=>> Building biology/cufflinks build started at Wed Apr 3 11:48:16 BST 2024 port directory: /usr/ports/biology/cufflinks package name: cufflinks-2.2.1.89_8 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1327 Feb 14 06:15 /usr/ports/biology/cufflinks/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: db616534ff Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/cufflinks/work/.cache HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/cufflinks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CCACHE_DIR="/root/.ccache" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/cufflinks/work/.cache HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/cufflinks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/eigen3 " CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cufflinks-2.2.1.89_8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> cufflinks-2.2.1.89_8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cufflinks-2.2.1.89_8 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cufflinks-2.2.1.89_8 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cufflinks-2.2.1.89_8 for building => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by cufflinks-2.2.1.89_8 for building ===> Extracting for cufflinks-2.2.1.89_8 => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz. => SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for cufflinks-2.2.1.89_8 ===> Applying distribution patches for cufflinks-2.2.1.89_8 ===> Applying FreeBSD patches for cufflinks-2.2.1.89_8 from /usr/ports/biology/cufflinks/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cufflinks-2.2.1.89_8 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.4.0_3.pkg [pkg-builder.dan.net.uk] Installing eigen-3.4.0_3... [pkg-builder.dan.net.uk] `-- Installing blas-3.12.0_1... [pkg-builder.dan.net.uk] | `-- Installing gcc13-13.2.0_4... [pkg-builder.dan.net.uk] | | `-- Installing binutils-2.40_5,1... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting binutils-2.40_5,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.1,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] | `-- Extracting gcc13-13.2.0_4: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] `-- Extracting blas-3.12.0_1: ..... done [pkg-builder.dan.net.uk] `-- Installing lapack-3.12.0_2... [pkg-builder.dan.net.uk] `-- Extracting lapack-3.12.0_2: .......... done [pkg-builder.dan.net.uk] Extracting eigen-3.4.0_3: .......... done ===== Message from gcc13-13.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> cufflinks-2.2.1.89_8 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of cufflinks-2.2.1.89_8 ===> cufflinks-2.2.1.89_8 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> cufflinks-2.2.1.89_8 depends on package: gmake>=4.4.1 - found ===> Returning to build of cufflinks-2.2.1.89_8 ===> cufflinks-2.2.1.89_8 depends on file: /usr/local/bin/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.18_1.pkg [pkg-builder.dan.net.uk] Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] Extracting python39-3.9.18_1: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> cufflinks-2.2.1.89_8 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of cufflinks-2.2.1.89_8 ===> cufflinks-2.2.1.89_8 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> cufflinks-2.2.1.89_8 depends on package: autoconf>=2.72 - found ===> Returning to build of cufflinks-2.2.1.89_8 ===> cufflinks-2.2.1.89_8 depends on package: automake>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> cufflinks-2.2.1.89_8 depends on package: automake>=1.16.5 - found ===> Returning to build of cufflinks-2.2.1.89_8 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cufflinks-2.2.1.89_8 depends on shared library: libboost_system.so - not found ===> Installing existing package /packages/All/boost-libs-1.84.0.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.84.0... [pkg-builder.dan.net.uk] `-- Installing icu-74.2,1... [pkg-builder.dan.net.uk] `-- Extracting icu-74.2,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.84.0: .......... done ===== Message from boost-libs-1.84.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> cufflinks-2.2.1.89_8 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> Returning to build of cufflinks-2.2.1.89_8 ===> cufflinks-2.2.1.89_8 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17_1.pkg [pkg-builder.dan.net.uk] Installing htslib-1.17_1... [pkg-builder.dan.net.uk] `-- Installing curl-8.6.0... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.7... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] | `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.6.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.17_1: .......... done ===> cufflinks-2.2.1.89_8 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of cufflinks-2.2.1.89_8 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for cufflinks-2.2.1.89_8 sh: svnversion: not found sh: svnversion: not found sh: svnversion: not found configure.ac:44: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:44: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... ax_check_zlib.m4:62: AX_CHECK_ZLIB is expanded from... configure.ac:44: the top level sh: svnversion: not found sh: svnversion: not found configure.ac:36: installing 'build-aux/ar-lib' configure.ac:32: installing 'build-aux/compile' configure.ac:38: installing 'build-aux/config.guess' configure.ac:38: installing 'build-aux/config.sub' configure.ac:17: installing 'build-aux/install-sh' configure.ac:17: installing 'build-aux/missing' src/Makefile.am:113: warning: source file 'locfit/adap.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:113: warning: source file 'locfit/ar_funs.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/arith.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/band.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_args.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_plot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/cmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_haz.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_int.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_odi.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/density.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dist.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_atree.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_interp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_kdtre.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_main.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_trian.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/family.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/fitted.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/frend.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/help.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_dercor.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_fitfun.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_robust.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_vari.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfstr.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/linalg.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/locfit.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_chol.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_eigen.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_jacob.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_max.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/makecmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/math.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/minmax.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/nbhd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pcomp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pout.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/preplot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/random.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/readfile.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb_cons.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/simul.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/solve.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/startlf.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/strings.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/vari.cpp' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/wdiag.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/weight.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am: installing 'build-aux/depcomp' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking how to create a pax tar archive... gnutar checking for gawk... (cached) /usr/bin/awk checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking whether gmake sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking whether /usr/local/bin/python3.9 version is >= 2.4... yes checking for /usr/local/bin/python3.9 version... 3.9 checking for /usr/local/bin/python3.9 platform... freebsd13 checking for GNU default /usr/local/bin/python3.9 prefix... ${prefix} checking for GNU default /usr/local/bin/python3.9 exec_prefix... ${exec_prefix} checking for /usr/local/bin/python3.9 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.9/site-packages checking for /usr/local/bin/python3.9 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.9/site-packages checking build system type... amd64-portbld-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 checking for boostlib >= 1.47.0 (104700)... yes checking for htslib or bamlib... yes checking whether the Boost::System library is available... yes checking for main in -lboost_system... yes configure: WARNING: BOOST_CPPFLAGS -I/usr/local/include checking whether the Boost::Serialization library is available... yes checking for main in -lboost_serialization... yes checking whether the Boost::Filesystem library is available... yes checking for main in -lboost_filesystem... yes checking whether the Boost::Thread library is available... yes checking for main in -lboost_thread... yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking for zlib.h... (cached) yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking for eigenlib... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... (cached) yes checking for stdbool.h that conforms to C99 or later... (cached) yes checking for inline... inline checking for pid_t... (cached) yes checking for size_t... (cached) yes checking for ptrdiff_t... (cached) yes checking if gcc accepts -m64... checking for struct sysinfo.totalram... no checking for cc options needed to detect all undeclared functions... -fno-builtin checking whether sysctl is declared... no checking whether CTL_HW is declared... no checking whether HW_PHYSMEM is declared... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- cufflinks 2.2.2 Configuration Results -- C++ compiler: c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong GCC version: FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Host System type: amd64-portbld-freebsd13.2 Install prefix: /usr/local Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for cufflinks-2.2.1.89_8 gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' Making all in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cufflinks.o -MD -MP -MF .deps/cufflinks.Tpo -c -o cufflinks.o cufflinks.cpp In file included from cufflinks.cpp:15: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from cufflinks.cpp:19: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ In file included from cufflinks.cpp:20: In file included from ./clustering.h:38: In file included from ./abundances.h:24: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from cufflinks.cpp:20: In file included from ./clustering.h:38: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :94:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from cufflinks.cpp:20: In file included from ./clustering.h:38: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from cufflinks.cpp:28: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cufflinks.cpp:693:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] bool ref_guided = (ref_scaffs != NULL); ^ cufflinks.cpp:690:5: note: previous statement is here if (bundle.hits().size() >= max_frags_per_bundle) ^ cufflinks.cpp:1279:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] if (!final_est_run && bundle_mode==REF_DRIVEN) // Bias needs to be learned ^ cufflinks.cpp:1275:5: note: previous statement is here if (allow_junk_filtering) ^ cufflinks.cpp:1176:17: warning: unused variable 'map_mass' [-Wunused-variable] long double map_mass = rg_props->normalized_map_mass(); ^ In file included from cufflinks.cpp:23: In file included from ./filters.h:18: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 49 warnings generated. mv -f .deps/cufflinks.Tpo .deps/cufflinks.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT clustering.o -MD -MP -MF .deps/clustering.Tpo -c -o clustering.o clustering.cpp In file included from clustering.cpp:10: In file included from ./clustering.h:38: In file included from ./abundances.h:23: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from clustering.cpp:10: In file included from ./clustering.h:38: In file included from ./abundances.h:24: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from clustering.cpp:10: In file included from ./clustering.h:38: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :294:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from clustering.cpp:10: In file included from ./clustering.h:38: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 43 warnings generated. mv -f .deps/clustering.Tpo .deps/clustering.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT differential.o -MD -MP -MF .deps/differential.Tpo -c -o differential.o differential.cpp In file included from differential.cpp:20: In file included from ./abundances.h:23: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from differential.cpp:20: In file included from ./abundances.h:24: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from differential.cpp:20: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :3:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from differential.cpp:20: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from differential.cpp:21: In file included from ./differential.h:29: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ In file included from differential.cpp:21: ./differential.h:215:5: warning: field 'sample_labels' will be initialized after field 'headers_written' [-Wreorder-ctor] sample_labels(sls), ^~~~~~~~~~~~~~~~~~ headers_written(false) ./differential.h:325:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ ./differential.h:407:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ ./differential.h:614:56: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n", ~~^ differential.cpp:134:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^ differential.cpp:163:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^ In file included from differential.cpp:24: ./sampling.h:50:13: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef M matrix_type; ^ ./sampling.h:113:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:114:42: warning: unused typedef 'vector_type' [-Wunused-local-typedef] typedef vector vector_type; ^ ./sampling.h:120:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:121:42: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef matrix matrix_type; ^ ./sampling.h:128:42: warning: unused typedef 'vector_type' [-Wunused-local-typedef] typedef vector vector_type; ^ ./sampling.h:127:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:135:42: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef matrix matrix_type; ^ ./sampling.h:134:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ 59 warnings generated. mv -f .deps/differential.Tpo .deps/differential.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp In file included from common.cpp:28: In file included from ./replicates.h:10: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :30:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from common.cpp:28: In file included from ./replicates.h:10: In file included from ./bundles.h:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from common.cpp:28: In file included from ./replicates.h:10: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from common.cpp:28: In file included from ./replicates.h:10: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from common.cpp:28: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ In file included from common.cpp:27: In file included from ./common.h:32: In file included from /usr/local/include/boost/archive/binary_iarchive.hpp:20: In file included from /usr/local/include/boost/archive/binary_iarchive_impl.hpp:21: In file included from /usr/local/include/boost/archive/basic_binary_iarchive.hpp:30: In file included from /usr/local/include/boost/archive/detail/common_iarchive.hpp:21: In file included from /usr/local/include/boost/archive/detail/basic_iarchive.hpp:23: In file included from /usr/local/include/boost/scoped_ptr.hpp:13: In file included from /usr/local/include/boost/smart_ptr/scoped_ptr.hpp:16: /usr/local/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ common.cpp:487:30: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here _mass_dispersion_model = boost::shared_ptr(new PoissonDispersionModel("")); ^ 45 warnings generated. mv -f .deps/common.Tpo .deps/common.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp In file included from assemble.cpp:19: In file included from ./lemon/topology.h:22: In file included from ./lemon/dfs.h:26: In file included from ./lemon/list_graph.h:26: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:108:10: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] std::auto_ptr buf; ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from assemble.cpp:19: In file included from ./lemon/topology.h:22: In file included from ./lemon/dfs.h:26: In file included from ./lemon/list_graph.h:26: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:93:10: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr<_Type> ptr; ^ ./lemon/error.h:248:34: note: in instantiation of template class 'lemon::ExceptionMember' requested here ExceptionMember _message; ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from assemble.cpp:19: In file included from ./lemon/topology.h:22: In file included from ./lemon/dfs.h:26: In file included from ./lemon/list_graph.h:26: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:464:9: warning: returning address of local temporary object [-Wreturn-stack-address] return ostr.str().c_str(); ^~~~~~~~~~ In file included from assemble.cpp:19: In file included from ./lemon/topology.h:28: In file included from ./lemon/concepts/graph.h:30: ./lemon/concepts/graph_components.h:102:9: warning: variable 'b' set but not used [-Wunused-but-set-variable] bool b; ^ In file included from assemble.cpp:44: In file included from ./transitive_closure.h:30: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :132:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from assemble.cpp:48: In file included from ./assemble.h:21: In file included from ./bundles.h:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from assemble.cpp:48: In file included from ./assemble.h:21: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from assemble.cpp:48: In file included from ./assemble.h:21: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ assemble.cpp:188:21: warning: unused variable 'a_for_b' [-Wunused-variable] ReachGraph::ANode a_for_b = b_to_a[b_id]; ^ assemble.cpp:123:17: warning: unused variable 'hits_for_node' [-Wunused-variable] HitsForNodeMap hits_for_node = get(vertex_name, dag); ^ assemble.cpp:262:21: warning: unused variable 'a_for_b' [-Wunused-variable] ReachGraph::ANode a_for_b = bp.nodeFromANodeId(a_id_for_b); ^ In file included from assemble.cpp:19: ./lemon/topology.h:249:34: warning: unused typedef 'Node' [-Wunused-local-typedef] typedef typename Graph::Node Node; ^ ./lemon/topology.h:313:36: warning: unused typedef 'EdgeIt' [-Wunused-local-typedef] typedef typename Graph::EdgeIt EdgeIt; ^ ./lemon/topology.h:311:34: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef typename Graph::Edge Edge; ^ ./lemon/topology.h:1213:34: warning: unused typedef 'Node' [-Wunused-local-typedef] typedef typename Graph::Node Node; ^ ./lemon/topology.h:1215:34: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef typename Graph::Edge Edge; ^ ./lemon/topology.h:1470:37: warning: unused typedef 'EdgeIt' [-Wunused-local-typedef] typedef typename UGraph::EdgeIt EdgeIt; ^ ./lemon/topology.h:1514:35: warning: unused typedef 'Node' [-Wunused-local-typedef] typedef typename UGraph::Node Node; ^ ./lemon/topology.h:1516:37: warning: unused typedef 'EdgeIt' [-Wunused-local-typedef] typedef typename UGraph::EdgeIt EdgeIt; ^ In file included from assemble.cpp:44: ./transitive_closure.h:224:73: warning: unused typedef 'tc_vertex' [-Wunused-local-typedef] typedef typename boost::graph_traits < GraphTC >::vertex_descriptor tc_vertex; ^ ./transitive_closure.h:83:69: warning: unused typedef 'edge' [-Wunused-local-typedef] typedef typename boost::graph_traits < Graph >::edge_descriptor edge; ^ ./transitive_closure.h:321:67: warning: unused typedef 'vertex' [-Wunused-local-typedef] typedef typename boost::graph_traits < G >::vertex_descriptor vertex; ^ ./transitive_closure.h:347:67: warning: unused typedef 'vertex' [-Wunused-local-typedef] typedef typename boost::graph_traits < G >::vertex_descriptor vertex; ^ In file included from assemble.cpp:45: ./transitive_reduction.h:53:63: warning: unused typedef 'VertexIterator' [-Wunused-local-typedef] typedef typename graph_traits::vertex_iterator VertexIterator; ^ 63 warnings generated. mv -f .deps/assemble.Tpo .deps/assemble.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -c -o tokenize.o tokenize.cpp mv -f .deps/tokenize.Tpo .deps/tokenize.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp In file included from abundances.cpp:16: In file included from ./abundances.h:23: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from abundances.cpp:16: In file included from ./abundances.h:24: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from abundances.cpp:16: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :391:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from abundances.cpp:16: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from abundances.cpp:43: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ abundances.cpp:552:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] return NUMERIC_OK; ^ abundances.cpp:549:5: note: previous statement is here if (has_ok_member == false) ^ abundances.cpp:526:10: warning: variable 'has_lowdata_member' set but not used [-Wunused-but-set-variable] bool has_lowdata_member = false; ^ abundances.cpp:1043:20: warning: unused variable 'curr_mass' [-Wunused-variable] double curr_mass = inserted.first->second; ^ abundances.cpp:1165:12: warning: variable 'total_mass_pre_collapse' set but not used [-Wunused-but-set-variable] double total_mass_pre_collapse = 0.0; ^ abundances.cpp:1346:12: warning: variable 'total_mass_post_collapse' set but not used [-Wunused-but-set-variable] double total_mass_post_collapse = 0.0; ^ abundances.cpp:1872:58: warning: unused variable 'sc_ab' [-Wunused-variable] const vector >& sc_ab = itr->second->abundances(); ^ abundances.cpp:2079:17: warning: variable 'bnb_mean' set but not used [-Wunused-but-set-variable] long double bnb_mean = 0.0; ^ abundances.cpp:2598:24: warning: unused variable 'fpkm' [-Wunused-variable] double fpkm = _abundances[i]->FPKM(); ^ abundances.cpp:2541:12: warning: variable 'abundance_weighted_length' set but not used [-Wunused-but-set-variable] double abundance_weighted_length = 0.0; ^ abundances.cpp:2542:12: warning: variable 'total_abundance' set but not used [-Wunused-but-set-variable] double total_abundance = 0.0; ^ abundances.cpp:2706:16: warning: variable 'avg_X_g' set but not used [-Wunused-but-set-variable] double avg_X_g = 0.0; ^ abundances.cpp:3280:12: warning: variable 'total_var' set but not used [-Wunused-but-set-variable] double total_var = 0.0; ^ abundances.cpp:3868:94: warning: unused variable 'al_itr' [-Wunused-variable] map, vector >::const_iterator al_itr = ^ abundances.cpp:4120:10: warning: variable 'logL' set but not used [-Wunused-but-set-variable] double logL; ^ abundances.cpp:4531:18: warning: implicit conversion from 'int' to 'float' changes value from 99999999 to 1.0E+8 [-Wimplicit-const-int-float-conversion] float min_doc = 99999999; ~~~~~~~ ^~~~~~~~ In file included from abundances.cpp:44: ./sampling.h:50:13: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef M matrix_type; ^ ./sampling.h:113:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:114:42: warning: unused typedef 'vector_type' [-Wunused-local-typedef] typedef vector vector_type; ^ ./sampling.h:120:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:121:42: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef matrix matrix_type; ^ ./sampling.h:127:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:128:42: warning: unused typedef 'vector_type' [-Wunused-local-typedef] typedef vector vector_type; ^ ./sampling.h:134:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:135:42: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef matrix matrix_type; ^ abundances.cpp:4056:15: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef M matrix_type; ^ In file included from abundances.cpp:42: In file included from ./filters.h:18: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 70 warnings generated. mv -f .deps/abundances.Tpo .deps/abundances.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT scaffolds.o -MD -MP -MF .deps/scaffolds.Tpo -c -o scaffolds.o scaffolds.cpp In file included from scaffolds.cpp:14: In file included from ./scaffolds.h:20: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from scaffolds.cpp:14: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ scaffolds.cpp:729:6: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = merged.left(); ^ scaffolds.cpp:803:6: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = merged.left(); ^ scaffolds.cpp:838:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] const vector& orig_ops = augmented_ops(); ^ scaffolds.cpp:835:5: note: previous statement is here if (filled_gap_size <= 0) ^ scaffolds.cpp:936:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] AugmentedCuffOp::merge_ops(overlapping, _augmented_ops, true); ^ scaffolds.cpp:933:5: note: previous statement is here if (overlapping.empty()) ^ 6 warnings generated. mv -f .deps/scaffolds.Tpo .deps/scaffolds.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT hits.o -MD -MP -MF .deps/hits.Tpo -c -o hits.o hits.cpp In file included from hits.cpp:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from hits.cpp:25: In file included from ./abundances.h:24: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from hits.cpp:25: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :102:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from hits.cpp:25: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ hits.cpp:44:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] int pos = _left; ^ hits.cpp:40:9: warning: variable 'new_left' set but not used [-Wunused-but-set-variable] int new_left = 0; ^ hits.cpp:723:23: warning: unused variable 'MAX_HEADER_LEN' [-Wunused-const-variable] static const unsigned MAX_HEADER_LEN = 64 * 1024 * 1024; // 4 MB ^ 46 warnings generated. mv -f .deps/hits.Tpo .deps/hits.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT genes.o -MD -MP -MF .deps/genes.Tpo -c -o genes.o genes.cpp In file included from genes.cpp:10: In file included from ./genes.h:17: In file included from ./scaffolds.h:20: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from genes.cpp:10: In file included from ./genes.h:17: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from genes.cpp:10: In file included from ./genes.h:18: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :73:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from genes.cpp:10: In file included from ./genes.h:18: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from genes.cpp:10: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 44 warnings generated. mv -f .deps/genes.Tpo .deps/genes.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT bundles.o -MD -MP -MF .deps/bundles.Tpo -c -o bundles.o bundles.cpp In file included from bundles.cpp:17: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :139:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from bundles.cpp:17: In file included from ./bundles.h:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from bundles.cpp:17: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from bundles.cpp:17: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ bundles.cpp:90:2: warning: misleading indentation; statement is not part of the previous 'else' [-Wmisleading-indentation] GList ref_rnas; ^ bundles.cpp:87:5: note: previous statement is here else ^ bundles.cpp:566:13: warning: 'random_shuffle>' is deprecated [-Wdeprecated-declarations] random_shuffle(_hits.begin(), _hits.end()); ^ /usr/include/c++/v1/__algorithm/shuffle.h:93:1: note: 'random_shuffle>' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX14 void ^ /usr/include/c++/v1/__config:1024:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ bundles.cpp:674:23: warning: integer literal is too large to be represented in a signed integer type, interpreting as unsigned [-Wimplicitly-unsigned-literal] if (tmp.ref_id() == 12638153115695167477) // corresponds to SAM "*" under FNV hash. unaligned read record ^ bundles.cpp:728:18: warning: variable 'found_scaff' set but not used [-Wunused-but-set-variable] bool found_scaff = false; ^ bundles.cpp:886:8: warning: variable 'last_hit_ref_id_seen' set but not used [-Wunused-but-set-variable] RefID last_hit_ref_id_seen = 0; ^ bundles.cpp:887:6: warning: variable 'last_hit_pos_seen' set but not used [-Wunused-but-set-variable] int last_hit_pos_seen = 0; ^ 49 warnings generated. mv -f .deps/bundles.Tpo .deps/bundles.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT filters.o -MD -MP -MF .deps/filters.Tpo -c -o filters.o filters.cpp In file included from filters.cpp:10: In file included from ./filters.h:17: In file included from ./scaffolds.h:20: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from filters.cpp:10: In file included from ./filters.h:17: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from filters.cpp:10: In file included from ./filters.h:18: In file included from ./genes.h:18: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :81:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from filters.cpp:10: In file included from ./filters.h:18: In file included from ./genes.h:18: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ filters.cpp:806:20: warning: variable 'mean_to_keep' set but not used [-Wunused-but-set-variable] double mean_to_keep = 0.0; ^ filters.cpp:807:20: warning: variable 'mean_to_trim' set but not used [-Wunused-but-set-variable] double mean_to_trim = 0.0; ^ filters.cpp:914:20: warning: variable 'total' set but not used [-Wunused-but-set-variable] double total = 0; ^ filters.cpp:934:36: warning: variable 'exon_3' set but not used [-Wunused-but-set-variable] const AugmentedCuffOp* exon_3 = NULL; ^ filters.cpp:935:17: warning: variable 'mult' set but not used [-Wunused-but-set-variable] int mult; ^ filters.cpp:936:17: warning: variable 'offset' set but not used [-Wunused-but-set-variable] int offset; ^ In file included from filters.cpp:10: In file included from ./filters.h:18: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 50 warnings generated. mv -f .deps/filters.Tpo .deps/filters.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT scaffold_graph.o -MD -MP -MF .deps/scaffold_graph.Tpo -c -o scaffold_graph.o scaffold_graph.cpp In file included from scaffold_graph.cpp:12: In file included from ./scaffolds.h:20: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from scaffold_graph.cpp:12: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ 2 warnings generated. mv -f .deps/scaffold_graph.Tpo .deps/scaffold_graph.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT matching_merge.o -MD -MP -MF .deps/matching_merge.Tpo -c -o matching_merge.o matching_merge.cpp In file included from matching_merge.cpp:10: In file included from ./matching_merge.h:16: In file included from ./lemon/smart_graph.h:30: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:108:10: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] std::auto_ptr buf; ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from matching_merge.cpp:10: In file included from ./matching_merge.h:16: In file included from ./lemon/smart_graph.h:30: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:93:10: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr<_Type> ptr; ^ ./lemon/error.h:248:34: note: in instantiation of template class 'lemon::ExceptionMember' requested here ExceptionMember _message; ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from matching_merge.cpp:10: In file included from ./matching_merge.h:16: In file included from ./lemon/smart_graph.h:30: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:464:9: warning: returning address of local temporary object [-Wreturn-stack-address] return ostr.str().c_str(); ^~~~~~~~~~ In file included from matching_merge.cpp:10: In file included from ./matching_merge.h:20: In file included from ./scaffolds.h:20: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from matching_merge.cpp:10: In file included from ./matching_merge.h:20: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ 5 warnings generated. mv -f .deps/matching_merge.Tpo .deps/matching_merge.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT graph_optimize.o -MD -MP -MF .deps/graph_optimize.Tpo -c -o graph_optimize.o graph_optimize.cpp In file included from graph_optimize.cpp:13: In file included from ./graph_optimize.h:17: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :90:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from graph_optimize.cpp:13: In file included from ./graph_optimize.h:17: In file included from ./bundles.h:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from graph_optimize.cpp:13: In file included from ./graph_optimize.h:17: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from graph_optimize.cpp:13: In file included from ./graph_optimize.h:17: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from graph_optimize.cpp:16: In file included from ./lemon/topology.h:22: In file included from ./lemon/dfs.h:26: In file included from ./lemon/list_graph.h:26: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:108:10: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr buf; ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from graph_optimize.cpp:16: In file included from ./lemon/topology.h:22: In file included from ./lemon/dfs.h:26: In file included from ./lemon/list_graph.h:26: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:93:10: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr<_Type> ptr; ^ ./lemon/error.h:248:34: note: in instantiation of template class 'lemon::ExceptionMember' requested here ExceptionMember _message; ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /usr/include/c++/v1/__config:1018:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from graph_optimize.cpp:16: In file included from ./lemon/topology.h:22: In file included from ./lemon/dfs.h:26: In file included from ./lemon/list_graph.h:26: In file included from ./lemon/bits/base_extender.h:23: ./lemon/error.h:464:9: warning: returning address of local temporary object [-Wreturn-stack-address] return ostr.str().c_str(); ^~~~~~~~~~ In file included from graph_optimize.cpp:16: In file included from ./lemon/topology.h:28: In file included from ./lemon/concepts/graph.h:30: ./lemon/concepts/graph_components.h:102:9: warning: variable 'b' set but not used [-Wunused-but-set-variable] bool b; ^ graph_optimize.cpp:264:30: warning: unused variable 'e' [-Wunused-variable] ContainmentGraph::UEdge e = containment.addEdge(nj.first, ^ In file included from graph_optimize.cpp:16: ./lemon/topology.h:249:34: warning: unused typedef 'Node' [-Wunused-local-typedef] typedef typename Graph::Node Node; ^ ./lemon/topology.h:311:34: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef typename Graph::Edge Edge; ^ ./lemon/topology.h:313:36: warning: unused typedef 'EdgeIt' [-Wunused-local-typedef] typedef typename Graph::EdgeIt EdgeIt; ^ ./lemon/topology.h:1213:34: warning: unused typedef 'Node' [-Wunused-local-typedef] typedef typename Graph::Node Node; ^ ./lemon/topology.h:1215:34: warning: unused typedef 'Edge' [-Wunused-local-typedef] typedef typename Graph::Edge Edge; ^ ./lemon/topology.h:1470:37: warning: unused typedef 'EdgeIt' [-Wunused-local-typedef] typedef typename UGraph::EdgeIt EdgeIt; ^ ./lemon/topology.h:1514:35: warning: unused typedef 'Node' [-Wunused-local-typedef] typedef typename UGraph::Node Node; ^ ./lemon/topology.h:1516:37: warning: unused typedef 'EdgeIt' [-Wunused-local-typedef] typedef typename UGraph::EdgeIt EdgeIt; ^ graph_optimize.cpp:342:31: warning: unused typedef 'ContainmentGraph' [-Wunused-local-typedef] typedef lemon::SmartBpUGraph ContainmentGraph; ^ In file included from graph_optimize.cpp:22: In file included from ./filters.h:18: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 58 warnings generated. mv -f .deps/graph_optimize.Tpo .deps/graph_optimize.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT biascorrection.o -MD -MP -MF .deps/biascorrection.Tpo -c -o biascorrection.o biascorrection.cpp In file included from biascorrection.cpp:11: In file included from ./scaffolds.h:20: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from biascorrection.cpp:11: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from biascorrection.cpp:12: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :7:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from biascorrection.cpp:12: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ biascorrection.cpp:797:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] return cond_prob; ^ biascorrection.cpp:794:5: note: previous statement is here if (isinf(cond_prob) || isnan(cond_prob)) ^ biascorrection.cpp:812:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] double tot_mass = accumulate( _rg_masses.begin(), _rg_masses.end(), 0.0 ); ^ biascorrection.cpp:809:5: note: previous statement is here if (no_length_correction) ^ 45 warnings generated. mv -f .deps/biascorrection.Tpo .deps/biascorrection.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT sampling.o -MD -MP -MF .deps/sampling.Tpo -c -o sampling.o sampling.cpp In file included from sampling.cpp:9: ./sampling.h:50:13: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef M matrix_type; ^ ./sampling.h:113:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:114:42: warning: unused typedef 'vector_type' [-Wunused-local-typedef] typedef vector vector_type; ^ ./sampling.h:120:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:121:42: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef matrix matrix_type; ^ ./sampling.h:127:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:128:42: warning: unused typedef 'vector_type' [-Wunused-local-typedef] typedef vector vector_type; ^ ./sampling.h:134:19: warning: unused typedef 'const_matrix_type' [-Wunused-local-typedef] typedef const M const_matrix_type; ^ ./sampling.h:135:42: warning: unused typedef 'matrix_type' [-Wunused-local-typedef] typedef matrix matrix_type; ^ 9 warnings generated. mv -f .deps/sampling.Tpo .deps/sampling.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT adap.o -MD -MP -MF .deps/adap.Tpo -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c locfit/adap.c:29:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] { int i, ii, j, p, p1; ^ locfit/adap.c:157:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] INT i, i0, d, n; ^ locfit/adap.c:157:14: warning: variable 'd' set but not used [-Wunused-but-set-variable] INT i, i0, d, n; ^ 3 warnings generated. mv -f .deps/adap.Tpo .deps/adap.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT ar_funs.o -MD -MP -MF .deps/ar_funs.Tpo -c -o ar_funs.o `test -f 'locfit/ar_funs.c' || echo './'`locfit/ar_funs.c mv -f .deps/ar_funs.Tpo .deps/ar_funs.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT arith.o -MD -MP -MF .deps/arith.Tpo -c -o arith.o `test -f 'locfit/arith.c' || echo './'`locfit/arith.c mv -f .deps/arith.Tpo .deps/arith.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT band.o -MD -MP -MF .deps/band.Tpo -c -o band.o `test -f 'locfit/band.c' || echo './'`locfit/band.c mv -f .deps/band.Tpo .deps/band.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT c_args.o -MD -MP -MF .deps/c_args.Tpo -c -o c_args.o `test -f 'locfit/c_args.c' || echo './'`locfit/c_args.c locfit/c_args.c:58:13: warning: variable 'nd' set but not used [-Wunused-but-set-variable] { int i, n, nd; ^ 1 warning generated. mv -f .deps/c_args.Tpo .deps/c_args.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT c_plot.o -MD -MP -MF .deps/c_plot.Tpo -c -o c_plot.o `test -f 'locfit/c_plot.c' || echo './'`locfit/c_plot.c locfit/c_plot.c:228:13: warning: variable 'sd' set but not used [-Wunused-but-set-variable] double c, sd, xl[2*MXDIM], xll[2]; ^ locfit/c_plot.c:226:36: warning: variable 'sef' set but not used [-Wunused-but-set-variable] { INT add, d, dp, i = 0, j = 0, n, sef; ^ locfit/c_plot.c:470:14: warning: incompatible pointer types passing 'char *' to parameter of type 'vari *' [-Wincompatible-pointer-types] setvarname(curstr,tname); ^~~~~~ locfit/vari.hpp:23:27: note: passing argument to parameter 'v' here void setvarname(vari* v, varname name); ^ 3 warnings generated. mv -f .deps/c_plot.Tpo .deps/c_plot.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT cmd.o -MD -MP -MF .deps/cmd.Tpo -c -o cmd.o `test -f 'locfit/cmd.c' || echo './'`locfit/cmd.c locfit/cmd.c:101:10: warning: variable 'nd' set but not used [-Wunused-but-set-variable] { INT i, nd; ^ locfit/cmd.c:353:29: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ locfit/cmd.c:357:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if (argvalis(v,k,"fit")|argvalis(v,k,"coef")) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || locfit/lffuns.h:169:25: note: expanded from macro 'argvalis' #define argvalis(v,i,z) (strcmp(argval(v,i),z)==0) ^ locfit/cmd.c:357:13: note: cast one or both operands to int to silence this warning locfit/lffuns.h:169:25: note: expanded from macro 'argvalis' #define argvalis(v,i,z) (strcmp(argval(v,i),z)==0) ^ locfit/cmd.c:358:25: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ locfit/cmd.c:362:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if (argvalis(v,k,"h")|argvalis(v,k,"band")) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ || locfit/lffuns.h:169:25: note: expanded from macro 'argvalis' #define argvalis(v,i,z) (strcmp(argval(v,i),z)==0) ^ locfit/cmd.c:362:13: note: cast one or both operands to int to silence this warning locfit/lffuns.h:169:25: note: expanded from macro 'argvalis' #define argvalis(v,i,z) (strcmp(argval(v,i),z)==0) ^ locfit/cmd.c:363:25: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ locfit/cmd.c:368:25: warning: incompatible pointer types passing 'char *' to parameter of type 'varname *' (aka 'char (*)[64]') [-Wincompatible-pointer-types] { vr = knotsvar(argarg(v,k),n); ^~~~~~~~~~~ locfit/lffuns.h:168:21: note: expanded from macro 'argarg' #define argarg(v,i) (((carg *)viptr(v,i))->arg) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ locfit/cmd.c:542:9: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] for (i=0; i<=mx; i++) ^ locfit/cmd.c:539:7: note: previous statement is here { if (my>0) ^ locfit/cmd.c:675:19: warning: variable 'nr' set but not used [-Wunused-but-set-variable] INT i, j, mn, nr; ^ 9 warnings generated. mv -f .deps/cmd.Tpo .deps/cmd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT dens_haz.o -MD -MP -MF .deps/dens_haz.Tpo -c -o dens_haz.o `test -f 'locfit/dens_haz.c' || echo './'`locfit/dens_haz.c mv -f .deps/dens_haz.Tpo .deps/dens_haz.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT dens_int.o -MD -MP -MF .deps/dens_int.Tpo -c -o dens_int.o `test -f 'locfit/dens_int.c' || echo './'`locfit/dens_int.c mv -f .deps/dens_int.Tpo .deps/dens_int.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT dens_odi.o -MD -MP -MF .deps/dens_odi.Tpo -c -o dens_odi.o `test -f 'locfit/dens_odi.c' || echo './'`locfit/dens_odi.c locfit/dens_odi.c:47:21: warning: variable 's' set but not used [-Wunused-but-set-variable] { double tc[40], f, s; ^ 1 warning generated. mv -f .deps/dens_odi.Tpo .deps/dens_odi.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT density.o -MD -MP -MF .deps/density.Tpo -c -o density.o `test -f 'locfit/density.c' || echo './'`locfit/density.c mv -f .deps/density.Tpo .deps/density.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT dist.o -MD -MP -MF .deps/dist.Tpo -c -o dist.o `test -f 'locfit/dist.c' || echo './'`locfit/dist.c mv -f .deps/dist.Tpo .deps/dist.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT ev_atree.o -MD -MP -MF .deps/ev_atree.Tpo -c -o ev_atree.o `test -f 'locfit/ev_atree.c' || echo './'`locfit/ev_atree.c mv -f .deps/ev_atree.Tpo .deps/ev_atree.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT ev_interp.o -MD -MP -MF .deps/ev_interp.Tpo -c -o ev_interp.o `test -f 'locfit/ev_interp.c' || echo './'`locfit/ev_interp.c mv -f .deps/ev_interp.Tpo .deps/ev_interp.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT ev_kdtre.o -MD -MP -MF .deps/ev_kdtre.Tpo -c -o ev_kdtre.o `test -f 'locfit/ev_kdtre.c' || echo './'`locfit/ev_kdtre.c mv -f .deps/ev_kdtre.Tpo .deps/ev_kdtre.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT ev_main.o -MD -MP -MF .deps/ev_main.Tpo -c -o ev_main.o `test -f 'locfit/ev_main.c' || echo './'`locfit/ev_main.c mv -f .deps/ev_main.Tpo .deps/ev_main.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT ev_trian.o -MD -MP -MF .deps/ev_trian.Tpo -c -o ev_trian.o `test -f 'locfit/ev_trian.c' || echo './'`locfit/ev_trian.c mv -f .deps/ev_trian.Tpo .deps/ev_trian.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT family.o -MD -MP -MF .deps/family.Tpo -c -o family.o `test -f 'locfit/family.c' || echo './'`locfit/family.c mv -f .deps/family.Tpo .deps/family.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT fitted.o -MD -MP -MF .deps/fitted.Tpo -c -o fitted.o `test -f 'locfit/fitted.c' || echo './'`locfit/fitted.c mv -f .deps/fitted.Tpo .deps/fitted.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT frend.o -MD -MP -MF .deps/frend.Tpo -c -o frend.o `test -f 'locfit/frend.c' || echo './'`locfit/frend.c locfit/frend.c:205:39: warning: variable 'ip' set but not used [-Wunused-but-set-variable] INT i, j, k = 0, d1, *mi, i0, p1, ip; ^ locfit/frend.c:382:17: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] i--; ^ locfit/frend.c:380:15: note: previous statement is here { for (j=0; jmi[MN]-lf->mi[MP]; ^ locfit/frend.c:401:7: note: previous statement is here { for (i=0; imi[MN]; i++) ^ 4 warnings generated. mv -f .deps/frend.Tpo .deps/frend.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o `test -f 'locfit/help.c' || echo './'`locfit/help.c mv -f .deps/help.Tpo .deps/help.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT lf_dercor.o -MD -MP -MF .deps/lf_dercor.Tpo -c -o lf_dercor.o `test -f 'locfit/lf_dercor.c' || echo './'`locfit/lf_dercor.c mv -f .deps/lf_dercor.Tpo .deps/lf_dercor.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT lf_fitfun.o -MD -MP -MF .deps/lf_fitfun.Tpo -c -o lf_fitfun.o `test -f 'locfit/lf_fitfun.c' || echo './'`locfit/lf_fitfun.c locfit/lf_fitfun.c:185:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] return; ^ locfit/lf_fitfun.c:182:7: note: previous statement is here { for (j=1; j<=deg; j++) ^ 1 warning generated. mv -f .deps/lf_fitfun.Tpo .deps/lf_fitfun.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT lf_robust.o -MD -MP -MF .deps/lf_robust.Tpo -c -o lf_robust.o `test -f 'locfit/lf_robust.c' || echo './'`locfit/lf_robust.c mv -f .deps/lf_robust.Tpo .deps/lf_robust.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT lf_vari.o -MD -MP -MF .deps/lf_vari.Tpo -c -o lf_vari.o `test -f 'locfit/lf_vari.c' || echo './'`locfit/lf_vari.c mv -f .deps/lf_vari.Tpo .deps/lf_vari.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT lfd.o -MD -MP -MF .deps/lfd.Tpo -c -o lfd.o `test -f 'locfit/lfd.c' || echo './'`locfit/lfd.c mv -f .deps/lfd.Tpo .deps/lfd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT lfstr.o -MD -MP -MF .deps/lfstr.Tpo -c -o lfstr.o `test -f 'locfit/lfstr.c' || echo './'`locfit/lfstr.c mv -f .deps/lfstr.Tpo .deps/lfstr.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT linalg.o -MD -MP -MF .deps/linalg.Tpo -c -o linalg.o `test -f 'locfit/linalg.c' || echo './'`locfit/linalg.c mv -f .deps/linalg.Tpo .deps/linalg.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT locfit.o -MD -MP -MF .deps/locfit.Tpo -c -o locfit.o `test -f 'locfit/locfit.c' || echo './'`locfit/locfit.c mv -f .deps/locfit.Tpo .deps/locfit.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT m_chol.o -MD -MP -MF .deps/m_chol.Tpo -c -o m_chol.o `test -f 'locfit/m_chol.c' || echo './'`locfit/m_chol.c mv -f .deps/m_chol.Tpo .deps/m_chol.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT m_eigen.o -MD -MP -MF .deps/m_eigen.Tpo -c -o m_eigen.o `test -f 'locfit/m_eigen.c' || echo './'`locfit/m_eigen.c mv -f .deps/m_eigen.Tpo .deps/m_eigen.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT m_jacob.o -MD -MP -MF .deps/m_jacob.Tpo -c -o m_jacob.o `test -f 'locfit/m_jacob.c' || echo './'`locfit/m_jacob.c mv -f .deps/m_jacob.Tpo .deps/m_jacob.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT m_max.o -MD -MP -MF .deps/m_max.Tpo -c -o m_max.o `test -f 'locfit/m_max.c' || echo './'`locfit/m_max.c mv -f .deps/m_max.Tpo .deps/m_max.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT makecmd.o -MD -MP -MF .deps/makecmd.Tpo -c -o makecmd.o `test -f 'locfit/makecmd.c' || echo './'`locfit/makecmd.c locfit/makecmd.c:88:36: warning: '&&' within '||' [-Wlogical-op-parentheses] } while ((instr) || (*z !=' ') && (!isterminator(*z))); ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ locfit/makecmd.c:88:36: note: place parentheses around the '&&' expression to silence this warning } while ((instr) || (*z !=' ') && (!isterminator(*z))); ^ ( ) locfit/makecmd.c:203:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sprintf((char *)vdptr(vs),cmdline); ^~~~~~~ locfit/makecmd.c:203:29: note: treat the string as an argument to avoid this sprintf((char *)vdptr(vs),cmdline); ^ "%s", 2 warnings generated. mv -f .deps/makecmd.Tpo .deps/makecmd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT math.o -MD -MP -MF .deps/math.Tpo -c -o math.o `test -f 'locfit/math.c' || echo './'`locfit/math.c mv -f .deps/math.Tpo .deps/math.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT minmax.o -MD -MP -MF .deps/minmax.Tpo -c -o minmax.o `test -f 'locfit/minmax.c' || echo './'`locfit/minmax.c mv -f .deps/minmax.Tpo .deps/minmax.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT nbhd.o -MD -MP -MF .deps/nbhd.Tpo -c -o nbhd.o `test -f 'locfit/nbhd.c' || echo './'`locfit/nbhd.c mv -f .deps/nbhd.Tpo .deps/nbhd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT pcomp.o -MD -MP -MF .deps/pcomp.Tpo -c -o pcomp.o `test -f 'locfit/pcomp.c' || echo './'`locfit/pcomp.c mv -f .deps/pcomp.Tpo .deps/pcomp.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT pout.o -MD -MP -MF .deps/pout.Tpo -c -o pout.o `test -f 'locfit/pout.c' || echo './'`locfit/pout.c locfit/pout.c:447:34: warning: variable 'vy' set but not used [-Wunused-but-set-variable] double z[3], z2[3], xx[2], vx, vy, vz; ^ locfit/pout.c:447:38: warning: variable 'vz' set but not used [-Wunused-but-set-variable] double z[3], z2[3], xx[2], vx, vy, vz; ^ locfit/pout.c:447:30: warning: variable 'vx' set but not used [-Wunused-but-set-variable] double z[3], z2[3], xx[2], vx, vy, vz; ^ 3 warnings generated. mv -f .deps/pout.Tpo .deps/pout.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT preplot.o -MD -MP -MF .deps/preplot.Tpo -c -o preplot.o `test -f 'locfit/preplot.c' || echo './'`locfit/preplot.c mv -f .deps/preplot.Tpo .deps/preplot.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT random.o -MD -MP -MF .deps/random.Tpo -c -o random.o `test -f 'locfit/random.c' || echo './'`locfit/random.c mv -f .deps/random.Tpo .deps/random.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT readfile.o -MD -MP -MF .deps/readfile.Tpo -c -o readfile.o `test -f 'locfit/readfile.c' || echo './'`locfit/readfile.c mv -f .deps/readfile.Tpo .deps/readfile.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT scb.o -MD -MP -MF .deps/scb.Tpo -c -o scb.o `test -f 'locfit/scb.c' || echo './'`locfit/scb.c locfit/scb.c:61:10: warning: variable 'b2i' set but not used [-Wunused-but-set-variable] { double b2i, b3i, b3j, b4i; ^ 1 warning generated. mv -f .deps/scb.Tpo .deps/scb.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT scb_cons.o -MD -MP -MF .deps/scb_cons.Tpo -c -o scb_cons.o `test -f 'locfit/scb_cons.c' || echo './'`locfit/scb_cons.c mv -f .deps/scb_cons.Tpo .deps/scb_cons.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT simul.o -MD -MP -MF .deps/simul.Tpo -c -o simul.o `test -f 'locfit/simul.c' || echo './'`locfit/simul.c mv -f .deps/simul.Tpo .deps/simul.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT solve.o -MD -MP -MF .deps/solve.Tpo -c -o solve.o `test -f 'locfit/solve.c' || echo './'`locfit/solve.c mv -f .deps/solve.Tpo .deps/solve.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT startlf.o -MD -MP -MF .deps/startlf.Tpo -c -o startlf.o `test -f 'locfit/startlf.c' || echo './'`locfit/startlf.c locfit/startlf.c:240:10: warning: comparison of array 'lf.mi' equal to a null pointer is always false [-Wtautological-pointer-compare] { if (lf.mi==NULL) return(1); ~~~^~ ~~~~ locfit/startlf.c:425:14: warning: comparison of array 'lf.mi' not equal to a null pointer is always true [-Wtautological-pointer-compare] { if (lf.mi!=NULL) lf.mi[MEV] = ENULL; ~~~^~ ~~~~ 2 warnings generated. mv -f .deps/startlf.Tpo .deps/startlf.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT strings.o -MD -MP -MF .deps/strings.Tpo -c -o strings.o `test -f 'locfit/strings.c' || echo './'`locfit/strings.c mv -f .deps/strings.Tpo .deps/strings.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT vari.o -MD -MP -MF .deps/vari.Tpo -c -o vari.o `test -f 'locfit/vari.cpp' || echo './'`locfit/vari.cpp mv -f .deps/vari.Tpo .deps/vari.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT wdiag.o -MD -MP -MF .deps/wdiag.Tpo -c -o wdiag.o `test -f 'locfit/wdiag.c' || echo './'`locfit/wdiag.c mv -f .deps/wdiag.Tpo .deps/wdiag.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MT weight.o -MD -MP -MF .deps/weight.Tpo -c -o weight.o `test -f 'locfit/weight.c' || echo './'`locfit/weight.c locfit/weight.c:162:10: warning: variable 'w' set but not used [-Wunused-but-set-variable] { double w; ^ 1 warning generated. mv -f .deps/weight.Tpo .deps/weight.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT replicates.o -MD -MP -MF .deps/replicates.Tpo -c -o replicates.o replicates.cpp In file included from replicates.cpp:12: ./locfit/local.h:126:9: warning: 'MAX' macro redefined [-Wmacro-redefined] #define MAX(a,b) (((a)>(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:315:9: note: previous definition is here #define MAX(a,b) (((a)>(b))?(a):(b)) ^ In file included from replicates.cpp:12: ./locfit/local.h:127:9: warning: 'MIN' macro redefined [-Wmacro-redefined] #define MIN(a,b) (((a)<(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:314:9: note: previous definition is here #define MIN(a,b) (((a)<(b))?(a):(b)) ^ In file included from replicates.cpp:18: In file included from ./replicates.h:10: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :76:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from replicates.cpp:18: In file included from ./replicates.h:10: In file included from ./bundles.h:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from replicates.cpp:18: In file included from ./replicates.h:10: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from replicates.cpp:18: In file included from ./replicates.h:10: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from replicates.cpp:18: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ replicates.cpp:661:16: warning: variable 'var' set but not used [-Wunused-but-set-variable] double var = 0.0; ^ replicates.cpp:833:12: warning: variable 'xim' set but not used [-Wunused-but-set-variable] double xim = 0; ^ In file included from replicates.cpp:9: In file included from /usr/local/include/boost/thread.hpp:13: In file included from /usr/local/include/boost/thread/thread.hpp:12: In file included from /usr/local/include/boost/thread/thread_only.hpp:17: In file included from /usr/local/include/boost/thread/pthread/thread_data.hpp:12: In file included from /usr/local/include/boost/thread/lock_types.hpp:18: In file included from /usr/local/include/boost/thread/thread_time.hpp:9: In file included from /usr/local/include/boost/date_time/time_clock.hpp:17: In file included from /usr/local/include/boost/shared_ptr.hpp:17: In file included from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:18: In file included from /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /usr/local/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /usr/local/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ replicates.cpp:793:21: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here disperser = boost::shared_ptr(new PoissonDispersionModel(condition_name)); ^ In file included from replicates.cpp:9: In file included from /usr/local/include/boost/thread.hpp:13: In file included from /usr/local/include/boost/thread/thread.hpp:12: In file included from /usr/local/include/boost/thread/thread_only.hpp:17: In file included from /usr/local/include/boost/thread/pthread/thread_data.hpp:12: In file included from /usr/local/include/boost/thread/lock_types.hpp:18: In file included from /usr/local/include/boost/thread/thread_time.hpp:9: In file included from /usr/local/include/boost/date_time/time_clock.hpp:17: In file included from /usr/local/include/boost/shared_ptr.hpp:17: In file included from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:18: In file included from /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:27: In file included from /usr/local/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27: /usr/local/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'MassDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ replicates.cpp:871:17: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here disperser = boost::shared_ptr(new MassDispersionModel(condition_name, compatible_count_means, raw_variances, fitted_values)); ^ 50 warnings generated. mv -f .deps/replicates.Tpo .deps/replicates.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT multireads.o -MD -MP -MF .deps/multireads.Tpo -c -o multireads.o multireads.cpp In file included from multireads.cpp:11: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from multireads.cpp:11: In file included from ./hits.h:32: ./multireads.h:27:11: warning: private field '_id' is not used [-Wunused-private-field] InsertID _id; ^ 2 warnings generated. mv -f .deps/multireads.Tpo .deps/multireads.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT jensen_shannon.o -MD -MP -MF .deps/jensen_shannon.Tpo -c -o jensen_shannon.o jensen_shannon.cpp jensen_shannon.cpp:31:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] return e; ^ jensen_shannon.cpp:29:5: note: previous statement is here if (e < 0) ^ jensen_shannon.cpp:67:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] return sqrt(js); ^ jensen_shannon.cpp:65:5: note: previous statement is here if (js < 0) // can happen due to underflow or rounding errors. ^ jensen_shannon.cpp:120:24: warning: variable 'alt_grad' set but not used [-Wunused-but-set-variable] double alt_grad = 0.0; ^ jensen_shannon.cpp:132:24: warning: unused variable 'curr_grad' [-Wunused-variable] double curr_grad = gradient(i*kappa_length + k); ^ 4 warnings generated. mv -f .deps/jensen_shannon.Tpo .deps/jensen_shannon.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT tracking.o -MD -MP -MF .deps/tracking.Tpo -c -o tracking.o tracking.cpp In file included from tracking.cpp:1: In file included from ./tracking.h:1: In file included from ./abundances.h:23: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from tracking.cpp:1: In file included from ./tracking.h:1: In file included from ./abundances.h:24: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from tracking.cpp:1: In file included from ./tracking.h:1: In file included from ./abundances.h:25: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :391:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from tracking.cpp:1: In file included from ./tracking.h:1: In file included from ./abundances.h:25: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 43 warnings generated. mv -f .deps/tracking.Tpo .deps/tracking.Po rm -f libcufflinks.a ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o tracking.o ranlib libcufflinks.a c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT codons.o -MD -MP -MF .deps/codons.Tpo -c -o codons.o codons.cpp mv -f .deps/codons.Tpo .deps/codons.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GArgs.o -MD -MP -MF .deps/GArgs.Tpo -c -o GArgs.o GArgs.cpp mv -f .deps/GArgs.Tpo .deps/GArgs.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GBase.o -MD -MP -MF .deps/GBase.Tpo -c -o GBase.o GBase.cpp GBase.cpp:237:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i=0; ^~~~~~~~~ GBase.cpp:247:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i=0; ^~~~~~~~~ GBase.cpp:256:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ua, ub; ^~~~~~~~~ GBase.cpp:256:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ua, ub; ^~~~~~~~~ GBase.cpp:630:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int h=0; ^~~~~~~~~ GBase.cpp:631:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int g; ^~~~~~~~~ 6 warnings generated. mv -f .deps/GBase.Tpo .deps/GBase.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gdna.o -MD -MP -MF .deps/gdna.Tpo -c -o gdna.o gdna.cpp gdna.cpp:56:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char c; ^~~~~~~~~ 1 warning generated. mv -f .deps/gdna.Tpo .deps/gdna.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GStr.o -MD -MP -MF .deps/GStr.Tpo -c -o GStr.o GStr.cpp GStr.cpp:411:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int istart; ^~~~~~~~~ GStr.cpp:412:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int iend; ^~~~~~~~~ GStr.cpp:431:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int istart; ^~~~~~~~~ GStr.cpp:432:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int iend; ^~~~~~~~~ GStr.cpp:452:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int iend; ^~~~~~~~~ GStr.cpp:470:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int iend; ^~~~~~~~~ GStr.cpp:488:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int iend; ^~~~~~~~~ GStr.cpp:511:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int istart; ^~~~~~~~~ GStr.cpp:528:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int istart; ^~~~~~~~~ GStr.cpp:669:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] for (register const char *p = chars(); *p; p++) ^~~~~~~~~ GStr.cpp:974:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] for (register char *p = chrs(); *p; p++) ^~~~~~~~~ GStr.cpp:985:10: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] for (register char *p = chrs(); *p; p++) ^~~~~~~~~ 12 warnings generated. mv -f .deps/GStr.Tpo .deps/GStr.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GFaSeqGet.o -MD -MP -MF .deps/GFaSeqGet.Tpo -c -o GFaSeqGet.o GFaSeqGet.cpp mv -f .deps/GFaSeqGet.Tpo .deps/GFaSeqGet.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT GFastaIndex.o -MD -MP -MF .deps/GFastaIndex.Tpo -c -o GFastaIndex.o GFastaIndex.cpp In file included from GFastaIndex.cpp:8: In file included from ./GFastaIndex.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 40 warnings generated. mv -f .deps/GFastaIndex.Tpo .deps/GFastaIndex.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gff.o -MD -MP -MF .deps/gff.Tpo -c -o gff.o gff.cpp In file included from gff.cpp:1: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 40 warnings generated. mv -f .deps/gff.Tpo .deps/gff.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gff_utils.o -MD -MP -MF .deps/gff_utils.Tpo -c -o gff_utils.o gff_utils.cpp In file included from gff_utils.cpp:1: In file included from ./gff_utils.h:3: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 40 warnings generated. mv -f .deps/gff_utils.Tpo .deps/gff_utils.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gtf_tracking.o -MD -MP -MF .deps/gtf_tracking.Tpo -c -o gtf_tracking.o gtf_tracking.cpp In file included from gtf_tracking.cpp:10: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ gtf_tracking.cpp:624:6: warning: variable 'loci_counter' set but not used [-Wunused-but-set-variable] int loci_counter=0; ^ 41 warnings generated. mv -f .deps/gtf_tracking.Tpo .deps/gtf_tracking.Po rm -f libgc.a ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o ranlib libgc.a c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffcompare.o -MD -MP -MF .deps/cuffcompare.Tpo -c -o cuffcompare.o cuffcompare.cpp In file included from cuffcompare.cpp:11: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from cuffcompare.cpp:14: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ cuffcompare.cpp:1676:12: warning: unused variable 'pre_mrna_threshold' [-Wunused-const-variable] const uint pre_mrna_threshold = 100; ^ 42 warnings generated. mv -f .deps/cuffcompare.Tpo .deps/cuffcompare.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -o cuffcompare cuffcompare.o libgc.a -lz c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffdiff.o -MD -MP -MF .deps/cuffdiff.Tpo -c -o cuffdiff.o cuffdiff.cpp In file included from cuffdiff.cpp:18: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from cuffdiff.cpp:19: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :200:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from cuffdiff.cpp:19: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from cuffdiff.cpp:19: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from cuffdiff.cpp:23: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ In file included from cuffdiff.cpp:36: In file included from ./differential.h:29: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ In file included from cuffdiff.cpp:36: ./differential.h:215:5: warning: field 'sample_labels' will be initialized after field 'headers_written' [-Wreorder-ctor] sample_labels(sls), ^~~~~~~~~~~~~~~~~~ headers_written(false) ./differential.h:325:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ ./differential.h:407:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ ./differential.h:614:56: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n", ~~^ In file included from cuffdiff.cpp:39: ./locfit/local.h:126:9: warning: 'MAX' macro redefined [-Wmacro-redefined] #define MAX(a,b) (((a)>(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:315:9: note: previous definition is here #define MAX(a,b) (((a)>(b))?(a):(b)) ^ In file included from cuffdiff.cpp:39: ./locfit/local.h:127:9: warning: 'MIN' macro redefined [-Wmacro-redefined] #define MIN(a,b) (((a)<(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:314:9: note: previous definition is here #define MIN(a,b) (((a)<(b))?(a):(b)) ^ cuffdiff.cpp:628:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ cuffdiff.cpp:719:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ cuffdiff.cpp:880:6: warning: variable 'significant' set but not used [-Wunused-but-set-variable] int significant = 0; ^ cuffdiff.cpp:2096:6: warning: variable 'total_diff_splice_tests' set but not used [-Wunused-but-set-variable] int total_diff_splice_tests = 0; ^ cuffdiff.cpp:1779:17: warning: variable 'total_norm_mass' set but not used [-Wunused-but-set-variable] long double total_norm_mass = 0.0; ^ cuffdiff.cpp:1662:10: warning: variable 'single_replicate_fac' set but not used [-Wunused-but-set-variable] bool single_replicate_fac = false; ^ cuffdiff.cpp:2043:6: warning: variable 'total_gene_de_tests' set but not used [-Wunused-but-set-variable] int total_gene_de_tests = 0; ^ cuffdiff.cpp:1991:6: warning: variable 'total_iso_de_tests' set but not used [-Wunused-but-set-variable] int total_iso_de_tests = 0; ^ cuffdiff.cpp:1660:9: warning: variable 'most_reps_idx' set but not used [-Wunused-but-set-variable] int most_reps_idx = 0; ^ cuffdiff.cpp:2069:6: warning: variable 'total_cds_de_tests' set but not used [-Wunused-but-set-variable] int total_cds_de_tests = 0; ^ cuffdiff.cpp:2147:6: warning: variable 'total_diff_cds_tests' set but not used [-Wunused-but-set-variable] int total_diff_cds_tests = 0; ^ cuffdiff.cpp:1780:17: warning: variable 'total_mass' set but not used [-Wunused-but-set-variable] long double total_mass = 0.0; ^ cuffdiff.cpp:2018:6: warning: variable 'total_group_de_tests' set but not used [-Wunused-but-set-variable] int total_group_de_tests = 0; ^ cuffdiff.cpp:2122:6: warning: variable 'total_diff_promoter_tests' set but not used [-Wunused-but-set-variable] int total_diff_promoter_tests = 0; ^ cuffdiff.cpp:1683:55: warning: overlapping comparisons always evaluate to true [-Wtautological-overlap-compare] if (most_reps == 1 && (dispersion_method != BLIND || dispersion_method != POISSON)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2332:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] srand48(random_seed); ^ cuffdiff.cpp:2327:5: note: previous statement is here if (random_seed == -1) ^ In file included from cuffdiff.cpp:17: In file included from ./common.h:32: In file included from /usr/local/include/boost/archive/binary_iarchive.hpp:20: In file included from /usr/local/include/boost/archive/binary_iarchive_impl.hpp:21: In file included from /usr/local/include/boost/archive/basic_binary_iarchive.hpp:30: In file included from /usr/local/include/boost/archive/detail/common_iarchive.hpp:21: In file included from /usr/local/include/boost/archive/detail/basic_iarchive.hpp:23: In file included from /usr/local/include/boost/scoped_ptr.hpp:13: In file included from /usr/local/include/boost/smart_ptr/scoped_ptr.hpp:16: /usr/local/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'MassDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffdiff.cpp:1514:28: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here pooled_model = boost::shared_ptr(new MassDispersionModel("pooled", compatible_mass, compatible_variances, est_fitted_var)); ^ In file included from cuffdiff.cpp:17: In file included from ./common.h:32: In file included from /usr/local/include/boost/archive/binary_iarchive.hpp:20: In file included from /usr/local/include/boost/archive/binary_iarchive_impl.hpp:21: In file included from /usr/local/include/boost/archive/basic_binary_iarchive.hpp:30: In file included from /usr/local/include/boost/archive/detail/common_iarchive.hpp:21: In file included from /usr/local/include/boost/archive/detail/basic_iarchive.hpp:23: In file included from /usr/local/include/boost/scoped_ptr.hpp:13: In file included from /usr/local/include/boost/smart_ptr/scoped_ptr.hpp:16: /usr/local/include/boost/core/checked_delete.hpp:44:5: warning: delete called on non-final 'PoissonDispersionModel' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete x; ^ /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:154:20: note: in instantiation of function template specialization 'boost::checked_delete' requested here boost::checked_delete( p ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:280:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count' requested here boost::detail::shared_count( p ).swap( pn ); ^ /usr/local/include/boost/smart_ptr/shared_ptr.hpp:374:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct' requested here boost::detail::sp_pointer_construct( this, p, pn ); ^ cuffdiff.cpp:1541:60: note: in instantiation of function template specialization 'boost::shared_ptr::shared_ptr' requested here boost::shared_ptr disperser = boost::shared_ptr(new PoissonDispersionModel("")); ^ 69 warnings generated. mv -f .deps/cuffdiff.Tpo .deps/cuffdiff.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o cuffdiff cuffdiff.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gtf_to_sam.o -MD -MP -MF .deps/gtf_to_sam.Tpo -c -o gtf_to_sam.o gtf_to_sam.cpp In file included from gtf_to_sam.cpp:22: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from gtf_to_sam.cpp:23: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :389:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from gtf_to_sam.cpp:23: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from gtf_to_sam.cpp:23: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ gtf_to_sam.cpp:142:86: warning: format specifies type 'int' but the argument has type 'RefID' (aka 'unsigned long') [-Wformat] fprintf(stderr, "Warning: Could not find contig name for ID %d, skipping\n", scaff.ref_id()); ~~ ^~~~~~~~~~~~~~ %lu 44 warnings generated. mv -f .deps/gtf_to_sam.Tpo .deps/gtf_to_sam.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o gtf_to_sam gtf_to_sam.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT compress_gtf.o -MD -MP -MF .deps/compress_gtf.Tpo -c -o compress_gtf.o compress_gtf.cpp In file included from compress_gtf.cpp:23: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from compress_gtf.cpp:24: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :389:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from compress_gtf.cpp:24: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from compress_gtf.cpp:24: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from compress_gtf.cpp:29: ./genes.h:210:6: warning: private field '_id' is not used [-Wunused-private-field] int _id; ^ 44 warnings generated. mv -f .deps/compress_gtf.Tpo .deps/compress_gtf.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o compress_gtf compress_gtf.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT gffread.o -MD -MP -MF .deps/gffread.Tpo -c -o gffread.o gffread.cpp In file included from gffread.cpp:2: In file included from ./gff_utils.h:3: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 40 warnings generated. mv -f .deps/gffread.Tpo .deps/gffread.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -o gffread gffread.o libgc.a -lz c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffquant.o -MD -MP -MF .deps/cuffquant.Tpo -c -o cuffquant.o cuffquant.cpp In file included from cuffquant.cpp:19: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from cuffquant.cpp:20: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :201:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from cuffquant.cpp:20: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from cuffquant.cpp:20: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from cuffquant.cpp:24: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ In file included from cuffquant.cpp:37: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ cuffquant.cpp:418:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ cuffquant.cpp:509:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ cuffquant.cpp:742:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^ cuffquant.cpp:760:25: warning: unused variable 'ab_group' [-Wunused-variable] const AbundanceGroup& ab_group = abundances[i]->transcripts; ^ cuffquant.cpp:1218:17: warning: variable 'total_norm_mass' set but not used [-Wunused-but-set-variable] long double total_norm_mass = 0.0; ^ cuffquant.cpp:1219:17: warning: variable 'total_mass' set but not used [-Wunused-but-set-variable] long double total_mass = 0.0; ^ cuffquant.cpp:1536:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] srand48(random_seed); ^ cuffquant.cpp:1531:5: note: previous statement is here if (random_seed == -1) ^ 52 warnings generated. mv -f .deps/cuffquant.Tpo .deps/cuffquant.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o cuffquant cuffquant.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -MT cuffnorm.o -MD -MP -MF .deps/cuffnorm.Tpo -c -o cuffnorm.o cuffnorm.cpp In file included from cuffnorm.cpp:18: ./hits.h:906:48: warning: field '_expression_file_name' will be initialized after field '_ifs' [-Wreorder-ctor] HitFactory(insert_table, reference_table), _expression_file_name(expression_file_name), _ifs(expression_file_name.c_str()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _ifs(expression_file_name.c_str()) _expression_file_name(expression_file_name) In file included from cuffnorm.cpp:19: In file included from ./bundles.h:15: /usr/local/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /usr/local/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :200:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ In file included from cuffnorm.cpp:19: In file included from ./bundles.h:23: ./scaffolds.h:270:7: warning: variable 'r_check' set but not used [-Wunused-but-set-variable] int r_check = left(); ^ In file included from cuffnorm.cpp:19: In file included from ./bundles.h:24: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from cuffnorm.cpp:23: ./update_check.h:81:29: warning: 'bzero' call operates on objects of type 'char' while the size is based on a different type 'char *' [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ~~~~~~~~~~~~ ^~~~~~~~~~~~ ./update_check.h:81:29: note: did you mean to provide an explicit length? bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~ In file included from cuffnorm.cpp:38: In file included from ./differential.h:29: ./replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^ In file included from cuffnorm.cpp:38: ./differential.h:215:5: warning: field 'sample_labels' will be initialized after field 'headers_written' [-Wreorder-ctor] sample_labels(sls), ^~~~~~~~~~~~~~~~~~ headers_written(false) ./differential.h:325:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ ./differential.h:407:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^ ./differential.h:614:56: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n", ~~^ In file included from cuffnorm.cpp:41: ./locfit/local.h:126:9: warning: 'MAX' macro redefined [-Wmacro-redefined] #define MAX(a,b) (((a)>(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:315:9: note: previous definition is here #define MAX(a,b) (((a)>(b))?(a):(b)) ^ In file included from cuffnorm.cpp:41: ./locfit/local.h:127:9: warning: 'MIN' macro redefined [-Wmacro-redefined] #define MIN(a,b) (((a)<(b)) ? (a) : (b)) ^ /usr/include/sys/param.h:314:9: note: previous definition is here #define MIN(a,b) (((a)<(b))?(a):(b)) ^ cuffnorm.cpp:711:17: warning: variable 'total_mass' set but not used [-Wunused-but-set-variable] long double total_mass = 0.0; ^ cuffnorm.cpp:710:17: warning: variable 'total_norm_mass' set but not used [-Wunused-but-set-variable] long double total_norm_mass = 0.0; ^ cuffnorm.cpp:1210:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] srand48(random_seed); ^ cuffnorm.cpp:1205:5: note: previous statement is here if (random_seed == -1) ^ 54 warnings generated. mv -f .deps/cuffnorm.Tpo .deps/cuffnorm.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++14 -pthread -I/usr/local/include -I/usr/local/include -I/usr/local/include/eigen3 -fstack-protector-strong -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -o cuffnorm cuffnorm.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> cufflinks-2.2.1.89_8 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for cufflinks-2.2.1.89_8 ===> Generating temporary packing list Making install in src gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' /bin/mkdir -p '/wrkdirs/usr/ports/biology/cufflinks/work/stage/usr/local/bin' install -s -m 555 cufflinks cuffcompare cuffdiff gtf_to_sam compress_gtf gffread cuffquant cuffnorm '/wrkdirs/usr/ports/biology/cufflinks/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/cufflinks/work/stage/usr/local/bin' install -m 555 cuffmerge '/wrkdirs/usr/ports/biology/cufflinks/work/stage/usr/local/bin' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-03T10:48:16+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=db616534ff' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for cufflinks-2.2.1.89_8 ===> Building cufflinks-2.2.1.89_8 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for cufflinks-2.2.1.89_8 build of biology/cufflinks | cufflinks-2.2.1.89_8 ended at Wed Apr 3 12:18:20 BST 2024 build time: 00:30:11