=>> Building biology/iolib build started at Fri May 2 06:19:26 BST 2025 port directory: /usr/ports/biology/iolib package name: io_lib-1.14.10_1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 583 Dec 29 14:16 /usr/ports/biology/iolib/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-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/14-amd64-default-dan/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/iolib/work/.cache HOME=/wrkdirs/usr/ports/biology/iolib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iolib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/iolib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 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/iolib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/iolib/work/.cache HOME=/wrkdirs/usr/ports/biology/iolib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iolib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/iolib/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 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/io_lib" EXAMPLESDIR="share/examples/io_lib" DATADIR="share/io_lib" WWWDIR="www/io_lib" ETCDIR="etc/io_lib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/io_lib DOCSDIR=/usr/local/share/doc/io_lib EXAMPLESDIR=/usr/local/share/examples/io_lib WWWDIR=/usr/local/www/io_lib ETCDIR=/usr/local/etc/io_lib --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 apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The io_lib port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> io_lib-1.14.10_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> io_lib-1.14.10_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of io_lib-1.14.10_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The io_lib port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by io_lib-1.14.10_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The io_lib port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by io_lib-1.14.10_1 for building => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The io_lib port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by io_lib-1.14.10_1 for building ===> Extracting for io_lib-1.14.10_1 => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for io_lib-1.14.10_1 ===> Applying FreeBSD patches for io_lib-1.14.10_1 from /usr/ports/biology/iolib/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> io_lib-1.14.10_1 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] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> io_lib-1.14.10_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of io_lib-1.14.10_1 ===> io_lib-1.14.10_1 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_3... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_3: .......... 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. ===> io_lib-1.14.10_1 depends on package: autoconf>=2.72 - found ===> Returning to build of io_lib-1.14.10_1 ===> io_lib-1.14.10_1 depends on package: automake>=1.17 - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg-builder.dan.net.uk] Installing automake-1.17... [pkg-builder.dan.net.uk] Extracting automake-1.17: .......... done ===> io_lib-1.14.10_1 depends on package: automake>=1.17 - found ===> Returning to build of io_lib-1.14.10_1 ===> io_lib-1.14.10_1 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.5.4.pkg [pkg-builder.dan.net.uk] Installing libtool-2.5.4... [pkg-builder.dan.net.uk] Extracting libtool-2.5.4: .......... done ===> io_lib-1.14.10_1 depends on executable: libtoolize - found ===> Returning to build of io_lib-1.14.10_1 ===> io_lib-1.14.10_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> io_lib-1.14.10_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of io_lib-1.14.10_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> io_lib-1.14.10_1 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.13.0_1.pkg [pkg-builder.dan.net.uk] Installing curl-8.13.0_1... [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 libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] Extracting curl-8.13.0_1: .......... done ===> io_lib-1.14.10_1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of io_lib-1.14.10_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for io_lib-1.14.10_1 autoreconf2.72: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:67: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.in:67: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.in:67: the top level configure.in:87: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:87: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.in:87: the top level configure.in:88: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:88: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.in:88: the top level configure.in:88: warning: The macro 'AC_LANG_C' is obsolete. configure.in:88: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.in:88: the top level configure.in:108: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:108: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from... configure.in:108: the top level configure.in:141: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:141: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:141: the top level configure.in:199: warning: AC_OUTPUT should be used without arguments. configure.in:199: You should run autoupdate. autoheader2.72: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:65: installing './compile' configure.in:67: installing './config.guess' configure.in:67: installing './config.sub' configure.in:5: installing './install-sh' configure.in:5: installing './missing' io_lib/Makefile.am:152: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' io_lib/Makefile.am: installing './depcomp' progs/Makefile.am:150: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') tests/Makefile.am:59: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') parallel-tests: installing './test-driver' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... cc 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 cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking build system type... amd64-portbld-freebsd14.2 checking host system type... amd64-portbld-freebsd14.2 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 524288 checking how to convert amd64-portbld-freebsd14.2 file names to amd64-portbld-freebsd14.2 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd14.2 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking command to parse /usr/bin/nm output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no 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 for sys/param.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd14.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) /usr/bin/awk checking for curl-config... /usr/local/bin/curl-config checking for the version of libcurl... 8.13.0 checking whether libcurl just needs -lcurl... no checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking for zlib.h... (cached) yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for egrep... (cached) /usr/bin/egrep checking for sys/wait.h that is POSIX.1 compatible... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for stdio_ext.h... no checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... (cached) yes checking for fileno... (cached) yes checking for fstat... (cached) yes checking for mallopt... no checking for cc option to enable large file support... none needed checking for declarations of fseeko and ftello... yes checking for getpagesize... (cached) yes checking for working mmap... (cached) yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... (cached) yes checking for fsync... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for io_lib-1.14.10_1 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' Making all in io_lib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/io_lib' /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. 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libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-compression.Tpo .deps/libstaden_read_la-compression.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-ztr.Tpo .deps/libstaden_read_la-ztr.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o ztr_translate.c:478:9: warning: variable 'nbytes' set but not used [-Wunused-but-set-variable] 478 | int nbytes = chunk->dlength; | ^ ztr_translate.c:614:9: warning: variable 'nbytes' set but not used [-Wunused-but-set-variable] 614 | int nbytes = chunk->dlength; | ^ 2 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-ztr_translate.Tpo .deps/libstaden_read_la-ztr_translate.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT 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libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-seqIOABI.Tpo .deps/libstaden_read_la-seqIOABI.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.o seqIOALF.c:274:9: warning: variable 'num_points' set but not used [-Wunused-but-set-variable] 274 | int num_points; /* keeps track of the actual number of points, | ^ 1 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-fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c -o libstaden_read_la-rANS_static.lo `test -f 'rANS_static.c' || echo './'`rANS_static.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c rANS_static.c -fPIC -DPIC -o .libs/libstaden_read_la-rANS_static.o rANS_static.c:274:20: warning: unused function 'RansDecSymbolInit' [-Wunused-function] 274 | static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq) | ^~~~~~~~~~~~~~~~~ rANS_static.c:318:20: warning: unused function 'RansDecAdvanceSymbol' [-Wunused-function] 318 | static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits) | ^~~~~~~~~~~~~~~~~~~~ rANS_static.c:336:20: warning: unused function 'RansDecAdvanceSymbolStep' [-Wunused-function] 336 | static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits) | ^~~~~~~~~~~~~~~~~~~~~~~~ rANS_static.c:348:20: warning: unused function 'RansDecRenorm' [-Wunused-function] 348 | static inline void RansDecRenorm(RansState* r, uint8_t** pptr) { | ^~~~~~~~~~~~~ rANS_static.c:470:20: warning: unused function 'RansDecAdvanceSymbol32' [-Wunused-function] 470 | static inline void RansDecAdvanceSymbol32(RansState* r, uint8_t** pptr, RansDecSymbol32 const* sym, uint32_t scale_bits) | ^~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c rANS_static.c -o libstaden_read_la-rANS_static.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-rANS_static.Tpo .deps/libstaden_read_la-rANS_static.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c -o libstaden_read_la-rANS_static4x16pr.lo `test -f 'rANS_static4x16pr.c' || echo './'`rANS_static4x16pr.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -fPIC -DPIC -o .libs/libstaden_read_la-rANS_static4x16pr.o rANS_static4x16pr.c:107:20: warning: unused function 'RansEncPut' [-Wunused-function] 107 | static inline void RansEncPut(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits) | ^~~~~~~~~~ rANS_static4x16pr.c:149:24: warning: unused function 'RansDecGet' [-Wunused-function] 149 | static inline uint32_t RansDecGet(RansState* r, uint32_t scale_bits) | ^~~~~~~~~~ rANS_static4x16pr.c:282:20: warning: unused function 'RansDecSymbolInit' [-Wunused-function] 282 | static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq) | ^~~~~~~~~~~~~~~~~ rANS_static4x16pr.c:334:20: warning: unused function 'RansDecAdvanceSymbol' [-Wunused-function] 334 | static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits) | ^~~~~~~~~~~~~~~~~~~~ rANS_static4x16pr.c:352:20: warning: unused function 'RansDecAdvanceSymbolStep' [-Wunused-function] 352 | static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits) | ^~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -o libstaden_read_la-rANS_static4x16pr.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-rANS_static4x16pr.Tpo .deps/libstaden_read_la-rANS_static4x16pr.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o cram_codecs.c:1395:19: warning: variable 'ntot' set but not used [-Wunused-but-set-variable] 1395 | int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k; | ^ 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o cram_decode.c:2292:9: warning: variable 'r' set but not used [-Wunused-but-set-variable] 2292 | int r = 0; | ^ 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_stats.Tpo .deps/libstaden_read_la-cram_stats.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3742 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../io_lib/cram_io.h:105:388: note: expanded from macro 'itf8_put' 105 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~^~~~~ cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3742 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../io_lib/cram_io.h:105:367: note: expanded from macro 'itf8_put' 105 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~~^~~~~ cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3742 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../io_lib/cram_io.h:105:345: note: expanded from macro 'itf8_put' 105 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~~~~~~^~~~~ cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] 3742 | cp += itf8_put(cp, -2); | ^~~~~~~~~~~~~~~~ ../io_lib/cram_io.h:105:311: note: expanded from macro 'itf8_put' 105 | #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) | ~~~~~^~~~~~~~~~~~~~~~~ 4 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_index.Tpo .deps/libstaden_read_la-cram_index.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-zfio.Tpo .deps/libstaden_read_la-zfio.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-string_alloc.Tpo .deps/libstaden_read_la-string_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_bambam.Tpo .deps/libstaden_read_la-cram_bambam.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-bgzip.Tpo .deps/libstaden_read_la-bgzip.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c -o libstaden_read_la-tokenise_name3.lo `test -f 'tokenise_name3.c' || echo './'`tokenise_name3.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o .libs/libstaden_read_la-tokenise_name3.o tokenise_name3.c:1302:9: warning: variable 'ndesc' set but not used [-Wunused-but-set-variable] 1302 | int ndesc = 0; | ^ 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -o libstaden_read_la-tokenise_name3.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-tokenise_name3.Tpo .deps/libstaden_read_la-tokenise_name3.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c -o libstaden_read_la-fqzcomp_qual.lo `test -f 'fqzcomp_qual.c' || echo './'`fqzcomp_qual.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o .libs/libstaden_read_la-fqzcomp_qual.o fqzcomp_qual.c:123:9: warning: variable 'ndup0' set but not used [-Wunused-but-set-variable] 123 | int ndup0 = 0, ndup1 = 0; | ^ fqzcomp_qual.c:123:20: warning: variable 'ndup1' set but not used [-Wunused-but-set-variable] 123 | int ndup0 = 0, ndup1 = 0; | ^ fqzcomp_qual.c:155:9: warning: variable 'nrun' set but not used [-Wunused-but-set-variable] 155 | int nrun = 0; | ^ fqzcomp_qual.c:156:9: warning: variable 'nswitch' set but not used [-Wunused-but-set-variable] 156 | int nswitch = 0; | ^ 4 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -o libstaden_read_la-fqzcomp_qual.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-fqzcomp_qual.Tpo .deps/libstaden_read_la-fqzcomp_qual.Plo /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -version-info 13:0:0 -lpthread -fstack-protector-strong -o libstaden-read.la -rpath /usr/local/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-rANS_static.lo libstaden_read_la-rANS_static4x16pr.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo libstaden_read_la-tokenise_name3.lo libstaden_read_la-fqzcomp_qual.lo -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2 libtool: link: cc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-rANS_static.o .libs/libstaden_read_la-rANS_static4x16pr.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o .libs/libstaden_read_la-tokenise_name3.o .libs/libstaden_read_la-fqzcomp_qual.o -lpthread -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2 -O2 -fstack-protector-strong -fstack-protector-strong -Wl,-soname -Wl,libstaden-read.so.13 -o .libs/libstaden-read.so.13.0.0 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.13" && ln -s "libstaden-read.so.13.0.0" "libstaden-read.so.13") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.13.0.0" "libstaden-read.so") libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-rANS_static.o libstaden_read_la-rANS_static4x16pr.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o 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-lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/srf2fastq srf2fastq.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf2fasta.o -MD -MP -MF .deps/srf2fasta.Tpo -c -o srf2fasta.o srf2fasta.c mv -f .deps/srf2fasta.Tpo .deps/srf2fasta.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/srf2fasta srf2fasta.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_filter.o -MD -MP -MF .deps/srf_filter.Tpo -c -o srf_filter.o srf_filter.c srf_filter.c:172:11: warning: variable 'lLineCount' set but not used [-Wunused-but-set-variable] 172 | long lLineCount; /* Current line number */ | ^ srf_filter.c:173:11: warning: variable 'lTotalChars' set but not used [-Wunused-but-set-variable] 173 | long lTotalChars; /* Total characters read */ | ^ 2 warnings generated. mv -f .deps/srf_filter.Tpo .deps/srf_filter.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_info.o -MD -MP -MF .deps/srf_info.Tpo -c -o srf_info.o srf_info.c mv -f .deps/srf_info.Tpo .deps/srf_info.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/srf_info srf_info.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_list.o -MD -MP -MF .deps/srf_list.Tpo -c -o srf_list.o srf_list.c mv -f .deps/srf_list.Tpo .deps/srf_list.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/srf_list srf_list.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT hash_exp.o -MD -MP -MF .deps/hash_exp.Tpo -c -o hash_exp.o hash_exp.c mv -f .deps/hash_exp.Tpo .deps/hash_exp.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_dump.o -MD -MP -MF .deps/cram_dump.Tpo -c -o cram_dump.o cram_dump.c mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_index.o -MD -MP -MF .deps/cram_index.Tpo -c -o cram_index.o cram_index.c mv -f .deps/cram_index.Tpo .deps/cram_index.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scramble.o -MD -MP -MF .deps/scramble.Tpo -c -o scramble.o scramble.c mv -f .deps/scramble.Tpo .deps/scramble.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_merge.o -MD -MP -MF .deps/scram_merge.Tpo -c -o scram_merge.o scram_merge.c mv -f .deps/scram_merge.Tpo .deps/scram_merge.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_pileup.o -MD -MP -MF .deps/scram_pileup.Tpo -c -o scram_pileup.o scram_pileup.c mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_flagstat.o -MD -MP -MF .deps/scram_flagstat.Tpo -c -o scram_flagstat.o scram_flagstat.c mv -f .deps/scram_flagstat.Tpo .deps/scram_flagstat.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_test.o -MD -MP -MF .deps/scram_test.Tpo -c -o scram_test.o scram_test.c mv -f .deps/scram_test.Tpo .deps/scram_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_size.o -MD -MP -MF .deps/cram_size.Tpo -c -o cram_size.o cram_size.c mv -f .deps/cram_size.Tpo .deps/cram_size.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_filter.o -MD -MP -MF .deps/cram_filter.Tpo -c -o cram_filter.o cram_filter.c mv -f .deps/cram_filter.Tpo .deps/cram_filter.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs' Making all in tests gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/tests' cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/tests' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for io_lib-1.14.10_1 ===> Generating temporary packing list if test -z 'strip'; then \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' Making install in io_lib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/io_lib' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/io_lib' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c -s libstaden-read.la '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.13.0.0 /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.so.13.0.0 libtool: install: strip --strip-unneeded /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.so.13.0.0 libtool: install: (cd /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib && { ln -s -f libstaden-read.so.13.0.0 libstaden-read.so.13 || { rm -f libstaden-read.so.13 && ln -s libstaden-read.so.13.0.0 libstaden-read.so.13; }; }) libtool: install: (cd /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib && { ln -s -f libstaden-read.so.13.0.0 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.13.0.0 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: install: strip --strip-debug /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: install: ranlib /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/io_lib' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/io_lib' Making install in progs gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ../libtool --mode=install /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/convert_trace /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/makeSCF /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/extract_seq /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/extract_qual /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/extract_fastq /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/extract_fastq libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s index_tar /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scf_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scf_info /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scf_update /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/get_comment /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/hash_tar /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/hash_extract /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/hash_list /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/trace_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/hash_sff /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/append_sff /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/ztr_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf_dump_all /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf_index_hash /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf_extract_linear /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf_extract_hash /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf2fastq /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf2fasta /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf_filter /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf_info /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/srf_list /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/hash_exp /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/cram_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/cram_index /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scramble /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scram_merge /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scram_pileup /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scram_flagstat /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/scram_test /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/cram_size /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/install-sh -c -s .libs/cram_filter /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_filter gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs' Making install in tests gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/tests' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/tests' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/tests' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/tests' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' install -m 555 io_lib-config '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man1' install -m 0644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man1' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man3' install -m 0644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man3' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man4' install -m 0644 man/man4/Read.4 '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man4' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/io_lib' install -m 0644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/zfio.h '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/io_lib' install -m 0644 io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib_config.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/io_lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' ====> 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=2025-05-02T05:19:26+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for io_lib-1.14.10_1 ===> Building io_lib-1.14.10_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for io_lib-1.14.10_1 build of biology/iolib | io_lib-1.14.10_1 ended at Fri May 2 06:21:16 BST 2025 build time: 00:01:50