=>> Building biology/jellyfish build started at Fri May 2 09:26:28 BST 2025 port directory: /usr/ports/biology/jellyfish package name: Jellyfish-2.3.0_4 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1067 Dec 29 14:16 /usr/ports/biology/jellyfish/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: 02 ---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/02/.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--- ===> The following configuration options are available for Jellyfish-2.3.0_4: NLS=on: Native Language Support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-nls --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/jellyfish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jellyfish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/jellyfish/work/.cache HOME=/wrkdirs/usr/ports/biology/jellyfish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/jellyfish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/jellyfish/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh 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/jellyfish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jellyfish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/jellyfish/work/.cache HOME=/wrkdirs/usr/ports/biology/jellyfish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/jellyfish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/jellyfish/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -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-- VER=2.3.0 NLS="" NO_NLS="@comment " OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/Jellyfish" EXAMPLESDIR="share/examples/Jellyfish" DATADIR="share/Jellyfish" WWWDIR="www/Jellyfish" ETCDIR="etc/Jellyfish" --End PLIST_SUB-- --SUB_LIST-- NLS="" NO_NLS="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Jellyfish DOCSDIR=/usr/local/share/doc/Jellyfish EXAMPLESDIR=/usr/local/share/examples/Jellyfish WWWDIR=/usr/local/www/Jellyfish ETCDIR=/usr/local/etc/Jellyfish --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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> Jellyfish-2.3.0_4 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 ===> Jellyfish-2.3.0_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of Jellyfish-2.3.0_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by Jellyfish-2.3.0_4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by Jellyfish-2.3.0_4 for building => SHA256 Checksum OK for jellyfish-2.3.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by Jellyfish-2.3.0_4 for building ===> Extracting for Jellyfish-2.3.0_4 => SHA256 Checksum OK for jellyfish-2.3.0.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 Jellyfish-2.3.0_4 ===> Applying FreeBSD patches for Jellyfish-2.3.0_4 from /usr/ports/biology/jellyfish/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> Jellyfish-2.3.0_4 depends on package: gettext-runtime>=0.22_1 - not found ===> Installing existing package /packages/All/gettext-runtime-0.23.1.pkg [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 ===> Jellyfish-2.3.0_4 depends on package: gettext-runtime>=0.22_1 - found ===> Returning to build of Jellyfish-2.3.0_4 ===> Jellyfish-2.3.0_4 depends on executable: msgfmt - not found ===> Installing existing package /packages/All/gettext-tools-0.23.1_1.pkg [pkg-builder.dan.net.uk] Installing gettext-tools-0.23.1_1... [pkg-builder.dan.net.uk] `-- Installing libtextstyle-0.23.1... [pkg-builder.dan.net.uk] `-- Extracting libtextstyle-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gettext-tools-0.23.1_1: .......... done ===> Jellyfish-2.3.0_4 depends on executable: msgfmt - found ===> Returning to build of Jellyfish-2.3.0_4 ===> Jellyfish-2.3.0_4 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. ===> Jellyfish-2.3.0_4 depends on file: /usr/local/bin/ccache - found ===> Returning to build of Jellyfish-2.3.0_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> Jellyfish-2.3.0_4 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.21.pkg [pkg-builder.dan.net.uk] Installing htslib-1.21... [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 [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.21: .......... done ===> Jellyfish-2.3.0_4 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of Jellyfish-2.3.0_4 ===> Jellyfish-2.3.0_4 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for Jellyfish-2.3.0_4 configure: WARNING: unrecognized options: --enable-nls configure: loading site script /usr/ports/Templates/config.site checking build system type... amd64-portbld-freebsd14.2 checking host system type... amd64-portbld-freebsd14.2 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking for style of include used by make... GNU 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 we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 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 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 ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib 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 how to run the C preprocessor... cpp checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.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 ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... no checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.2 ld.so checking how to hardcode library paths into programs... immediate checking for HTSLIB... no checking for samtools... no checking for unix2dos... no checking for md5sum... md5sum checking for yaggo... false checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 406f0:15200800:fffa3203:1f8bfbff checking for x86 cpuid 0x00000007 output... 0:1c27ab:0:bc000400 checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C++ compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C++ compiler accepts -madx... yes checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... no configure: WARNING: Your processor and OS supports ABM instructions but not your compiler, can you try another compiler? checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... yes checking for std::numeric_limits<__int128>... yes checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... no checking for sys/syscall.h... yes checking for siginfo_t.si_int... no checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --enable-nls =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for Jellyfish-2.3.0_4 /usr/bin/make all-am depbase=`echo lib/rectangular_binary_matrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/rectangular_binary_matrix.lo -MD -MP -MF $depbase.Tpo -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/rectangular_binary_matrix.lo -MD -MP -MF lib/.deps/rectangular_binary_matrix.Tpo -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/rectangular_binary_matrix.lo -MD -MP -MF lib/.deps/rectangular_binary_matrix.Tpo -c lib/rectangular_binary_matrix.cc -o lib/rectangular_binary_matrix.o >/dev/null 2>&1 depbase=`echo lib/mer_dna.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/mer_dna.lo -MD -MP -MF $depbase.Tpo -c -o lib/mer_dna.lo lib/mer_dna.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/mer_dna.lo -MD -MP -MF lib/.deps/mer_dna.Tpo -c lib/mer_dna.cc -fPIC -DPIC -o lib/.libs/mer_dna.o In file included from lib/mer_dna.cc:10: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ 3 warnings generated. libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/mer_dna.lo -MD -MP -MF lib/.deps/mer_dna.Tpo -c lib/mer_dna.cc -o lib/mer_dna.o >/dev/null 2>&1 depbase=`echo lib/storage.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/storage.lo -MD -MP -MF $depbase.Tpo -c -o lib/storage.lo lib/storage.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/storage.lo -MD -MP -MF lib/.deps/storage.Tpo -c lib/storage.cc -fPIC -DPIC -o lib/.libs/storage.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/storage.lo -MD -MP -MF lib/.deps/storage.Tpo -c lib/storage.cc -o lib/storage.o >/dev/null 2>&1 depbase=`echo lib/allocators_mmap.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/allocators_mmap.lo -MD -MP -MF $depbase.Tpo -c -o lib/allocators_mmap.lo lib/allocators_mmap.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/allocators_mmap.lo -MD -MP -MF lib/.deps/allocators_mmap.Tpo -c lib/allocators_mmap.cc -fPIC -DPIC -o lib/.libs/allocators_mmap.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/allocators_mmap.lo -MD -MP -MF lib/.deps/allocators_mmap.Tpo -c lib/allocators_mmap.cc -o lib/allocators_mmap.o >/dev/null 2>&1 depbase=`echo lib/misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/misc.lo -MD -MP -MF $depbase.Tpo -c -o lib/misc.lo lib/misc.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/misc.lo -MD -MP -MF lib/.deps/misc.Tpo -c lib/misc.cc -fPIC -DPIC -o lib/.libs/misc.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/misc.lo -MD -MP -MF lib/.deps/misc.Tpo -c lib/misc.cc -o lib/misc.o >/dev/null 2>&1 depbase=`echo lib/int128.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/int128.lo -MD -MP -MF $depbase.Tpo -c -o lib/int128.lo lib/int128.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/int128.lo -MD -MP -MF lib/.deps/int128.Tpo -c lib/int128.cc -fPIC -DPIC -o lib/.libs/int128.o In file included from lib/int128.cc:14: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ 3 warnings generated. libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/int128.lo -MD -MP -MF lib/.deps/int128.Tpo -c lib/int128.cc -o lib/int128.o >/dev/null 2>&1 depbase=`echo lib/thread_exec.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/thread_exec.lo -MD -MP -MF $depbase.Tpo -c -o lib/thread_exec.lo lib/thread_exec.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/thread_exec.lo -MD -MP -MF lib/.deps/thread_exec.Tpo -c lib/thread_exec.cc -fPIC -DPIC -o lib/.libs/thread_exec.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/thread_exec.lo -MD -MP -MF lib/.deps/thread_exec.Tpo -c lib/thread_exec.cc -o lib/thread_exec.o >/dev/null 2>&1 depbase=`echo lib/jsoncpp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/jsoncpp.lo -MD -MP -MF $depbase.Tpo -c -o lib/jsoncpp.lo lib/jsoncpp.cpp && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/jsoncpp.lo -MD -MP -MF lib/.deps/jsoncpp.Tpo -c lib/jsoncpp.cpp -fPIC -DPIC -o lib/.libs/jsoncpp.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/jsoncpp.lo -MD -MP -MF lib/.deps/jsoncpp.Tpo -c lib/jsoncpp.cpp -o lib/jsoncpp.o >/dev/null 2>&1 depbase=`echo lib/time.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/time.lo -MD -MP -MF $depbase.Tpo -c -o lib/time.lo lib/time.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/time.lo -MD -MP -MF lib/.deps/time.Tpo -c lib/time.cc -fPIC -DPIC -o lib/.libs/time.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/time.lo -MD -MP -MF lib/.deps/time.Tpo -c lib/time.cc -o lib/time.o >/dev/null 2>&1 depbase=`echo lib/generator_manager.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/generator_manager.lo -MD -MP -MF $depbase.Tpo -c -o lib/generator_manager.lo lib/generator_manager.cc && mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/generator_manager.lo -MD -MP -MF lib/.deps/generator_manager.Tpo -c lib/generator_manager.cc -fPIC -DPIC -o lib/.libs/generator_manager.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT lib/generator_manager.lo -MD -MP -MF lib/.deps/generator_manager.Tpo -c lib/generator_manager.cc -o lib/generator_manager.o >/dev/null 2>&1 /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -version-info 2:0:0 -fstack-protector-strong -o libjellyfish-2.0.la -rpath /usr/local/lib lib/rectangular_binary_matrix.lo lib/mer_dna.lo lib/storage.lo lib/allocators_mmap.lo lib/misc.lo lib/int128.lo lib/thread_exec.lo lib/jsoncpp.lo lib/time.lo lib/generator_manager.lo libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o lib/.libs/rectangular_binary_matrix.o lib/.libs/mer_dna.o lib/.libs/storage.o lib/.libs/allocators_mmap.o lib/.libs/misc.o lib/.libs/int128.o lib/.libs/thread_exec.o lib/.libs/jsoncpp.o lib/.libs/time.o lib/.libs/generator_manager.o -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -fstack-protector-strong -Wl,-soname -Wl,libjellyfish-2.0.so.2 -o .libs/libjellyfish-2.0.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so.2" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so.2") libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so") libtool: link: ar cru .libs/libjellyfish-2.0.a lib/rectangular_binary_matrix.o lib/mer_dna.o lib/storage.o lib/allocators_mmap.o lib/misc.o lib/int128.o lib/thread_exec.o lib/jsoncpp.o lib/time.o lib/generator_manager.o libtool: link: ranlib .libs/libjellyfish-2.0.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-2.0.la" && ln -s "../libjellyfish-2.0.la" "libjellyfish-2.0.la" ) depbase=`echo sub_commands/jellyfish.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/jellyfish.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc && mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/count_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/count_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/count_main.o sub_commands/count_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/count_main.cc:38: In file included from ./include/jellyfish/hash_counter.hpp:14: In file included from ./include/jellyfish/large_hash_array.hpp:18: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/count_main.cc:45: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: In file included from ./include/jellyfish/sorted_dumper.hpp:21: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ In file included from sub_commands/count_main.cc:45: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: ./include/jellyfish/sorted_dumper.hpp:76:34: warning: variable 'count' set but not used [-Wunused-but-set-variable] 76 | size_t count = 0; | ^ sub_commands/count_main.cc:153:12: warning: variable 'count' set but not used [-Wunused-but-set-variable] 153 | size_t count = 0; | ^ In file included from sub_commands/count_main.cc:38: In file included from ./include/jellyfish/hash_counter.hpp:14: In file included from ./include/jellyfish/large_hash_array.hpp:18: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/count_main.cc:47: In file included from ./include/jellyfish/mer_dna_bloom_counter.hpp:13: ./include/jellyfish/bloom_counter2.hpp:112:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 112 | typename super::prefetch_info pinfo[super::k_]; | ^~~~~~~~~ ./include/jellyfish/bloom_common.hpp:78:47: note: in instantiation of member function 'jellyfish::bloom_counter2_base>::check__' requested here 78 | return static_cast(this)->check__(hashes); | ^ sub_commands/count_main.cc:116:31: note: in instantiation of member function 'jellyfish::bloom_base, jellyfish::bloom_counter2_base>>::check' requested here 116 | unsigned int c = counter_.check(m); | ^ ./include/jellyfish/bloom_counter2.hpp:112:41: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function 112 | typename super::prefetch_info pinfo[super::k_]; | ^ In file included from sub_commands/count_main.cc:47: In file included from ./include/jellyfish/mer_dna_bloom_counter.hpp:14: ./include/jellyfish/bloom_filter.hpp:47:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 47 | typename super::prefetch_info pinfo[super::k_]; | ^~~~~~~~~ ./include/jellyfish/bloom_common.hpp:72:41: note: in instantiation of member function 'jellyfish::bloom_filter_base>::insert__' requested here 72 | return static_cast(this)->insert__(hashes); | ^ sub_commands/count_main.cc:128:26: note: in instantiation of member function 'jellyfish::bloom_base, jellyfish::bloom_filter_base>>::insert' requested here 128 | unsigned int c = bf_.insert(m); | ^ ./include/jellyfish/bloom_filter.hpp:47:41: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function 47 | typename super::prefetch_info pinfo[super::k_]; | ^ In file included from sub_commands/count_main.cc:38: In file included from ./include/jellyfish/hash_counter.hpp:14: In file included from ./include/jellyfish/large_hash_array.hpp:18: ./include/jellyfish/mer_dna.hpp:682:10: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 682 | char s[mer.k() + 1]; | ^~~~~~~~~~~ ./include/jellyfish/text_dumper.hpp:19:8: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator<<>' requested here 19 | out << key << " " << val << "\n"; | ^ ./include/jellyfish/text_dumper.hpp:44:12: note: in instantiation of member function 'jellyfish::text_writer, unsigned long>::write' requested here 44 | writer.write(out, item->key_, item->val_); | ^ ./include/jellyfish/sorted_dumper.hpp:87:34: note: in instantiation of member function 'jellyfish::text_dumper>>::write_key_value_pair' requested here 87 | static_cast(this)->write_key_value_pair(buffer, item); | ^ ./include/jellyfish/text_dumper.hpp:31:3: note: in instantiation of member function 'jellyfish::sorted_dumper>>, jellyfish::large_hash::array>>::start' requested here 31 | text_dumper(int nb_threads, const char* file_prefix, file_header* header = 0) : | ^ sub_commands/count_main.cc:281:22: note: in instantiation of member function 'jellyfish::text_dumper>>::text_dumper' requested here 281 | dumper.reset(new text_dumper(args.threads_arg, args.output_arg, &header)); | ^ ./include/jellyfish/mer_dna.hpp:682:10: note: function parameter 'mer' with unknown value cannot be used in a constant expression 682 | char s[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:680:76: note: declared here 680 | inline std::ostream& operator<<(std::ostream& os, const mer_base& mer) { | ^ 11 warnings generated. depbase=`echo sub_commands/info_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/info_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/info_main.o sub_commands/info_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/info_main.cc:6: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ 3 warnings generated. depbase=`echo sub_commands/dump_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/dump_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/dump_main.o sub_commands/dump_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/dump_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/dump_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: In file included from ./include/jellyfish/sorted_dumper.hpp:21: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ In file included from sub_commands/dump_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: ./include/jellyfish/sorted_dumper.hpp:76:34: warning: variable 'count' set but not used [-Wunused-but-set-variable] 76 | size_t count = 0; | ^ In file included from sub_commands/dump_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/dump_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:13: ./include/jellyfish/mer_dna.hpp:682:10: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 682 | char s[mer.k() + 1]; | ^~~~~~~~~~~ sub_commands/dump_main.cc:43:11: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator<<>' requested here 43 | out << it.key() << spacer << it.val() << "\n"; | ^ sub_commands/dump_main.cc:77:5: note: in instantiation of function template specialization 'dump, unsigned long>>' requested here 77 | dump(reader, out, args.lower_count_arg, args.upper_count_arg); | ^ ./include/jellyfish/mer_dna.hpp:682:10: note: function parameter 'mer' with unknown value cannot be used in a constant expression 682 | char s[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:680:76: note: declared here 680 | inline std::ostream& operator<<(std::ostream& os, const mer_base& mer) { | ^ ./include/jellyfish/mer_dna.hpp:694:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 694 | char buffer[mer.k() + 1]; | ^~~~~~~~~~~ ./include/jellyfish/text_dumper.hpp:74:9: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator>>>' requested here 74 | is_ >> key_ >> val_; | ^ sub_commands/dump_main.cc:40:14: note: in instantiation of member function 'jellyfish::text_reader, unsigned long>::next' requested here 40 | while(it.next()) { | ^ sub_commands/dump_main.cc:80:5: note: in instantiation of function template specialization 'dump, unsigned long>>' requested here 80 | dump(reader, out, args.lower_count_arg, args.upper_count_arg); | ^ ./include/jellyfish/mer_dna.hpp:694:15: note: function parameter 'mer' with unknown value cannot be used in a constant expression 694 | char buffer[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:689:70: note: declared here 689 | inline std::istream& operator>>(std::istream& is, mer_base& mer) { | ^ 9 warnings generated. depbase=`echo sub_commands/histo_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/histo_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/histo_main.o sub_commands/histo_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/histo_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/histo_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: In file included from ./include/jellyfish/sorted_dumper.hpp:21: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ In file included from sub_commands/histo_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: ./include/jellyfish/sorted_dumper.hpp:76:34: warning: variable 'count' set but not used [-Wunused-but-set-variable] 76 | size_t count = 0; | ^ In file included from sub_commands/histo_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/histo_main.cc:28: In file included from ./include/jellyfish/jellyfish.hpp:13: ./include/jellyfish/mer_dna.hpp:694:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 694 | char buffer[mer.k() + 1]; | ^~~~~~~~~~~ ./include/jellyfish/text_dumper.hpp:74:9: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator>>>' requested here 74 | is_ >> key_ >> val_; | ^ sub_commands/histo_main.cc:36:16: note: in instantiation of member function 'jellyfish::text_reader, unsigned long>::next' requested here 36 | while(reader.next()) { | ^ sub_commands/histo_main.cc:77:5: note: in instantiation of function template specialization 'compute_histo, unsigned long>>' requested here 77 | compute_histo(reader, base, ceil, histo, nb_buckets, inc); | ^ ./include/jellyfish/mer_dna.hpp:694:15: note: function parameter 'mer' with unknown value cannot be used in a constant expression 694 | char buffer[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:689:70: note: declared here 689 | inline std::istream& operator>>(std::istream& is, mer_base& mer) { | ^ 8 warnings generated. depbase=`echo sub_commands/stats_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/stats_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/stats_main.o sub_commands/stats_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/stats_main.cc:27: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/stats_main.cc:27: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: In file included from ./include/jellyfish/sorted_dumper.hpp:21: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ In file included from sub_commands/stats_main.cc:27: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: ./include/jellyfish/sorted_dumper.hpp:76:34: warning: variable 'count' set but not used [-Wunused-but-set-variable] 76 | size_t count = 0; | ^ In file included from sub_commands/stats_main.cc:27: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/stats_main.cc:27: In file included from ./include/jellyfish/jellyfish.hpp:13: ./include/jellyfish/mer_dna.hpp:694:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 694 | char buffer[mer.k() + 1]; | ^~~~~~~~~~~ ./include/jellyfish/text_dumper.hpp:74:9: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator>>>' requested here 74 | is_ >> key_ >> val_; | ^ sub_commands/stats_main.cc:38:16: note: in instantiation of member function 'jellyfish::text_reader, unsigned long>::next' requested here 38 | while(reader.next()) { | ^ sub_commands/stats_main.cc:71:5: note: in instantiation of function template specialization 'compute_stats, unsigned long>>' requested here 71 | compute_stats(reader, args.lower_count_arg, args.upper_count_arg, uniq, distinct, total, max); | ^ ./include/jellyfish/mer_dna.hpp:694:15: note: function parameter 'mer' with unknown value cannot be used in a constant expression 694 | char buffer[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:689:70: note: declared here 689 | inline std::istream& operator>>(std::istream& is, mer_base& mer) { | ^ 8 warnings generated. depbase=`echo sub_commands/merge_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/merge_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/merge_main.o sub_commands/merge_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/merge_main.cc:17: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ 3 warnings generated. depbase=`echo sub_commands/bc_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/bc_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/bc_main.o sub_commands/bc_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/bc_main.cc:26: In file included from ./include/jellyfish/mer_iterator.hpp:14: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/bc_main.cc:31: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ In file included from sub_commands/bc_main.cc:26: In file included from ./include/jellyfish/mer_iterator.hpp:14: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/bc_main.cc:29: In file included from ./include/jellyfish/mer_dna_bloom_counter.hpp:13: ./include/jellyfish/bloom_counter2.hpp:59:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 59 | typename super::prefetch_info pinfo[super::k_]; | ^~~~~~~~~ ./include/jellyfish/bloom_common.hpp:72:41: note: in instantiation of member function 'jellyfish::bloom_counter2_base>::insert__' requested here 72 | return static_cast(this)->insert__(hashes); | ^ sub_commands/bc_main.cc:69:15: note: in instantiation of member function 'jellyfish::bloom_base, jellyfish::bloom_counter2_base>>::insert' requested here 69 | filter_.insert(*mers); | ^ sub_commands/bc_main.cc:132:50: note: in instantiation of member function 'mer_bloom_counter>::start' requested here 132 | mer_bloom_counter counter(args.threads_arg, filter, | ^ ./include/jellyfish/bloom_counter2.hpp:59:41: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function 59 | typename super::prefetch_info pinfo[super::k_]; | ^ 7 warnings generated. depbase=`echo sub_commands/query_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/query_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/query_main.o sub_commands/query_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/query_main.cc:21: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ In file included from sub_commands/query_main.cc:24: In file included from ./include/jellyfish/mer_iterator.hpp:14: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/query_main.cc:27: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: ./include/jellyfish/sorted_dumper.hpp:76:34: warning: variable 'count' set but not used [-Wunused-but-set-variable] 76 | size_t count = 0; | ^ In file included from sub_commands/query_main.cc:24: In file included from ./include/jellyfish/mer_iterator.hpp:14: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from sub_commands/query_main.cc:24: In file included from ./include/jellyfish/mer_iterator.hpp:14: ./include/jellyfish/mer_dna.hpp:682:10: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 682 | char s[mer.k() + 1]; | ^~~~~~~~~~~ sub_commands/query_main.cc:50:9: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator<<>' requested here 50 | out << *mers << " " << db.check(*mers) << "\n"; | ^ sub_commands/query_main.cc:105:5: note: in instantiation of function template specialization 'query_from_sequence, jellyfish::bloom_counter2>>' requested here 105 | query_from_sequence(args.sequence_arg.begin(), args.sequence_arg.end(), filter, out, header.canonical()); | ^ ./include/jellyfish/mer_dna.hpp:682:10: note: function parameter 'mer' with unknown value cannot be used in a constant expression 682 | char s[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:680:76: note: declared here 680 | inline std::ostream& operator<<(std::ostream& os, const mer_base& mer) { | ^ In file included from sub_commands/query_main.cc:25: In file included from ./include/jellyfish/mer_dna_bloom_counter.hpp:13: ./include/jellyfish/bloom_counter2.hpp:112:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 112 | typename super::prefetch_info pinfo[super::k_]; | ^~~~~~~~~ ./include/jellyfish/bloom_common.hpp:78:47: note: in instantiation of member function 'jellyfish::bloom_counter2_base>::check__' requested here 78 | return static_cast(this)->check__(hashes); | ^ sub_commands/query_main.cc:50:31: note: in instantiation of member function 'jellyfish::bloom_base, jellyfish::bloom_counter2_base>>::check' requested here 50 | out << *mers << " " << db.check(*mers) << "\n"; | ^ sub_commands/query_main.cc:105:5: note: in instantiation of function template specialization 'query_from_sequence, jellyfish::bloom_counter2>>' requested here 105 | query_from_sequence(args.sequence_arg.begin(), args.sequence_arg.end(), filter, out, header.canonical()); | ^ ./include/jellyfish/bloom_counter2.hpp:112:41: note: implicit use of 'this' pointer is only allowed within the evaluation of a call to a 'constexpr' member function 112 | typename super::prefetch_info pinfo[super::k_]; | ^ 9 warnings generated. depbase=`echo sub_commands/cite_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/cite_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/cite_main.o sub_commands/cite_main.cc && mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/mem_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sub_commands/mem_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/mem_main.o sub_commands/mem_main.cc && mv -f $depbase.Tpo $depbase.Po In file included from sub_commands/mem_main.cc:20: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ 3 warnings generated. depbase=`echo jellyfish/merge_files.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT jellyfish/merge_files.o -MD -MP -MF $depbase.Tpo -c -o jellyfish/merge_files.o jellyfish/merge_files.cc && mv -f $depbase.Tpo $depbase.Po In file included from jellyfish/merge_files.cc:9: In file included from ./jellyfish/merge_files.hpp:14: In file included from ./include/jellyfish/file_header.hpp:13: ./include/jellyfish/generic_file_header.hpp:107:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 107 | char pad[align - padding]; | ^~~~~~~~~~~~~~~ ./include/jellyfish/generic_file_header.hpp:107:16: note: read of non-const variable 'align' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:94:9: note: declared here 94 | int align = alignment(); | ^ ./include/jellyfish/generic_file_header.hpp:187:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 187 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:187:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:183:12: note: declared here 183 | size_t len = PATH_MAX; | ^ ./include/jellyfish/generic_file_header.hpp:232:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 232 | char path[len + 1]; | ^~~~~~~ ./include/jellyfish/generic_file_header.hpp:232:15: note: read of non-const variable 'len' is not allowed in a constant expression ./include/jellyfish/generic_file_header.hpp:227:12: note: declared here 227 | size_t len = PATH_MAX; | ^ In file included from jellyfish/merge_files.cc:20: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from jellyfish/merge_files.cc:20: In file included from ./include/jellyfish/jellyfish.hpp:15: In file included from ./include/jellyfish/text_dumper.hpp:12: ./include/jellyfish/sorted_dumper.hpp:76:34: warning: variable 'count' set but not used [-Wunused-but-set-variable] 76 | size_t count = 0; | ^ jellyfish/merge_files.cc:136:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 136 | size_t reprobes[h.max_reprobe() + 1]; | ^~~~~~~~~~~~~~~~~~~ jellyfish/merge_files.cc:136:23: note: initializer of 'h' is not a constant expression jellyfish/merge_files.cc:125:18: note: declared here 125 | file_header& h = files[i].header; | ^ In file included from jellyfish/merge_files.cc:20: In file included from ./include/jellyfish/jellyfish.hpp:13: In file included from ./include/jellyfish/mer_dna.hpp:27: ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:109:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 109 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ ./include/jellyfish/int128.hpp:94:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 94 | char padding[nb_padding]; | ^~~~~~~~~~ ./include/jellyfish/int128.hpp:115:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 115 | __int128_ns::__print(os, x); | ^ ./include/jellyfish/int128.hpp:94:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 94 | char padding[nb_padding]; | ^ ./include/jellyfish/int128.hpp:87:11: note: declared here 87 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from jellyfish/merge_files.cc:20: In file included from ./include/jellyfish/jellyfish.hpp:13: ./include/jellyfish/mer_dna.hpp:694:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 694 | char buffer[mer.k() + 1]; | ^~~~~~~~~~~ ./include/jellyfish/text_dumper.hpp:74:9: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator>>>' requested here 74 | is_ >> key_ >> val_; | ^ jellyfish/merge_files.cc:55:19: note: in instantiation of member function 'jellyfish::text_reader, unsigned long>::next' requested here 55 | if(readers[i].next()) | ^ jellyfish/merge_files.cc:172:5: note: in instantiation of function template specialization 'do_merge, unsigned long>, jellyfish::text_writer, unsigned long>>' requested here 172 | do_merge(files, out, writer, min, max, op); | ^ ./include/jellyfish/mer_dna.hpp:694:15: note: function parameter 'mer' with unknown value cannot be used in a constant expression 694 | char buffer[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:689:70: note: declared here 689 | inline std::istream& operator>>(std::istream& is, mer_base& mer) { | ^ ./include/jellyfish/mer_dna.hpp:682:10: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 682 | char s[mer.k() + 1]; | ^~~~~~~~~~~ ./include/jellyfish/text_dumper.hpp:19:8: note: in instantiation of function template specialization 'jellyfish::mer_dna_ns::operator<<>' requested here 19 | out << key << " " << val << "\n"; | ^ jellyfish/merge_files.cc:89:16: note: in instantiation of member function 'jellyfish::text_writer, unsigned long>::write' requested here 89 | writer.write(out, key, val); | ^ jellyfish/merge_files.cc:172:5: note: in instantiation of function template specialization 'do_merge, unsigned long>, jellyfish::text_writer, unsigned long>>' requested here 172 | do_merge(files, out, writer, min, max, op); | ^ ./include/jellyfish/mer_dna.hpp:682:10: note: function parameter 'mer' with unknown value cannot be used in a constant expression 682 | char s[mer.k() + 1]; | ^ ./include/jellyfish/mer_dna.hpp:680:76: note: declared here 680 | inline std::ostream& operator<<(std::ostream& os, const mer_base& mer) { | ^ 10 warnings generated. /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -fstack-protector-strong -o bin/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o libjellyfish-2.0.la libtool: link: c++ -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -fstack-protector-strong -o bin/.libs/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/usr/local/lib =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for Jellyfish-2.3.0_4 ===> Generating temporary packing list if test -z 'strip'; then /usr/bin/make INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/jellyfish/work/jellyfish-2.3.0/install-sh -c -s" install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/jellyfish/work/jellyfish-2.3.0/install-sh -c -s" INSTALL_STRIP_FLAG=-s install; else /usr/bin/make INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/jellyfish/work/jellyfish-2.3.0/install-sh -c -s" install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/jellyfish/work/jellyfish-2.3.0/install-sh -c -s" INSTALL_STRIP_FLAG=-s "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; fi /usr/bin/make install-am /bin/mkdir -p '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c -s libjellyfish-2.0.la '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/libjellyfish-2.0.so.2.0.0 libtool: install: strip --strip-unneeded /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: strip --strip-debug /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: ranlib /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ./libtool --mode=install /bin/sh /wrkdirs/usr/ports/biology/jellyfish/work/jellyfish-2.3.0/install-sh -c -s bin/jellyfish '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/jellyfish/work/jellyfish-2.3.0/install-sh -c -s bin/.libs/jellyfish /wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/bin/jellyfish /bin/mkdir -p '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/include/jellyfish-2.3.0/jellyfish' install -m 0644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/include/jellyfish-2.3.0/jellyfish' install -m 0644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/include/jellyfish-2.3.0/jellyfish' /bin/mkdir -p '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/share/man/man1' install -m 0644 'doc/jellyfish.man' '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/share/man/man1/jellyfish.1' /bin/mkdir -p '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/pkgconfig' install -m 0644 jellyfish-2.0.pc '/wrkdirs/usr/ports/biology/jellyfish/work/stage/usr/local/lib/pkgconfig' ====> 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=2025-05-02T08:26:28+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 Jellyfish-2.3.0_4 ===> Building Jellyfish-2.3.0_4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for Jellyfish-2.3.0_4 build of biology/jellyfish | Jellyfish-2.3.0_4 ended at Fri May 2 09:28:36 BST 2025 build time: 00:02:09