=>> Building biology/iolib build started at Sun Mar 15 11:31:08 EDT 2026 port directory: /usr/ports/biology/iolib package name: io_lib-1.15.1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: alven@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 609 Feb 17 19:06 /usr/ports/biology/iolib/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 6620ae9fa686 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 13 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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/freebsd_15_0_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- alven@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/iolib/work/.cache HOME=/wrkdirs/usr/ports/biology/iolib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iolib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/iolib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/iolib/work/.cache HOME=/wrkdirs/usr/ports/biology/iolib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iolib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/iolib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/io_lib" EXAMPLESDIR="share/examples/io_lib" DATADIR="share/io_lib" WWWDIR="www/io_lib" ETCDIR="etc/io_lib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/io_lib DOCSDIR=/usr/local/share/doc/io_lib EXAMPLESDIR=/usr/local/share/examples/io_lib WWWDIR=/usr/local/www/io_lib ETCDIR=/usr/local/etc/io_lib --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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 ===> io_lib-1.15.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> io_lib-1.15.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of io_lib-1.15.1 =========================================================================== =================================================== ===== 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 io_lib-1.15.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by io_lib-1.15.1 for building => SHA256 Checksum OK for io_lib-1.15.1.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 io_lib-1.15.1 for building ===> Extracting for io_lib-1.15.1 => SHA256 Checksum OK for io_lib-1.15.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for io_lib-1.15.1 ===> Applying FreeBSD patches for io_lib-1.15.1 from /usr/ports/biology/iolib/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> io_lib-1.15.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> io_lib-1.15.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of io_lib-1.15.1 ===> io_lib-1.15.1 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing m4-1.4.21,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.21,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> io_lib-1.15.1 depends on package: autoconf>=2.72_1 - found ===> Returning to build of io_lib-1.15.1 ===> io_lib-1.15.1 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> io_lib-1.15.1 depends on package: automake>=1.18.1 - found ===> Returning to build of io_lib-1.15.1 ===> io_lib-1.15.1 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.5.4_1.pkg [pkg.DaveG.ca] Installing libtool-2.5.4_1... [pkg.DaveG.ca] Extracting libtool-2.5.4_1: .......... done ===> io_lib-1.15.1 depends on executable: libtoolize - found ===> Returning to build of io_lib-1.15.1 ===> io_lib-1.15.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> io_lib-1.15.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of io_lib-1.15.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> io_lib-1.15.1 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.17.0.pkg [pkg.DaveG.ca] Installing curl-8.17.0... [pkg.DaveG.ca] `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] Extracting curl-8.17.0: .......... done ===> io_lib-1.15.1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of io_lib-1.15.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for io_lib-1.15.1 libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:81: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:81: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:81: the top level configure.ac:101: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:101: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.ac:101: the top level configure.ac:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:102: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:156: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:156: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from... configure.ac:156: the top level configure.ac:157: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:157: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_zstd.m4:31: AX_ZSTD is expanded from... configure.ac:157: the top level configure.ac:190: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:190: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:190: the top level configure.ac:255: warning: AC_OUTPUT should be used without arguments. configure.ac:255: You should run autoupdate. configure.ac:79: installing './compile' configure.ac:10: installing './missing' io_lib/Makefile.am: installing './depcomp' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking build system type... amd64-portbld-freebsd15.0 checking host system type... amd64-portbld-freebsd15.0 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) 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-freebsd15.0 file names to amd64-portbld-freebsd15.0 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd15.0 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd15.0 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) /usr/bin/awk checking for curl-config... /usr/local/bin/curl-config checking for the version of libcurl... 8.17.0 checking whether libcurl just needs -lcurl... no checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking for zlib.h... (cached) yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for egrep... (cached) /usr/bin/egrep checking for sys/wait.h that is POSIX.1 compatible... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for stdio_ext.h... no checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... (cached) yes checking for fileno... (cached) yes checking for fstat... (cached) yes checking for mallopt... no checking for cc option to enable large file support... none needed checking for declarations of fseeko and ftello... yes checking for getpagesize... (cached) yes checking for working mmap... (cached) yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... (cached) yes checking for fsync... (cached) yes checking that generated files are newer than configure... done === configuring in htscodecs (/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs) configure: running /bin/sh ./configure '--prefix=/usr/local' --disable-option-checking '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=amd64-portbld-freebsd15.0' 'build_alias=amd64-portbld-freebsd15.0' 'CC=cc' 'CFLAGS=-O2 -pipe -fstack-protector-strong -fno-strict-aliasing ' 'LDFLAGS= ' 'LIBS=' 'CPPFLAGS=' '--disable-shared' '--with-pic' '--srcdir=.' --cache-file= configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking build system type... amd64-portbld-freebsd15.0 checking host system type... amd64-portbld-freebsd15.0 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) 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-freebsd15.0 file names to amd64-portbld-freebsd15.0 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd15.0 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for 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 dynamic linker characteristics... freebsd15.0 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... no checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for __builtin_prefetch... yes checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for sys/wait.h that is POSIX.1 compatible... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for function pthread_join... -lthr checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating htscodecs/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------- CONFIGURE SUMMARY -------------------------------------------------- Bzip2 enabled: yes lzma enabled: yes custom-buffering enabled: yes Using own crc: yes Libcurl enabled: yes Libdeflate enabled: no have libbsc: no Have zstd: no CC: cc CFLAGS: -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing LDFLAGS: LIBS: -lm -llzma -lbz2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for io_lib-1.15.1 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' Making all in htscodecs gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' /usr/local/bin/gmake all-recursive gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' Making all in htscodecs gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' Update version.h: #define HTSCODECS_VERSION_TEXT "1.5.0" /usr/local/bin/gmake all-am gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c -o pack.lo pack.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c -o rle.lo rle.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c -o fqzcomp_qual.lo fqzcomp_qual.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c -o rANS_static.lo rANS_static.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c -o rANS_static4x16pr.lo rANS_static4x16pr.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static32x16pr.lo -MD -MP -MF .deps/rANS_static32x16pr.Tpo -c -o rANS_static32x16pr.lo rANS_static32x16pr.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static32x16pr_neon.lo -MD -MP -MF .deps/rANS_static32x16pr_neon.Tpo -c -o rANS_static32x16pr_neon.lo rANS_static32x16pr_neon.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT tokenise_name3.lo -MD -MP -MF .deps/tokenise_name3.Tpo -c -o tokenise_name3.lo tokenise_name3.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c -o arith_dynamic.lo arith_dynamic.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c -o htscodecs.lo htscodecs.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c -o utils.lo utils.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -msse4.1 -mssse3 -mpopcnt -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -MD -MP -MF .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo -c -o librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo `test -f 'rANS_static32x16pr_sse4.c' || echo './'`rANS_static32x16pr_sse4.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -mavx2 -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -MD -MP -MF .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo -c -o librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo `test -f 'rANS_static32x16pr_avx2.c' || echo './'`rANS_static32x16pr_avx2.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -mavx512f -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -MD -MP -MF .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo -c -o librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo `test -f 'rANS_static32x16pr_avx512.c' || echo './'`rANS_static32x16pr_avx512.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c pack.c -fPIC -DPIC -o pack.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c rle.c -fPIC -DPIC -o rle.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.c -fPIC -DPIC -o utils.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static32x16pr.lo -MD -MP -MF .deps/rANS_static32x16pr.Tpo -c rANS_static32x16pr.c -fPIC -DPIC -o rANS_static32x16pr.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c htscodecs.c -fPIC -DPIC -o htscodecs.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c rANS_static.c -fPIC -DPIC -o rANS_static.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -fPIC -DPIC -o rANS_static4x16pr.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c arith_dynamic.c -fPIC -DPIC -o arith_dynamic.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static32x16pr_neon.lo -MD -MP -MF .deps/rANS_static32x16pr_neon.Tpo -c rANS_static32x16pr_neon.c -fPIC -DPIC -o rANS_static32x16pr_neon.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o fqzcomp_qual.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -msse4.1 -mssse3 -mpopcnt -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -MD -MP -MF .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo -c rANS_static32x16pr_sse4.c -fPIC -DPIC -o librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT tokenise_name3.lo -MD -MP -MF .deps/tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o tokenise_name3.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -mavx512f -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -MD -MP -MF .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo -c rANS_static32x16pr_avx512.c -fPIC -DPIC -o librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -mavx2 -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -MD -MP -MF .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo -c rANS_static32x16pr_avx2.c -fPIC -DPIC -o librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o mv -f .deps/rANS_static32x16pr_neon.Tpo .deps/rANS_static32x16pr_neon.Plo mv -f .deps/htscodecs.Tpo .deps/htscodecs.Plo mv -f .deps/utils.Tpo .deps/utils.Plo mv -f .deps/rle.Tpo .deps/rle.Plo mv -f .deps/pack.Tpo .deps/pack.Plo mv -f .deps/rANS_static.Tpo .deps/rANS_static.Plo mv -f .deps/rANS_static32x16pr.Tpo .deps/rANS_static32x16pr.Plo mv -f .deps/arith_dynamic.Tpo .deps/arith_dynamic.Plo mv -f .deps/tokenise_name3.Tpo .deps/tokenise_name3.Plo mv -f .deps/rANS_static4x16pr.Tpo .deps/rANS_static4x16pr.Plo mv -f .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Plo /bin/sh ../libtool --tag=CC --mode=link cc -msse4.1 -mssse3 -mpopcnt -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o librANS_static32x16pr_sse4.la librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -lthr -lbz2 libtool: link: ar cr .libs/librANS_static32x16pr_sse4.a librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o libtool: link: ranlib .libs/librANS_static32x16pr_sse4.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_sse4.la" && ln -s "../librANS_static32x16pr_sse4.la" "librANS_static32x16pr_sse4.la" ) mv -f .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Plo /bin/sh ../libtool --tag=CC --mode=link cc -mavx2 -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o librANS_static32x16pr_avx2.la librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -lthr -lbz2 mv -f .deps/fqzcomp_qual.Tpo .deps/fqzcomp_qual.Plo libtool: link: ar cr .libs/librANS_static32x16pr_avx2.a librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o libtool: link: ranlib .libs/librANS_static32x16pr_avx2.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_avx2.la" && ln -s "../librANS_static32x16pr_avx2.la" "librANS_static32x16pr_avx2.la" ) mv -f .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Plo /bin/sh ../libtool --tag=CC --mode=link cc -mavx512f -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o librANS_static32x16pr_avx512.la librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -lthr -lbz2 libtool: link: ar cr .libs/librANS_static32x16pr_avx512.a librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o libtool: link: ranlib .libs/librANS_static32x16pr_avx512.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_avx512.la" && ln -s "../librANS_static32x16pr_avx512.la" "librANS_static32x16pr_avx512.la" ) /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -version-info 3:2:1 -o libhtscodecs.la -rpath /usr/local/lib pack.lo rle.lo fqzcomp_qual.lo rANS_static.lo rANS_static4x16pr.lo rANS_static32x16pr.lo rANS_static32x16pr_neon.lo tokenise_name3.lo arith_dynamic.lo htscodecs.lo utils.lo librANS_static32x16pr_sse4.la librANS_static32x16pr_avx2.la librANS_static32x16pr_avx512.la -lm -lthr -lbz2 libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_sse4.a && ar x "/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs/./.libs/librANS_static32x16pr_sse4.a") libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_avx2.a && ar x "/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs/./.libs/librANS_static32x16pr_avx2.a") libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_avx512.a && ar x "/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs/./.libs/librANS_static32x16pr_avx512.a") libtool: link: ar cr .libs/libhtscodecs.a pack.o rle.o fqzcomp_qual.o rANS_static.o rANS_static4x16pr.o rANS_static32x16pr.o rANS_static32x16pr_neon.o tokenise_name3.o arith_dynamic.o htscodecs.o utils.o .libs/libhtscodecs.lax/librANS_static32x16pr_sse4.a/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o .libs/libhtscodecs.lax/librANS_static32x16pr_avx2.a/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o .libs/libhtscodecs.lax/librANS_static32x16pr_avx512.a/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o libtool: link: ranlib .libs/libhtscodecs.a libtool: link: rm -fr .libs/libhtscodecs.lax libtool: link: ( cd ".libs" && rm -f "libhtscodecs.la" && ln -s "../libhtscodecs.la" "libhtscodecs.la" ) gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' Making all in . gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' Making all in tests gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/tests' cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static4x16pr_test.o -MD -MP -MF .deps/rANS_static4x16pr_test.Tpo -c -o rANS_static4x16pr_test.o rANS_static4x16pr_test.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT tokenise_name3_test.o -MD -MP -MF .deps/tokenise_name3_test.Tpo -c -o tokenise_name3_test.o tokenise_name3_test.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT arith_dynamic_test.o -MD -MP -MF .deps/arith_dynamic_test.Tpo -c -o arith_dynamic_test.o arith_dynamic_test.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT rANS_static_test.o -MD -MP -MF .deps/rANS_static_test.Tpo -c -o rANS_static_test.o rANS_static_test.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT fqzcomp_qual_test.o -MD -MP -MF .deps/fqzcomp_qual_test.Tpo -c -o fqzcomp_qual_test.o fqzcomp_qual_test.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT varint_test.o -MD -MP -MF .deps/varint_test.Tpo -c -o varint_test.o varint_test.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT entropy.o -MD -MP -MF .deps/entropy.Tpo -c -o entropy.o entropy.c mv -f .deps/entropy.Tpo .deps/entropy.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o entropy entropy.o ../htscodecs/libhtscodecs.la -lthr -lbz2 mv -f .deps/tokenise_name3_test.Tpo .deps/tokenise_name3_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o tokenise_name3 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-fstack-protector-strong -fno-strict-aliasing -o tokenise_name3 tokenise_name3_test.o ../htscodecs/.libs/libhtscodecs.a -lm -lthr -lbz2 mv -f .deps/fqzcomp_qual_test.Tpo .deps/fqzcomp_qual_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o fqzcomp_qual fqzcomp_qual_test.o ../htscodecs/libhtscodecs.la -lthr -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o rans4x8 rANS_static_test.o ../htscodecs/.libs/libhtscodecs.a -lm -lthr -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o arith_dynamic arith_dynamic_test.o ../htscodecs/.libs/libhtscodecs.a -lm -lthr -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o rans4x16pr rANS_static4x16pr_test.o ../htscodecs/.libs/libhtscodecs.a -lm -lthr -lbz2 mv -f .deps/varint_test.Tpo .deps/varint_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe 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-MD -MP -MF .deps/libstaden_read_la-find.Tpo -c find.c -fPIC -DPIC -o .libs/libstaden_read_la-find.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-seqIOPlain.lo -MD -MP -MF .deps/libstaden_read_la-seqIOPlain.Tpo -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-misc_scf.lo -MD -MP -MF .deps/libstaden_read_la-misc_scf.Tpo -c misc_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-misc_scf.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe 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-o libstaden_read_la-write_scf.o >/dev/null 2>&1 ztr_translate.c:479:9: warning: variable 'nbytes' set but not used [-Wunused-but-set-variable] 479 | int nbytes = chunk->dlength; | ^ ztr_translate.c:615:9: warning: variable 'nbytes' set but not used [-Wunused-but-set-variable] 615 | int nbytes = chunk->dlength; | ^ 2 warnings generated. seqIOALF.c:274:9: warning: variable 'num_points' set but not used [-Wunused-but-set-variable] 274 | int num_points; /* keeps track of the actual number of points, | ^ 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-array.lo -MD -MP -MF .deps/libstaden_read_la-array.Tpo -c array.c -o libstaden_read_la-array.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c sff.c -fPIC -DPIC -o .libs/libstaden_read_la-sff.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-read_scf.lo -MD -MP -MF .deps/libstaden_read_la-read_scf.Tpo -c read_scf.c -o libstaden_read_la-read_scf.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-error.lo -MD -MP -MF .deps/libstaden_read_la-error.Tpo -c error.c -o libstaden_read_la-error.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c read_alloc.c -o libstaden_read_la-read_alloc.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-scf_extras.Tpo .deps/libstaden_read_la-scf_extras.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-fpoint.Tpo .deps/libstaden_read_la-fpoint.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c expFileIO.c -o libstaden_read_la-expFileIO.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-misc_scf.lo -MD -MP -MF .deps/libstaden_read_la-misc_scf.Tpo -c misc_scf.c -o libstaden_read_la-misc_scf.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-xalloc.Tpo .deps/libstaden_read_la-xalloc.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-seqIOPlain.Tpo .deps/libstaden_read_la-seqIOPlain.Plo mv -f .deps/libstaden_read_la-string_alloc.Tpo .deps/libstaden_read_la-string_alloc.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong 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pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-zfio.Tpo .deps/libstaden_read_la-zfio.Plo mv -f .deps/libstaden_read_la-traceType.Tpo .deps/libstaden_read_la-traceType.Plo mv -f .deps/libstaden_read_la-files.Tpo .deps/libstaden_read_la-files.Plo mv -f .deps/libstaden_read_la-compress.Tpo .deps/libstaden_read_la-compress.Plo mv -f .deps/libstaden_read_la-mach-io.Tpo .deps/libstaden_read_la-mach-io.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-strings.lo -MD -MP -MF .deps/libstaden_read_la-strings.Tpo -c strings.c -o libstaden_read_la-strings.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_stats.Tpo .deps/libstaden_read_la-cram_stats.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-array.Tpo .deps/libstaden_read_la-array.Plo mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-jenkins_lookup3.Tpo .deps/libstaden_read_la-jenkins_lookup3.Plo mv -f .deps/libstaden_read_la-read_scf.Tpo .deps/libstaden_read_la-read_scf.Plo mv -f .deps/libstaden_read_la-misc_scf.Tpo .deps/libstaden_read_la-misc_scf.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-write_scf.Tpo .deps/libstaden_read_la-write_scf.Plo open_trace_file.c:595:14: warning: call to 'Wcurl_easy_setopt_err_long' declared with 'warning' attribute: curl_easy_setopt expects a long argument [-Wattribute-warning] 595 | if (0 != curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1)) | ^ /usr/local/include/curl/typecheck-gcc.h:50:15: note: expanded from macro 'curl_easy_setopt' 50 | Wcurl_easy_setopt_err_long(); \ | ^ 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-srf.lo -MD -MP -MF .deps/libstaden_read_la-srf.Tpo -c srf.c -o libstaden_read_la-srf.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-seqIOALF.Tpo .deps/libstaden_read_la-seqIOALF.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-open_trace_file.lo -MD -MP -MF .deps/libstaden_read_la-open_trace_file.Tpo -c open_trace_file.c -o libstaden_read_la-open_trace_file.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-seqIOABI.Tpo .deps/libstaden_read_la-seqIOABI.Plo mv -f .deps/libstaden_read_la-read_alloc.Tpo .deps/libstaden_read_la-read_alloc.Plo mv -f .deps/libstaden_read_la-error.Tpo .deps/libstaden_read_la-error.Plo mv -f .deps/libstaden_read_la-mFILE.Tpo .deps/libstaden_read_la-mFILE.Plo mv -f .deps/libstaden_read_la-cram_bambam.Tpo .deps/libstaden_read_la-cram_bambam.Plo mv -f .deps/libstaden_read_la-find.Tpo .deps/libstaden_read_la-find.Plo mv -f .deps/libstaden_read_la-vlen.Tpo .deps/libstaden_read_la-vlen.Plo mv -f .deps/libstaden_read_la-Read.Tpo .deps/libstaden_read_la-Read.Plo mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c sff.c -o libstaden_read_la-sff.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-pooled_alloc.Tpo .deps/libstaden_read_la-pooled_alloc.Plo mv -f .deps/libstaden_read_la-ztr.Tpo .deps/libstaden_read_la-ztr.Plo mv -f .deps/libstaden_read_la-strings.Tpo .deps/libstaden_read_la-strings.Plo mv -f .deps/libstaden_read_la-cram_index.Tpo .deps/libstaden_read_la-cram_index.Plo mv -f .deps/libstaden_read_la-bgzip.Tpo .deps/libstaden_read_la-bgzip.Plo mv -f .deps/libstaden_read_la-translate.Tpo .deps/libstaden_read_la-translate.Plo mv -f .deps/libstaden_read_la-ztr_translate.Tpo .deps/libstaden_read_la-ztr_translate.Plo mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo mv -f .deps/libstaden_read_la-expFileIO.Tpo .deps/libstaden_read_la-expFileIO.Plo mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo mv -f .deps/libstaden_read_la-sff.Tpo .deps/libstaden_read_la-sff.Plo mv -f .deps/libstaden_read_la-deflate_interlaced.Tpo .deps/libstaden_read_la-deflate_interlaced.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-open_trace_file.Tpo .deps/libstaden_read_la-open_trace_file.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-compression.Tpo .deps/libstaden_read_la-compression.Plo mv -f .deps/libstaden_read_la-srf.Tpo .deps/libstaden_read_la-srf.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-hash_table.Tpo .deps/libstaden_read_la-hash_table.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -I/usr/local/include -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -version-info 15:4:1 -o libstaden-read.la -rpath /usr/local/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -L/usr/local/lib -lcurl ../htscodecs/htscodecs/libhtscodecs.la -lm -llzma -lbz2 libtool: link: cc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -L/usr/local/lib -lcurl ../htscodecs/htscodecs/.libs/libhtscodecs.a -lthr -lm -llzma -lbz2 -O2 -fstack-protector-strong -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.4 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.4" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.4" "libstaden-read.so") libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/io_lib' Making all in progs gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/progs' cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT makeSCF.o -MD -MP -MF .deps/makeSCF.Tpo -c -o makeSCF.o makeSCF.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT extract_seq.o -MD -MP -MF .deps/extract_seq.Tpo -c -o extract_seq.o extract_seq.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT extract_qual.o -MD -MP -MF .deps/extract_qual.Tpo -c -o extract_qual.o extract_qual.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT extract_fastq.o -MD -MP -MF .deps/extract_fastq.Tpo -c -o extract_fastq.o extract_fastq.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT index_tar.o -MD -MP -MF .deps/index_tar.Tpo -c -o index_tar.o index_tar.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scf_dump.o -MD -MP -MF .deps/scf_dump.Tpo -c -o scf_dump.o scf_dump.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scf_info.o -MD -MP -MF .deps/scf_info.Tpo -c -o scf_info.o scf_info.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scf_update.o -MD -MP -MF .deps/scf_update.Tpo -c -o scf_update.o scf_update.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT get_comment.o -MD -MP -MF .deps/get_comment.Tpo -c -o get_comment.o get_comment.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT hash_tar.o -MD -MP -MF .deps/hash_tar.Tpo -c -o hash_tar.o hash_tar.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT hash_extract.o -MD -MP -MF .deps/hash_extract.Tpo -c -o hash_extract.o hash_extract.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT hash_list.o -MD -MP -MF .deps/hash_list.Tpo -c -o hash_list.o hash_list.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT trace_dump.o -MD -MP -MF .deps/trace_dump.Tpo -c -o trace_dump.o trace_dump.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT hash_sff.o -MD -MP -MF .deps/hash_sff.Tpo -c -o hash_sff.o hash_sff.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT append_sff.o -MD -MP -MF .deps/append_sff.Tpo -c -o append_sff.o append_sff.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT ztr_dump.o -MD -MP -MF .deps/ztr_dump.Tpo -c -o ztr_dump.o ztr_dump.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_dump_all.o -MD -MP -MF .deps/srf_dump_all.Tpo -c -o srf_dump_all.o srf_dump_all.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_index_hash.o -MD -MP -MF .deps/srf_index_hash.Tpo -c -o srf_index_hash.o srf_index_hash.c mv -f .deps/extract_seq.Tpo .deps/extract_seq.Po mv -f .deps/scf_info.Tpo .deps/scf_info.Po mv -f .deps/scf_update.Tpo .deps/scf_update.Po mv -f .deps/index_tar.Tpo .deps/index_tar.Po mv -f .deps/extract_qual.Tpo .deps/extract_qual.Po mv -f .deps/extract_fastq.Tpo .deps/extract_fastq.Po mv -f .deps/scf_dump.Tpo .deps/scf_dump.Po mv -f .deps/append_sff.Tpo .deps/append_sff.Po mv -f .deps/hash_list.Tpo .deps/hash_list.Po mv -f .deps/get_comment.Tpo .deps/get_comment.Po mv -f .deps/hash_sff.Tpo .deps/hash_sff.Po mv -f .deps/makeSCF.Tpo .deps/makeSCF.Po mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po mv -f .deps/trace_dump.Tpo .deps/trace_dump.Po mv -f .deps/srf_index_hash.Tpo .deps/srf_index_hash.Po mv -f .deps/ztr_dump.Tpo .deps/ztr_dump.Po mv -f .deps/hash_extract.Tpo .deps/hash_extract.Po mv -f .deps/hash_tar.Tpo .deps/hash_tar.Po cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_extract_linear.o -MD -MP -MF .deps/srf_extract_linear.Tpo -c -o srf_extract_linear.o srf_extract_linear.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_extract_hash.o -MD -MP -MF .deps/srf_extract_hash.Tpo -c -o srf_extract_hash.o srf_extract_hash.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf2fastq.o -MD -MP -MF .deps/srf2fastq.Tpo -c -o srf2fastq.o srf2fastq.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf2fasta.o -MD -MP -MF .deps/srf2fasta.Tpo -c -o srf2fasta.o srf2fasta.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_filter.o -MD -MP -MF .deps/srf_filter.Tpo -c -o srf_filter.o srf_filter.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_info.o -MD -MP -MF .deps/srf_info.Tpo -c -o srf_info.o srf_info.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT srf_list.o -MD -MP -MF .deps/srf_list.Tpo -c -o srf_list.o srf_list.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT hash_exp.o -MD -MP -MF .deps/hash_exp.Tpo -c -o hash_exp.o hash_exp.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_dump.o -MD -MP -MF .deps/cram_dump.Tpo -c -o cram_dump.o cram_dump.c srf_dump_all.c:498:11: warning: variable 'lLineCount' set but not used [-Wunused-but-set-variable] 498 | long lLineCount; /* Current line number */ | ^ srf_dump_all.c:499:11: warning: variable 'lTotalChars' set but not used [-Wunused-but-set-variable] 499 | long lTotalChars; /* Total characters read */ | ^ 2 warnings generated. mv -f .deps/srf_dump_all.Tpo .deps/srf_dump_all.Po cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_index.o -MD -MP -MF .deps/cram_index.Tpo -c -o cram_index.o cram_index.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scramble.o -MD -MP -MF .deps/scramble.Tpo -c -o scramble.o scramble.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_merge.o -MD -MP -MF .deps/scram_merge.Tpo -c -o scram_merge.o scram_merge.c mv -f .deps/srf_list.Tpo .deps/srf_list.Po cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_pileup.o -MD -MP -MF .deps/scram_pileup.Tpo -c -o scram_pileup.o scram_pileup.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_flagstat.o -MD -MP -MF .deps/scram_flagstat.Tpo -c -o scram_flagstat.o scram_flagstat.c mv -f .deps/srf2fasta.Tpo .deps/srf2fasta.Po mv -f .deps/srf_extract_linear.Tpo .deps/srf_extract_linear.Po cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT scram_test.o -MD -MP -MF .deps/scram_test.Tpo -c -o scram_test.o scram_test.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_size.o -MD -MP -MF .deps/cram_size.Tpo -c -o cram_size.o cram_size.c mv -f .deps/srf_extract_hash.Tpo .deps/srf_extract_hash.Po cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_filter.o -MD -MP -MF .deps/cram_filter.Tpo -c -o cram_filter.o cram_filter.c mv -f .deps/hash_exp.Tpo .deps/hash_exp.Po mv -f .deps/srf_info.Tpo .deps/srf_info.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 srf_filter.c:172:11: warning: variable 'lLineCount' set but not used [-Wunused-but-set-variable] 172 | long lLineCount; /* Current line number */ | ^ srf_filter.c:173:11: warning: variable 'lTotalChars' set but not used [-Wunused-but-set-variable] 173 | long lTotalChars; /* Total characters read */ | ^ 2 warnings generated. /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po mv -f .deps/scram_merge.Tpo .deps/scram_merge.Po mv -f .deps/cram_size.Tpo .deps/cram_size.Po mv -f .deps/scram_flagstat.Tpo .deps/scram_flagstat.Po mv -f .deps/scramble.Tpo .deps/scramble.Po mv -f .deps/cram_index.Tpo .deps/cram_index.Po mv -f .deps/srf_filter.Tpo .deps/srf_filter.Po mv -f .deps/srf2fastq.Tpo .deps/srf2fastq.Po mv -f .deps/scram_test.Tpo .deps/scram_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 mv -f .deps/cram_filter.Tpo .deps/cram_filter.Po mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o index_tar index_tar.o -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scf_update scf_update.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scf_info scf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o get_comment get_comment.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o hash_list hash_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o append_sff append_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o index_tar index_tar.o -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scf_dump scf_dump.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/extract_fastq extract_fastq.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scf_info scf_info.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/hash_tar hash_tar.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/hash_extract hash_extract.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/trace_dump trace_dump.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/get_comment get_comment.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/hash_sff hash_sff.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scf_update scf_update.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/hash_list hash_list.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf_list srf_list.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf_extract_linear srf_extract_linear.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf_info srf_info.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/append_sff append_sff.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf_index_hash srf_index_hash.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/ztr_dump ztr_dump.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf2fastq srf2fastq.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf_extract_hash srf_extract_hash.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf2fasta srf2fasta.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/srf_dump_all srf_dump_all.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/progs' Making all in tests gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/tests' cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lthr -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/tests' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for io_lib-1.15.1 ===> Generating temporary packing list if test -z 'strip'; then \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' Making install in htscodecs gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' Making install in htscodecs gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' /usr/local/bin/gmake install-am gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c -s libhtscodecs.la '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libhtscodecs.lai /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libhtscodecs.la libtool: install: /usr/bin/install -c .libs/libhtscodecs.a /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libhtscodecs.a libtool: install: strip --strip-debug /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libhtscodecs.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libhtscodecs.a libtool: install: ranlib /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libhtscodecs.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/htscodecs' Making install in . gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' gmake[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/htscodecs' install -m 0644 htscodecs/arith_dynamic.h htscodecs/fqzcomp_qual.h htscodecs/rANS_static.h htscodecs/rANS_static4x16.h htscodecs/tokenise_name3.h htscodecs/pack.h htscodecs/rle.h htscodecs/varint.h htscodecs/htscodecs.h '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/htscodecs' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' Making install in tests gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/tests' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/tests' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/tests' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs/tests' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/htscodecs' Making install in io_lib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/io_lib' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/io_lib' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c -s libstaden-read.la '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.4 /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.so.14.1.4 libtool: install: strip --strip-unneeded /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.so.14.1.4 libtool: install: (cd /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib && { ln -s -f libstaden-read.so.14.1.4 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.4 libstaden-read.so.14; }; }) libtool: install: (cd /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib && { ln -s -f libstaden-read.so.14.1.4 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.4 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: install: strip --strip-debug /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: install: ranlib /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/lib/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/io_lib' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/io_lib' Making install in progs gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/progs' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/progs' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ../libtool --mode=install /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/convert_trace /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/makeSCF /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/extract_seq /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/extract_qual /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/extract_fastq /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/extract_fastq libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s index_tar /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scf_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scf_info /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scf_update /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/get_comment /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/hash_tar /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/hash_extract /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/hash_list /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/trace_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/hash_sff /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/append_sff /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/ztr_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf_dump_all /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf_index_hash /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf_extract_linear /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf_extract_hash /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf2fastq /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf2fasta /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf_filter /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf_info /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/srf_list /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/hash_exp /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/cram_dump /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/cram_index /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scramble /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scram_merge /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scram_pileup /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scram_flagstat /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/scram_test /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/cram_size /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/install-sh -c -s .libs/cram_filter /wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin/cram_filter gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/progs' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/progs' Making install in tests gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/tests' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/tests' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/tests' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1/tests' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' install -m 555 io_lib-config '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man1' install -m 0644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man1' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man3' install -m 0644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man3' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man4' install -m 0644 man/man4/Read.4 '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/share/man/man4' /bin/mkdir -p '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/io_lib' install -m 0644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/io_lib' install -m 0644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/wrkdirs/usr/ports/biology/iolib/work/stage/usr/local/include/io_lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-1.15.1' ====> 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=2026-03-15T15:31:08+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=6620ae9fa686' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for io_lib-1.15.1 ===> Building io_lib-1.15.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for io_lib-1.15.1 build of biology/iolib | io_lib-1.15.1 ended at Sun Mar 15 11:35:01 EDT 2026 build time: 00:03:54