* Package: sci-libs/htslib-1.17:0/3 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_32 bzip2 elibc_glibc kernel_linux lzma x86 * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; This ebuild was merged at the following commit: https://github.com/gentoo-mirror/gentoo/commit/d766a1511c35a5fa2a1aef84c3bdabfc1f0066dc (Mon Mar 25 22:49:17 UTC 2024) @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.63 (python 3.12.2-final-0, default/linux/x86/17.0, gcc-14, glibc-2.39-r2, 6.1.66-gentoo-dist i686) ================================================================= System uname: Linux-6.1.66-gentoo-dist-i686-AMD_EPYC_7513_32-Core_Processor-with-glibc2.39 KiB Mem: 263452516 total, 54068944 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 25 Mar 2024 22:49:16 +0000 sh bash 5.2_p26 ld GNU ld (Gentoo 2.42 p3) 2.42.0 app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p26::gentoo dev-build/autoconf: 2.72-r1::gentoo dev-build/automake: 1.16.5-r2::gentoo dev-build/cmake: 3.29.0::gentoo dev-build/libtool: 2.4.7-r3::gentoo dev-build/make: 4.4.1-r1::gentoo dev-build/meson: 1.4.0-r1::gentoo dev-lang/perl: 5.38.2-r2::gentoo dev-lang/python: 3.10.14::gentoo, 3.11.8_p1::gentoo, 3.12.2_p1::gentoo sys-apps/baselayout: 2.15::gentoo sys-apps/openrc: 0.53.1::gentoo sys-apps/sandbox: 2.38::gentoo sys-devel/binutils: 2.42-r1::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/gcc: 14.0.1_pre20240324::gentoo sys-devel/gcc-config: 2.11::gentoo sys-kernel/linux-headers: 6.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.39-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 volatile: True sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-max-age: 3 Binary Repositories: gentoobinhost priority: 1 sync-uri: https://gentoo.osuosl.org/releases/x86/binpackages/17.0/i686 ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* MIT" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" DISTDIR="/var/tmp/portage/sci-libs/htslib-1.17/distdir" EMERGE_DEFAULT_OPTS="--complete-graph y --with-bdeps=y -1 -k -b --backtrack=100" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME" FCFLAGS="-O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://distfiles.gentoo.org" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" LEX="flex" MAKEOPTS="-j16" PKGDIR="/root/tbci/binpkg" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" SHELL="/bin/bash" USE="acl bzip2 cli crypt debug dri elogind fortran gdbm iconv ipv6 jumbo-build libtirpc lzma native-symlinks ncurses nls openmp pam pcre readline seccomp split-usr ssl test-rust unicode x86 xattr zlib" ABI_X86="32" ELIBC="glibc" KERNEL="linux" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ############################## # emerge history (qlop -mv): # ############################## ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/audio-0-r3:0 acct-group/cdrom-0-r3:0 acct-group/dialout-0-r3:0 acct-group/disk-0-r3:0 acct-group/floppy-0-r1:0 acct-group/input-0-r3:0 acct-group/kmem-0-r3:0 acct-group/kvm-0-r3:0 acct-group/lp-0-r3:0 acct-group/man-0-r3:0 acct-group/messagebus-0-r3:0 acct-group/polkitd-0-r3:0 acct-group/portage-0-r2:0 acct-group/render-0-r3:0 acct-group/root-0-r2:0 acct-group/sgx-0-r2:0 acct-group/sshd-0-r3:0 acct-group/tape-0-r3:0 acct-group/tty-0-r3:0 acct-group/usb-0-r3:0 acct-group/video-0-r3:0 acct-user/man-1-r3:0 acct-user/messagebus-0-r3:0 acct-user/polkitd-0-r3:0 acct-user/portage-0-r3:0 acct-user/sshd-0-r3:0 app-admin/eselect-1.4.27-r1:0 -doc -emacs 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-gui -verify-sig app-text/asciidoc-10.2.0:0 -python_single_target_pypy3 -python_single_target_python3_10 python_single_target_python3_11 -python_single_target_python3_12 app-text/build-docbook-catalog-2.4:0 app-text/docbook-xml-dtd-4.5-r2:4.5 app-text/docbook-xml-dtd-4.4-r3:4.4 app-text/docbook-xml-dtd-4.2-r3:4.2 app-text/docbook-xml-dtd-4.1.2-r7:4.1.2 app-text/docbook-xsl-ns-stylesheets-1.79.1:0 -ruby app-text/docbook-xsl-stylesheets-1.79.1-r4:0 -ruby app-text/manpager-1:0 app-text/opensp-1.5.2-r10:0 -doc nls -static-libs -test app-text/po4a-0.71:0 -test -test app-text/sgml-common-0.6.3-r7:0 app-text/xmlto-0.0.28-r11:0 -latex text dev-build/autoconf-2.72-r1:2.72 -emacs -verify-sig dev-build/autoconf-archive-2023.02.20:0 dev-build/autoconf-wrapper-20231224:0 dev-build/automake-1.16.5-r2:1.16 -test dev-build/automake-wrapper-20221207:0 dev-build/cmake-3.29.0:0 -dap -doc -gui ncurses -qt6 -test -test -verify-sig dev-build/gtk-doc-am-1.33.2:0 dev-build/libtool-2.4.7-r3:2 -vanilla 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x11-misc/xdg-utils-1.2.1-r1:0 -X -dbus -doc -gnome ############# # build.log # ############# >>> Unpacking source... >>> Unpacking htslib-1.17.tar.bz2 to /var/tmp/portage/sci-libs/htslib-1.17/work >>> Source unpacked in /var/tmp/portage/sci-libs/htslib-1.17/work >>> Preparing source in /var/tmp/portage/sci-libs/htslib-1.17/work/htslib-1.17 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/htslib-1.17/work/htslib-1.17 ... ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --docdir=/usr/share/doc/htslib-1.17 --htmldir=/usr/share/doc/htslib-1.17/html --libdir=/usr/lib --disable-gcs --disable-plugins --disable-s3 --enable-bz2 --disable-libcurl --enable-lzma checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes checking whether C compiler accepts -mavx2... no checking whether C compiler accepts -mavx512f... yes checking whether C compiler supports ARM Neon... no checking for i686-pc-linux-gnu-pkg-config... /usr/bin/i686-pc-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking shared library type for i686-pc-linux-gnu... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/htslib-1.17/work/htslib-1.17 ... make -j16 AR=i686-pc-linux-gnu-ar i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o kfunc.o kfunc.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o kstring.o kstring.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o bgzf.o bgzf.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o errmod.o errmod.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o faidx.o faidx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o header.o header.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.17"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'i686-pc-linux-gnu-gcc' \ '' \ '-Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden' \ '-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden ' \ '-llzma -lbz2 -lz -lm ' > config_vars.h i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o hts_os.o hts_os.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o md5.o md5.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o multipart.o multipart.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o probaln.o probaln.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o realn.o realn.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o regidx.o regidx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o region.o region.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o sam.o sam.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o tbx.o tbx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o textutils.o textutils.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o vcf.o vcf.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -mavx512f -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o header.pico header.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o region.pico region.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -mavx512f -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o bgzip.o bgzip.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htsfile.o htsfile.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o tabix.o tabix.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/sam.o test/sam.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_faidx.o test/test_faidx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc i686-pc-linux-gnu-gcc -Wall -O2 -march=i686 -mfpmath=sse -msse2 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o hts.o hts.c i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_time_funcs test/test_time_funcs.o i686-pc-linux-gnu-gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 i686-pc-linux-gnu-ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o i686-pc-linux-gnu-ranlib libhts.a i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_faidx test/test_faidx.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -lpthread >>> Source compiled. >>> Test phase [not enabled]: sci-libs/htslib-1.17 >>> Install sci-libs/htslib-1.17 into /var/tmp/portage/sci-libs/htslib-1.17/image make -j16 DESTDIR=/var/tmp/portage/sci-libs/htslib-1.17/image install mkdir -p -m 755 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/bin /var/tmp/portage/sci-libs/htslib-1.17/image/usr/include /var/tmp/portage/sci-libs/htslib-1.17/image/usr/include/htslib /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib /var/tmp/portage/sci-libs/htslib-1.17/image/usr/share/man/man1 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/share/man/man5 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/share/man/man7 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib/pkgconfig if test -n ""; then mkdir -p -m 755 /var/tmp/portage/sci-libs/htslib-1.17/image; fi install -p -m 644 libhts.so /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib/libhts.so.1.17 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib#g;s#@-PACKAGE_VERSION@#1.17#g' htslib.pc.tmp > /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib/pkgconfig/htslib.pc chmod 644 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib/pkgconfig/htslib.pc ln -sf libhts.so.1.17 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib/libhts.so ln -sf libhts.so.1.17 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib/libhts.so.3 install -p bgzip htsfile tabix /var/tmp/portage/sci-libs/htslib-1.17/image/usr/bin if test -n ""; then install -p /var/tmp/portage/sci-libs/htslib-1.17/image; fi install -p -m 644 htslib/*.h /var/tmp/portage/sci-libs/htslib-1.17/image/usr/include/htslib install -p -m 644 libhts.a /var/tmp/portage/sci-libs/htslib-1.17/image/usr/lib/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /var/tmp/portage/sci-libs/htslib-1.17/image/usr/share/man/man7 >>> Completed installing sci-libs/htslib-1.17 into /var/tmp/portage/sci-libs/htslib-1.17/image * Final size of build directory: 43144 KiB (42.1 MiB) * Final size of installed tree: 4692 KiB ( 4.5 MiB) making executable: /usr/lib/libhts.so.1.17 * QA Notice: Found the following implicit function declarations in configure logs: * /var/tmp/portage/sci-libs/htslib-1.17/work/htslib-1.17/config.log:122 - _mm256_extract_epi64 * Check that no features were accidentally disabled. * See https://wiki.gentoo.org/wiki/Modern_C_porting. strip: i686-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/lib/libhts.so.1.17 /usr/bin/bgzip /usr/bin/htsfile /usr/bin/tabix >>> Done.