* Package: sci-libs/htslib-1.15.1:0/3 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 bzip2 elibc_musl kernel_linux lzma userland_GNU * FEATURES: network-sandbox preserve-libs sandbox test 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/b0367acf5b4394a62a8794bd6176464a38c1ddbe (Wed Sep 28 14:02:00 UTC 2022) @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.37 (python 3.10.7-final-0, default/linux/amd64/17.0/musl/hardened, gcc-12.2.0, musl-1.2.3-r4, 5.10.133-gentoo x86_64) ================================================================= System uname: Linux-5.10.133-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-libc KiB Mem: 264024340 total, 61267844 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Wed, 28 Sep 2022 14:02:00 +0000 sh bash 5.1_p16-r2 ld GNU ld (Gentoo 2.39 p4) 2.39.0 app-misc/pax-utils: 1.3.5::gentoo app-shells/bash: 5.1_p16-r2::gentoo dev-lang/perl: 5.36.0::gentoo dev-lang/python: 3.8.14::gentoo, 3.9.14::gentoo, 3.10.7::gentoo, 3.11.0_rc2::gentoo dev-util/cmake: 3.24.2::gentoo dev-util/meson: 0.63.2-r1::gentoo sys-apps/baselayout: 2.9::gentoo sys-apps/openrc: 0.45.2::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.71-r4::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.39-r2::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/gcc: 12.2.0::gentoo sys-devel/gcc-config: 2.6::gentoo sys-devel/libtool: 2.4.7::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.19::gentoo (virtual/os-headers) sys-libs/musl: 1.2.3-r4::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* MIT" CBUILD="x86_64-gentoo-linux-musl" CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" CHOST="x86_64-gentoo-linux-musl" 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 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" DISTDIR="/var/tmp/portage/sci-libs/htslib-1.15.1/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY 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" FCFLAGS="-O2 -pipe -march=x86-64 -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 network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=x86-64 -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" INSTALL_MASK="charset.alias /usr/share/locale/locale.alias" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j4" 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 amd64 bzip2 cli crypt dri elogind fortran hardened iconv ipv6 jumbo-build libglvnd libtirpc lzma native-symlinks ncurses nls nptl openmp pam pcre pie readline seccomp split-usr ssl ssp test unicode xattr xtpax zlib" ABI_X86="64" ELIBC="musl" KERNEL="linux" USERLAND="GNU" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ############################## # emerge history (qlop -mv): # ############################## ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/audio-0-r1:0 acct-group/cdrom-0-r1:0 acct-group/dialout-0-r1:0 acct-group/disk-0-r1:0 acct-group/input-0-r1:0 acct-group/kmem-0-r1:0 acct-group/kvm-0-r1:0 acct-group/lp-0-r1:0 acct-group/man-0-r1:0 acct-group/messagebus-0-r1:0 acct-group/portage-0:0 acct-group/render-0-r1:0 acct-group/sgx-0:0 acct-group/sshd-0-r1:0 acct-group/tape-0-r1:0 acct-group/tty-0-r1:0 acct-group/video-0-r1:0 acct-user/man-1-r1:0 acct-user/messagebus-0-r1:0 acct-user/portage-0:0 acct-user/sshd-0-r1:0 app-admin/eselect-1.4.20:0 -doc -emacs -vim-syntax app-admin/perl-cleaner-2.30:0 app-arch/bzip2-1.0.8-r3:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static -static-libs -verify-sig app-arch/gzip-1.12-r2:0 -pic -static 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x11-misc/xdg-utils-1.1.3_p20210805:0 -dbus -doc -gnome ####################### # build.log # ####################### >>> Unpacking source... >>> Unpacking htslib-1.15.1.tar.bz2 to /var/tmp/portage/sci-libs/htslib-1.15.1/work >>> Source unpacked in /var/tmp/portage/sci-libs/htslib-1.15.1/work >>> Preparing source in /var/tmp/portage/sci-libs/htslib-1.15.1/work/htslib-1.15.1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/htslib-1.15.1/work/htslib-1.15.1 ... ./configure --prefix=/usr --build=x86_64-gentoo-linux-musl --host=x86_64-gentoo-linux-musl --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --docdir=/usr/share/doc/htslib-1.15.1 --htmldir=/usr/share/doc/htslib-1.15.1/html --libdir=/usr/lib --disable-gcs --disable-plugins --disable-s3 --enable-bz2 --disable-libcurl --enable-lzma checking for x86_64-gentoo-linux-musl-gcc... x86_64-gentoo-linux-musl-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 x86_64-gentoo-linux-musl-gcc accepts -g... yes checking for x86_64-gentoo-linux-musl-gcc option to accept ISO C89... none needed checking for x86_64-gentoo-linux-musl-ranlib... x86_64-gentoo-linux-musl-ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for x86_64-gentoo-linux-musl-pkg-config... /usr/bin/x86_64-gentoo-linux-musl-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... no checking shared library type for x86_64-gentoo-linux-musl... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... x86_64-gentoo-linux-musl-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... none required 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-1.15.1/work/htslib-1.15.1 ... make -j4 AR=x86_64-gentoo-linux-musl-ar x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o kfunc.o kfunc.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o kstring.o kstring.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o bgzf.o bgzf.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o errmod.o errmod.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o faidx.o faidx.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o header.o header.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "x86_64-gentoo-linux-musl-gcc"' > config_vars.h echo '#define HTS_CPPFLAGS ""' >> config_vars.h echo '#define HTS_CFLAGS "-Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden"' >> config_vars.h x86_64-gentoo-linux-musl-gcc -Wall 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probaln.o probaln.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o realn.o realn.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o regidx.o regidx.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o region.o region.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o sam.o sam.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o tbx.o tbx.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o textutils.o textutils.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o vcf.o vcf.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c In file included from htscodecs/htscodecs/rANS_static4x16pr.c:74: In function 'RansEncFlush', inlined from 'rans_compress_O1_4x16.isra' at htscodecs/htscodecs/rANS_static4x16pr.c:840:5: htscodecs/htscodecs/rANS_word.h:109:9: warning: 'ptr' may be used uninitialized [-Wmaybe-uninitialized[https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wmaybe-uninitialized]] 109 | ptr -= 4; | ~~~~^~~~ htscodecs/htscodecs/rANS_static4x16pr.c: In function 'rans_compress_O1_4x16.isra': htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: 'ptr' was declared here 793 | uint8_t* ptr = out_end; | ^~~ x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o header.pico header.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o region.pico region.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c In file included from htscodecs/htscodecs/rANS_static4x16pr.c:74: In function 'RansEncFlush', inlined from 'rans_compress_O1_4x16.isra' at htscodecs/htscodecs/rANS_static4x16pr.c:840:5: htscodecs/htscodecs/rANS_word.h:109:9: warning: 'ptr' may be used uninitialized [-Wmaybe-uninitialized[https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wmaybe-uninitialized]] 109 | ptr -= 4; | ~~~~^~~~ htscodecs/htscodecs/rANS_static4x16pr.c: In function 'rans_compress_O1_4x16.isra': htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: 'ptr' was declared here 793 | uint8_t* ptr = out_end; | ^~~ x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o bgzip.o bgzip.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o htsfile.o htsfile.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o tabix.o tabix.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/sam.o test/sam.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.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 x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -c -o hts.o hts.c x86_64-gentoo-linux-musl-gcc -shared -Wl,-soname,libhts.so.3 -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_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico -llzma -lbz2 -lz -lpthread x86_64-gentoo-linux-musl-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 x86_64-gentoo-linux-musl-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 ln -sf libhts.so libhts.so.3 x86_64-gentoo-linux-musl-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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o x86_64-gentoo-linux-musl-ranlib libhts.a x86_64-gentoo-linux-musl-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lpthread x86_64-gentoo-linux-musl-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lpthread x86_64-gentoo-linux-musl-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread x86_64-gentoo-linux-musl-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 -lpthread >>> Source compiled. >>> Test phase: sci-libs/htslib-1.15.1 make -j4 check x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c x86_64-gentoo-linux-musl-gcc -Wall -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.c x86_64-gentoo-linux-musl-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lpthread x86_64-gentoo-linux-musl-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lpthread x86_64-gentoo-linux-musl-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lpthread x86_64-gentoo-linux-musl-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fvisibility=hidden -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test Testing rans4x8 -r -o0 on ./dat/q4 cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test 11674 Testing rans4x8 -r -o1 on ./dat/q4 10870 Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 ./rans4x16.test: line 12: 7908 Segmentation fault ./rans4x16pr -r -o$o $out/r4x16-nl $out/r4x16.comp 2>> $out/r4x16.stderr make: *** [Makefile:626: test_htscodecs_rans4x16] Error 1 make: *** Waiting for unfinished jobs.... Testing rans4x8 -r -o0 on ./dat/q40+dir 50258 Testing rans4x8 -r -o1 on ./dat/q40+dir 50537 Testing rans4x8 -r -o0 on ./dat/q8 33099 Testing rans4x8 -r -o1 on ./dat/q8 31428 Testing rans4x8 -r -o0 on ./dat/qvar 32997 Testing rans4x8 -r -o1 on ./dat/qvar 32832 * ERROR: sci-libs/htslib-1.15.1::gentoo failed (test phase): * Make check failed. See above for details. * * Call stack: * ebuild.sh, line 122: Called src_test * environment, line 1273: Called default * phase-functions.sh, line 872: Called default_src_test * phase-functions.sh, line 901: Called __eapi0_src_test * phase-helpers.sh, line 832: Called die * The specific snippet of code: * ${emake_cmd} ${internal_opts} check || \ * die "Make check failed. See above for details." * * If you need support, post the output of `emerge --info '=sci-libs/htslib-1.15.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/htslib-1.15.1::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-libs/htslib-1.15.1:20220928-140714.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/htslib-1.15.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/htslib-1.15.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/htslib-1.15.1/work/htslib-1.15.1' * S: '/var/tmp/portage/sci-libs/htslib-1.15.1/work/htslib-1.15.1'