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Gentoo's Bugzilla – Attachment 623926 Details for
Bug 713816
dev-perl/Bio-DB-HTS does not respect LDFLAGS
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build.log
build.log (text/plain), 15.71 KB, created by
Agostino Sarubbo
on 2020-03-21 16:28:24 UTC
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hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-03-21 16:28:24 UTC
Size:
15.71 KB
patch
obsolete
> * Package: dev-perl/Bio-DB-HTS-3.10.0 > * Repository: gentoo > * Maintainer: marecki@gentoo.org sci-biology@gentoo.org > * USE: abi_x86_32 elibc_glibc kernel_linux userland_GNU x86 > * FEATURES: network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox > * Applying 2.11-build_split_htslib_opts.patch ... > [ ok ] > * Using Module::Build > * perl Build.PL --installdirs=vendor --libdoc= --destdir=/var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/ --create_packlist=1 --htslib-includedir=/usr/include/htslib --htslib-libdir=/usr/lib >Created MYMETA.yml and MYMETA.json >Creating new 'Build' script for 'Bio-DB-HTS' version '3.01' >Building Bio-DB-HTS >i686-pc-linux-gnu-gcc -I/usr/include -I/usr/lib/perl5/5.30.1/i686-linux/CORE -DVERSION="3.01" -DXS_VERSION="3.01" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -g -ggdb -Werror=format-security -O2 -pipe -march=native -g -ggdb -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c >[01m[Klib/Bio/DB/HTS.xs:[m[K In function â[01m[KXS_Bio__DB__HTS__VCF__Header_fmt_text[m[Kâ: >[01m[Klib/Bio/DB/HTS.xs:1769:5:[m[K [01;35m[Kwarning: [m[Kâ[01m[Kbcf_hdr_fmt_text[m[Kâ is deprecated: use bcf_hdr_format() instead [[01;35m[K-Wdeprecated-declarations[m[K] > 1769 | [01;35m[KRETVAL[m[K = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0); > | [01;35m[K^~~~~~[m[K >In file included from [01m[Klib/Bio/DB/HTS.xs:59[m[K: >[01m[K/usr/include/htslib/vcf.h:439:11:[m[K [01;36m[Knote: [m[Kdeclared here > 439 | char *[01;36m[Kbcf_hdr_fmt_text[m[K(const bcf_hdr_t *hdr, int is_bcf, int *len) > | [01;36m[K^~~~~~~~~~~~~~~~[m[K >ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs') >i686-pc-linux-gnu-gcc -shared -O2 -pipe -march=native -g -ggdb -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz >i686-pc-linux-gnu-gcc -I/usr/include -I/usr/lib/perl5/5.30.1/i686-linux/CORE -DVERSION="3.01" -DXS_VERSION="3.01" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -g -ggdb -Werror=format-security -O2 -pipe -march=native -g -ggdb -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c >ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs') >i686-pc-linux-gnu-gcc -shared -O2 -pipe -march=native -g -ggdb -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/usr/lib -Wl,-rpath,/usr/lib -lhts -lpthread -lz > * Skipping make test/check due to ebuild restriction. > * ./Build install --pure >Building Bio-DB-HTS >Files found in blib/arch: installing files in blib/lib into architecture dependent library tree >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/auto/Bio/DB/HTS/HTS.so >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/auto/Bio/DB/HTS/HTS.bs >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/auto/Bio/DB/HTS/Faidx/Faidx.so >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/auto/Bio/DB/HTS/Faidx/Faidx.bs >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/FetchIterator.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/ReadIterator.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/ConfigData.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/AlignWrapper.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Segment.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/PileupWrapper.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/VCF.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Target.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Tabix.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Pileup.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Kseq.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Alignment.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Faidx.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Constants.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Query.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Tabix/Iterator.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Kseq/Iterator.pod >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/Kseq/Record.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/VCF/HeaderPtr.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/VCF/Header.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/VCF/Row.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/VCF/Iterator.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/lib/perl5/vendor_perl/5.30.1/i686-linux/Bio/DB/HTS/VCF/RowPtr.pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Kseq.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Faidx.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Constants.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::PileupWrapper.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Pileup.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Alignment.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Target.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Query.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Kseq::Record.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::ConfigData.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::VCF::Iterator.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Segment.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::AlignWrapper.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Kseq::Iterator.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Tabix::Iterator.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::VCF.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::ReadIterator.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::FetchIterator.3pm >Installing /var/tmp/portage/dev-perl/Bio-DB-HTS-3.10.0/image/usr/share/man/man3/Bio::DB::HTS::Tabix.3pm > * Fixing packlist file /usr/lib/perl5/vendor_perl/5.30.1/i686-linux/auto/Bio/DB/HTS/.packlist > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::AlignWrapper.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Alignment.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::ConfigData.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Constants.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Faidx.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::FetchIterator.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Kseq.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Kseq::Iterator.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Kseq::Record.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Pileup.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::PileupWrapper.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Query.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::ReadIterator.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Segment.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Tabix.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Tabix::Iterator.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::Target.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::VCF.3pm > * Pruning surplus packlist entry /usr/share/man/man3/Bio::DB::HTS::VCF::Iterator.3pm > * Final size of build directory: 8780 KiB (8.5 MiB) > * Final size of installed tree: 820 KiB > > > >emerge --info: >Portage 2.3.89 (python 3.6.10-final-0, default/linux/x86/17.0, gcc-9.2.0, glibc-2.29-r7, 4.14.34-gentoo-infra38 i686) >================================================================= >System uname: Linux-4.14.34-gentoo-infra38-i686-Intel-R-_Xeon-R-_CPU_E5-2620_v4_@_2.10GHz-with-gentoo-2.6 >KiB Mem: 16426740 total, 5942776 free >KiB Swap: 4194268 total, 4194268 free >Timestamp of repository gentoo: Sat, 21 Mar 2020 15:38:38 +0000 >sh bash 4.4_p23-r1 >ld GNU ld (Gentoo 2.33.1 p2) 2.33.1 >app-shells/bash: 4.4_p23-r1::gentoo >dev-lang/perl: 5.30.1::gentoo >dev-lang/python: 2.7.17-r1::gentoo, 3.6.10::gentoo, 3.7.6::gentoo >dev-util/cmake: 3.16.5::gentoo >sys-apps/baselayout: 2.6-r1::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.13::gentoo >sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r4::gentoo >sys-devel/automake: 1.16.1-r1::gentoo >sys-devel/binutils: 2.33.1-r1::gentoo >sys-devel/gcc: 9.2.0-r2::gentoo >sys-devel/gcc-config: 2.2.1::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.2.1-r4::gentoo >sys-kernel/linux-headers: 4.19::gentoo (virtual/os-headers) >sys-libs/glibc: 2.29-r7::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-jobs: 1 > sync-rsync-verify-max-age: 24 > >ACCEPT_KEYWORDS="x86" >ACCEPT_LICENSE="*" >CBUILD="i686-pc-linux-gnu" >CFLAGS="-O2 -pipe -march=native -g -ggdb -Werror=format-security" >CHOST="i686-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.4/ext-active/ /etc/php/cgi-php7.4/ext-active/ /etc/php/cli-php7.4/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXXFLAGS="-O2 -pipe -march=native -g -ggdb -Werror=format-security" >DISTDIR="/usr/portage/distfiles" >EMERGE_DEFAULT_OPTS="--with-bdeps y --keep-going y --quiet-fail y -1" >ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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 -march=i686 -pipe" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -march=i686 -pipe" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="en_US.utf8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -Wl,--defsym=__gentoo_check_ldflags__=0" >LINGUAS="en en_GB" >MAKEOPTS="-j8" >PKGDIR="/root/.packages" >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" >USE="X acl berkdb bzip2 cli consolekit crypt dri fortran gdbm iconv ipv6 jumbo-build libtirpc ncurses nls nptl openmp openssl pam pcre readline seccomp split-usr ssl tcpd unicode x86 xattr zlib" ABI_X86="32" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en en_GB en-GB" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" >Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS >
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bug 713816
: 623926