Attachment 623930 Details for Bug 713818 – build log

build log

file_713818.txt (text/plain), 10.20 KB, created by Agostino Sarubbo on 2020-03-21 16:39:23 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Agostino Sarubbo

Created: 2020-03-21 16:39:23 UTC

Size: 10.20 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
>lib/Bio/DB/HTS.xs: In function âXS_Bio__DB__HTS__VCF__Header_fmt_textâ:
>lib/Bio/DB/HTS.xs:1769:5: warning: âbcf_hdr_fmt_textâ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
> 1769 |     RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0);
>      |     ^~~~~~
>In file included from lib/Bio/DB/HTS.xs:59:
>/usr/include/htslib/vcf.h:439:11: note: declared here
>  439 |     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
>      |           ^~~~~~~~~~~~~~~~
>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

Actions: View

Attachments on bug 713818: 623930