* Package: dev-perl/go-db-perl-0.04-r1 * Repository: science * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking go-db-perl-0.04.tar.gz to /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/work >>> Source unpacked in /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/work >>> Preparing source in /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/work/go-db-perl-0.04 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/work/go-db-perl-0.04 ... * Using ExtUtils::MakeMaker * perl Makefile.PL PREFIX=/usr INSTALLDIRS=vendor INSTALLMAN3DIR=none DESTDIR=/var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image ** WARNING ** You do not have the environment variable GO_ROOT set. This is required for building the database, so that the system known where the XSL files live. You should set this to wherever your go-dev distribution lives; eg setenv GO_ROOT /go-dev/ If you are having problems installing XML::LibXSLT, please consult http://www.godatabase.org/dev/xml/doc/xml-doc.html go-db-perl: Gene Ontology Database API Online documentation - http://www.godatabase.org/dev Local documentation - see go-dev/go-db-perl/doc/go-db-perl-doc.html In order to test and install the API, you need database creation privileges on a mysql database server. this is so that I can build a few test databases to check everything is working. if you dont have network access to any nearby servers, consider installing mysql locally - see www.mysql.org you will also need read access to a fully populated GO database. You can use the main GO one or populate your own from the exports here: http://www.godatabase.org/dev/database mysql server address [localhost]: name of readonly populated GO database[go]: name of dbuser (optional)[]: db password (optional)[]: ** WARNING ** You do not have the environment variable GO_ROOT set; you should set this to wherever you have the go-dev repository checked out (this should be the directory one above this one) Unparsable version '0.0/Carp' for prerequisite Carp treated as 0 at /usr/lib64/perl5/5.30.3/CPAN/Meta/Requirements.pm line 140. Unparsable version '0.0/Stag' for prerequisite Data::Stag treated as 0 at /usr/lib64/perl5/5.30.3/CPAN/Meta/Requirements.pm line 140. Unparsable version '0.0/bioperl' for prerequisite Bio::Seq treated as 0 at /usr/lib64/perl5/5.30.3/CPAN/Meta/Requirements.pm line 140. Unparsable version '0.0/Scalar' for prerequisite Set::Scalar treated as 0 at /usr/lib64/perl5/5.30.3/CPAN/Meta/Requirements.pm line 140. Unparsable version '0.0/DBI for DbUtils::SqlWrapper' for prerequisite DBI treated as 0 at /usr/lib64/perl5/5.30.3/CPAN/Meta/Requirements.pm line 140. Unparsable version '0.0/MD5' for prerequisite Digest::MD5 treated as 0 at /usr/lib64/perl5/5.30.3/CPAN/Meta/Requirements.pm line 140. Checking if your kit is complete... Warning: the following files are missing in your kit: META.yml Please inform the author. Warning: prerequisite Bio::Seq 0 not found. Generating a Unix-style Makefile Writing Makefile for GO Writing MYMETA.yml and MYMETA.json >>> Source configured. >>> Compiling source in /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/work/go-db-perl-0.04 ... * emake OTHERLDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 make -j1 'OTHERLDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' cp GO/Handlers/genericdb.pm blib/lib/GO/Handlers/genericdb.pm cp GO/AppHandles/AppHandleChadoSqlImpl.pm blib/lib/GO/AppHandles/AppHandleChadoSqlImpl.pm cp GO/Reasoner.pm blib/lib/GO/Reasoner.pm cp GO/TestHarness.pm blib/lib/GO/TestHarness.pm cp GO/AppHandles/AppHandleAbstractSqlImpl.pm blib/lib/GO/AppHandles/AppHandleAbstractSqlImpl.pm cp GO/Handlers/db.pm blib/lib/GO/Handlers/db.pm cp GO/Admin.pm blib/lib/GO/Admin.pm cp GO/DebugUtils.pm blib/lib/GO/DebugUtils.pm cp GO/AppHandles/AppHandleSqlImpl.pm blib/lib/GO/AppHandles/AppHandleSqlImpl.pm cp GO.pm blib/lib/GO.pm cp GO/SqlWrapper.pm blib/lib/GO/SqlWrapper.pm cp GO/AppHandles/AppHandleCachingImpl.pm blib/lib/GO/AppHandles/AppHandleCachingImpl.pm cp GO/AppHandle.pm blib/lib/GO/AppHandle.pm cp GO/AppHandles/AppHandleCWrapper.pm blib/lib/GO/AppHandles/AppHandleCWrapper.pm cp GO/Tango.pm blib/lib/GO/Tango.pm cp GO/AppHandles/AppHandlePgImpl.pm blib/lib/GO/AppHandles/AppHandlePgImpl.pm cp GO/Handlers/godb.pm blib/lib/GO/Handlers/godb.pm >>> Source compiled. >>> Test phase [not enabled]: dev-perl/go-db-perl-0.04-r1 >>> Install dev-perl/go-db-perl-0.04-r1 into /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image make -j1 pure_install Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/Tango.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/AppHandle.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/SqlWrapper.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/DebugUtils.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/Admin.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/TestHarness.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/Reasoner.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/AppHandles/AppHandlePgImpl.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/AppHandles/AppHandleCWrapper.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/AppHandles/AppHandleCachingImpl.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/AppHandles/AppHandleSqlImpl.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/AppHandles/AppHandleAbstractSqlImpl.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/AppHandles/AppHandleChadoSqlImpl.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/Handlers/godb.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/Handlers/db.pm Installing /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image/usr/lib64/perl5/vendor_perl/5.30.3/GO/Handlers/genericdb.pm * Fixing packlist file //usr/lib64/perl5/vendor_perl/5.30.3/x86_64-linux/auto/GO/.packlist * Pruning surplus packlist entry /usr/bin/go-apply-xslt * Pruning surplus packlist entry /usr/bin/go-dag-summary.pl * Pruning surplus packlist entry 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/usr/lib64/perl5/vendor_perl/5.30.3/GO/ObjFactory.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/ParserEventNames.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/base_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/generic_tagval_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/go_assoc_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/go_def_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/go_ids_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/go_ont_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/go_xref_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/locuslink_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/mesh_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/mgi_assoc_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/ncbi_taxon_names_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/ncbi_taxonomy_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/obj_emitter.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/obj_storable_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/obj_yaml_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/obo_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/obo_text_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/obo_xml_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/owl_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/references_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/refgenomes_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/unknown_format_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Parsers/xrf_abbs_parser.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/Utils.pm * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/chadoxml_to_oboxml.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/ipr_to_oboxml.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_filter.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_chadoxml.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_dig.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_godb_prestore.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_obd_prestore.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_obotext.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_owl.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_racer.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_simple_owl.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/oboxml_to_summary_table.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/owl_to_oboxml.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/GO/xsl/text_html.xsl * Pruning surplus packlist entry /usr/lib64/perl5/vendor_perl/5.30.3/go-perl.pod * Pruning surplus packlist entry /usr/share/man/man1/go-apply-xslt.1 * Pruning surplus packlist entry /usr/share/man/man1/go-dag-summary.pl.1 * Pruning surplus packlist entry /usr/share/man/man1/go-export-graph.pl.1 * Pruning surplus packlist entry /usr/share/man/man1/go-export-prolog.pl.1 * Pruning surplus packlist entry /usr/share/man/man1/go-filter-subset.pl.1 * Pruning surplus packlist entry /usr/share/man/man1/go-show-assocs-by-node.pl.1 * Pruning surplus packlist entry /usr/share/man/man1/go-show-paths-to-root.pl.1 * Pruning surplus packlist entry /usr/share/man/man1/go2error_report.1 * Pruning surplus packlist entry /usr/share/man/man1/go2fmt.pl.1 * Pruning surplus packlist entry /usr/share/man/man1/map2slim.1 >>> Completed installing dev-perl/go-db-perl-0.04-r1 into /var/tmp/portage/dev-perl/go-db-perl-0.04-r1/image * Final size of build directory: 4048 KiB (3.9 MiB) * Final size of installed tree: 512 KiB * checking 20 files for package collisions * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / ` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at https://bugs.gentoo.org/ unless you report exactly * which two packages install the same file(s). See * https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how * to solve the problem. And once again, please do NOT file a bug report * unless you have completely understood the above message. * * Detected file collision(s): * * /usr/lib64/perl5/vendor_perl/5.30.3/x86_64-linux/auto/GO/.packlist * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * dev-perl/go-perl-0.150.0:0::gentoo * /usr/lib64/perl5/vendor_perl/5.30.3/x86_64-linux/auto/GO/.packlist * * Package 'dev-perl/go-db-perl-0.04-r1' NOT merged due to file * collisions. If necessary, refer to your elog messages for the whole * content of the above message.