------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/perl5-5.30.3.txz ===== Message from perl5-5.30.3: -- The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Installing /packages/All/p5-IO-String-1.08_1.txz Installing /packages/All/p5-Data-Stag-0.14_2.txz Installing /packages/All/p5-Error-0.17029.txz Installing /packages/All/p5-Heap-0.80_1.txz Installing /packages/All/p5-Graph-0.9704,1.txz Installing /packages/All/p5-Clone-0.45.txz Installing /packages/All/p5-Encode-Locale-1.05.txz Installing /packages/All/p5-TimeDate-2.33,1.txz Installing /packages/All/p5-HTTP-Date-6.05.txz Installing /packages/All/p5-IO-HTML-1.001_1.txz Installing /packages/All/p5-LWP-MediaTypes-6.04.txz Installing /packages/All/p5-URI-1.76.txz Installing /packages/All/p5-HTTP-Message-6.24.txz Installing /packages/All/p5-IO-stringy-2.111.txz Installing /packages/All/p5-IO-Tty-1.14.txz Installing /packages/All/p5-IPC-Run-0.99.txz Installing /packages/All/p5-Exporter-Tiny-1.002002.txz Installing /packages/All/p5-List-MoreUtils-XS-0.428.txz Installing /packages/All/p5-List-MoreUtils-0.428.txz Installing /packages/All/p5-Module-Build-0.4231.txz Installing /packages/All/p5-Set-Scalar-1.29.txz Installing /packages/All/p5-Class-Data-Inheritable-0.08_1.txz Installing /packages/All/p5-Devel-StackTrace-2.04.txz Installing /packages/All/p5-Exception-Class-1.44.txz Installing /packages/All/p5-Test-Deep-1.130.txz Installing /packages/All/p5-Algorithm-Diff-1.1903.txz Installing /packages/All/p5-Text-Diff-1.45.txz Installing /packages/All/p5-Test-Differences-0.650,1.txz Installing /packages/All/p5-Sub-Uplevel-0.2800.txz Installing /packages/All/p5-Test-Exception-0.43.txz Installing /packages/All/p5-Test-Warn-0.36.txz Installing /packages/All/p5-Test-Most-0.35.txz Installing /packages/All/p5-Test-RequiresInternet-0.05.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/p5-XML-Parser-2.44.txz Installing /packages/All/p5-libxml-0.08_1.txz Installing /packages/All/p5-Digest-HMAC-1.03_1.txz Installing /packages/All/p5-Authen-NTLM-1.09_1.txz Installing /packages/All/p5-File-Listing-6.04_1.txz Installing /packages/All/p5-HTML-Tagset-3.20_1.txz Installing /packages/All/p5-HTML-Parser-3.72.txz Installing /packages/All/p5-HTTP-Cookies-6.08.txz Installing /packages/All/p5-HTTP-Daemon-6.10.txz Installing /packages/All/p5-HTTP-Negotiate-6.01_1.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/p5-Net-SSLeay-1.88.txz Installing /packages/All/p5-Mozilla-CA-20180117.txz Installing /packages/All/p5-Socket6-0.29.txz Installing /packages/All/p5-IO-Socket-INET6-2.72_1.txz Installing /packages/All/p5-IO-Socket-SSL-2.068.txz Installing /packages/All/p5-Net-HTTP-6.19.txz Installing /packages/All/p5-Try-Tiny-0.30.txz Installing /packages/All/p5-WWW-RobotRules-6.02_1.txz Installing /packages/All/p5-libwww-6.44.txz Installing /packages/All/p5-XML-RegExp-0.04_1.txz Installing /packages/All/p5-XML-DOM-1.44_1.txz Installing /packages/All/p5-XML-XPathEngine-0.14_1.txz Installing /packages/All/p5-XML-DOM-XPath-0.14_1.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/p5-XML-NamespaceSupport-1.12.txz Installing /packages/All/p5-XML-SAX-Base-1.09.txz Installing /packages/All/p5-XML-SAX-1.02.txz could not find ParserDetails.ini in /usr/local/lib/perl5/site_perl/XML/SAX Installing /packages/All/p5-XML-LibXML-2.0204,1.txz Installing /packages/All/p5-XML-Filter-BufferText-1.01_1.txz Installing /packages/All/p5-XML-SAX-Writer-0.57.txz Installing /packages/All/p5-HTML-Tree-5.07.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/p5-Text-Iconv-1.7_3.txz Installing /packages/All/p5-Tie-IxHash-1.23_1.txz Installing /packages/All/p5-XML-XPath-1.44.txz Installing /packages/All/p5-XML-Twig-3.52.txz Installing /packages/All/p5-XML-Writer-0.625_1.txz Installing /packages/All/p5-YAML-1.30.txz Installing /packages/All/p5-BioPerl-1.007007.txz Installing /packages/All/p5-Bio-Variation-1.7.5.txz Installing /packages/All/p5-Bio-Cluster-1.7.3_1.txz Installing /packages/All/p5-Bio-ASN1-EntrezGene-1.73_2,1.txz Installing /packages/All/p5-CGI-4.47.txz Installing /packages/All/p5-File-NFSLock-1.29.txz Installing /packages/All/p5-Cache-2.11.txz Installing /packages/All/p5-Digest-SHA1-2.13_1.txz Installing /packages/All/p5-IPC-ShareLite-0.17_1.txz Installing /packages/All/p5-Cache-Cache-1.08.txz Installing /packages/All/p5-LWP-Protocol-https-6.07_1.txz SUCCEEDED 00:00:17 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by p5-Bio-DB-NCBIHelper-1.7.6 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by p5-Bio-DB-NCBIHelper-1.7.6 for building => SHA256 Checksum OK for Bio-DB-NCBIHelper-1.7.6.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by p5-Bio-DB-NCBIHelper-1.7.6 for building ===> Extracting for p5-Bio-DB-NCBIHelper-1.7.6 => SHA256 Checksum OK for Bio-DB-NCBIHelper-1.7.6.tar.gz. Extracted Memory Use: 0.22M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for p5-Bio-DB-NCBIHelper-1.7.6 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Bio-ASN1-EntrezGene>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-BioPerl>=1.007007 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-CGI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Cache-Cache>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-HTTP-Message>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-LWP-Protocol-https>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-URI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-XML-Twig>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-libwww>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: perl5>=5.30.r1<5.31 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: perl5>=5.30.r1<5.31 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Bio-ASN1-EntrezGene>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-BioPerl>=1.007007 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-CGI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Cache-Cache>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-HTTP-Message>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-LWP-Protocol-https>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-URI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-XML-Twig>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-libwww>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: perl5>=5.30.r1<5.31 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: perl5>=5.30.r1<5.31 - found ===> Configuring for p5-Bio-DB-NCBIHelper-1.7.6 Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::DB::NCBIHelper Writing MYMETA.yml and MYMETA.json SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for p5-Bio-DB-NCBIHelper-1.7.6 --- blib/lib/Bio/DB/.exists --- --- blib/arch/.exists --- --- blib/lib/auto/Bio/DB/NCBIHelper/.exists --- --- blib/arch/auto/Bio/DB/NCBIHelper/.exists --- --- blib/bin/.exists --- --- blib/script/.exists --- --- blib/man1/.exists --- --- blib/man3/.exists --- --- config --- --- subdirs --- --- dynamic --- --- pm_to_blib --- --- blib/script/bp_biofetch_genbank_proxy --- --- blib/script/bp_download_query_genbank --- --- blib/script/bp_query_entrez_taxa --- --- blib/script/bp_biofetch_genbank_proxy --- cp bin/bp_biofetch_genbank_proxy blib/script/bp_biofetch_genbank_proxy --- blib/script/bp_download_query_genbank --- cp bin/bp_download_query_genbank blib/script/bp_download_query_genbank --- blib/script/bp_biofetch_genbank_proxy --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biofetch_genbank_proxy --- blib/script/bp_download_query_genbank --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_download_query_genbank --- blib/script/bp_query_entrez_taxa --- cp bin/bp_query_entrez_taxa blib/script/bp_query_entrez_taxa "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_query_entrez_taxa --- blibdirs --- --- config --- --- dynamic --- --- linkext --- --- pm_to_blib --- cp lib/Bio/DB/GenPept.pm blib/lib/Bio/DB/GenPept.pm cp lib/Bio/DB/GenBank.pm blib/lib/Bio/DB/GenBank.pm cp lib/Bio/DB/EntrezGene.pm blib/lib/Bio/DB/EntrezGene.pm cp lib/Bio/DB/NCBIHelper.pm blib/lib/Bio/DB/NCBIHelper.pm cp lib/Bio/DB/Query/GenBank.pm blib/lib/Bio/DB/Query/GenBank.pm cp lib/Bio/DB/Taxonomy/entrez.pm blib/lib/Bio/DB/Taxonomy/entrez.pm --- pure_all --- --- pure_all --- --- manifypods --- Manifying 3 pod documents Manifying 6 pod documents --- all --- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Bio-ASN1-EntrezGene>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-BioPerl>=1.007007 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-CGI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Cache-Cache>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-HTTP-Message>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-LWP-Protocol-https>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-URI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-XML-Twig>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-libwww>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: perl5>=5.30.r1<5.31 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for p5-Bio-DB-NCBIHelper-1.7.6 ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Bio-ASN1-EntrezGene>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-BioPerl>=1.007007 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-CGI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-Cache-Cache>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-HTTP-Message>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-LWP-Protocol-https>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-URI>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-XML-Twig>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: p5-libwww>=0 - found ===> p5-Bio-DB-NCBIHelper-1.7.6 depends on package: perl5>=5.30.r1<5.31 - found ===> Generating temporary packing list Manifying 3 pod documents Manifying 6 pod documents Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/Bio/DB/GenPept.pm Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/Bio/DB/GenBank.pm Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/Bio/DB/EntrezGene.pm Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/Bio/DB/NCBIHelper.pm Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/Bio/DB/Taxonomy/entrez.pm Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/Bio/DB/Query/GenBank.pm Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man1/bp_biofetch_genbank_proxy.1 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man1/bp_query_entrez_taxa.1 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man1/bp_download_query_genbank.1 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Taxonomy::entrez.3 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::EntrezGene.3 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::GenBank.3 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::NCBIHelper.3 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Query::GenBank.3 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::GenPept.3 Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/bin/bp_biofetch_genbank_proxy Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/bin/bp_query_entrez_taxa Installing /construction/biology/p5-Bio-DB-NCBIHelper/stage/usr/local/bin/bp_download_query_genbank ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: www/p5-CGI was in Perl CORE. Check with `corelist CGI 0` and `corelist -a CGI` if it should be conditionally added depending on PERL_LEVEL Notice: You have some Perl modules as dependencies but you do not have devel/p5-Module-CoreList installed, the perlcore QA check gets better results when using it, especially with older Perl versions. Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for p5-Bio-DB-NCBIHelper-1.7.6 file sizes/checksums [19]: 0% file sizes/checksums [19]: 100% packing files [19]: 0% packing files [19]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:26