diff --git a/recipes/perl-bioperl-core/build.sh b/recipes/perl-bioperl-core/build.sh index 37bc07175aaf4..2eeaadf306838 100644 --- a/recipes/perl-bioperl-core/build.sh +++ b/recipes/perl-bioperl-core/build.sh @@ -8,18 +8,26 @@ set -o pipefail # * skipping test that require network access export PERL_MM_USE_DEFAULT=1 +# ensure perl-gd is loaded properly or die trying +perl -e 'die "GD module missing!" unless(eval{require GD});'; + # If it has Build.PL use that, otherwise use Makefile.PL if [ -f Build.PL ]; then - perl Build.PL 2>&1 | tee configure.log +# perl Build.PL 2>&1 | tee configure.log + perl Build.PL ./Build - ./Build test 2>&1 | tee tests.log +# ./Build test 2>&1 | tee tests.log + ./Build test # Make sure this goes in site ./Build install --installdirs site + ./Build install --install_path script=site elif [ -f Makefile.PL ]; then # Make sure this goes in site - perl Makefile.PL INSTALLDIRS=site 2>&1 | tee configure.log +# perl Makefile.PL INSTALLDIRS=site 2>&1 | tee configure.log + perl Makefile.PL INSTALLDIRS=site make - make test 2>&1 | tee tests.log +# make test 2>&1 | tee tests.log + make test make install else echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' diff --git a/recipes/perl-bioperl-core/meta.yaml b/recipes/perl-bioperl-core/meta.yaml index 3f1b523a2b7cd..e54988fa6812a 100644 --- a/recipes/perl-bioperl-core/meta.yaml +++ b/recipes/perl-bioperl-core/meta.yaml @@ -1,88 +1,159 @@ package: name: perl-bioperl-core - version: "1.6.924" + version: 1.7.1 source: - fn: BioPerl-1.6.924.tar.gz - url: http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz - md5: 3090437478919f2a1bd1bcb3d6df5839 + fn: BioPerl-1.007001.tar.gz + url: https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz + md5: 2fe9e716acb53f000f37d422197c2610 build: number: 1 - + # disable osx since deps perl-db-file and perl-dbd-mysql not available + # TODO: either enable dep module OR configure build interactively + skip: True # [osx] + requirements: build: - - perl-threaded - # Required packages - - perl-data-stag - - perl-io-string - # Testing packages - - perl-test-most - - perl-module-build - - perl-uri - # Recommended packages + - perl-threaded >=5.8.3 + - expat + # Recommended and required packages - perl-aceperl - perl-algorithm-munkres - perl-array-compare + - perl-archive-tar + - perl-array-compare + - perl-bio-asn1-entrezgene ## cyclic dependency : update separately !!! - perl-bio-phylo +# - perl-bioperl-ext ## needed? + - perl-cgi - perl-clone - perl-convert-binary-c + - perl-data-stag >=0.11 + - perl-db-file - perl-dbd-sqlite + - perl-dbd-mysql + - perl-dbd-pg - perl-dbi - perl-error + - perl-extutils-manifest >=1.52 - perl-gd - perl-graphviz + - perl-graph + - perl-html-parser - perl-html-tableextract + - perl-http-message + - perl-inline-c >=0.67 + - perl-io-compress - perl-io-stringy + - perl-io-string + - perl-libwww-perl >=5.64 + - perl-libxml-perl - perl-list-moreutils + - perl-math-random + - perl-memoize +# - perl-mod_perl ## Apache APR dependency .. uaks + - perl-module-build >=0.42 - perl-postscript + - perl-scalar-list-utils - perl-set-scalar - - perl-soap-lite +# - perl-soap-lite ## not found in v1.7 build.sh; obsolete? - perl-sort-naturally - perl-spreadsheet-parseexcel - - perl-svg - - perl-svg-graph + - perl-spreadsheet-writeexcel + - perl-statistics-frequency + - perl-svg >=2.26 + - perl-svg-graph >=0.01 + - perl-test-exception + - perl-test-most + - perl-test-simple + - perl-test-warn + - perl-text-parsewords + - perl-tie-cacher + - perl-time-hires + - perl-tree-dag_node + - perl-uri +# - perl-www-mechanize # try first without.. many dependencies.. - perl-xml-dom - perl-xml-dom-xpath + - perl-xml-libxml + - perl-xml-parser + - perl-xml-sax >=0.15 - perl-xml-sax-writer - perl-xml-simple - perl-xml-twig - - perl-xml-writer + - perl-xml-writer >=0.4 - perl-yaml run: - - perl-threaded - # Required packages... - - perl-data-stag - - perl-io-string - # Recommended packages... + - perl-threaded >=5.8.3 + - expat + # Recommended and required packages - perl-aceperl - perl-algorithm-munkres - perl-array-compare + - perl-archive-tar + - perl-array-compare + - perl-bio-asn1-entrezgene - perl-bio-phylo +# - perl-bioperl-ext + - perl-cgi - perl-clone - perl-convert-binary-c + - perl-data-stag >=0.11 + - perl-db-file - perl-dbd-sqlite + - perl-dbd-mysql + - perl-dbd-pg - perl-dbi - perl-error + - perl-extutils-manifest >=1.52 - perl-gd - perl-graphviz + - perl-graph + - perl-html-parser - perl-html-tableextract + - perl-http-message + - perl-inline-c >=0.67 + - perl-io-compress - perl-io-stringy + - perl-io-string + - perl-libwww-perl >=5.64 + - perl-libxml-perl - perl-list-moreutils + - perl-math-random + - perl-memoize +# - perl-mod_perl + - perl-module-build >=0.42 - perl-postscript + - perl-scalar-list-utils - perl-set-scalar - - perl-soap-lite +# - perl-soap-lite - perl-sort-naturally - perl-spreadsheet-parseexcel - - perl-svg - - perl-svg-graph + - perl-spreadsheet-writeexcel + - perl-statistics-frequency + - perl-svg >=2.26 + - perl-svg-graph >=0.01 + - perl-test-exception + - perl-test-most + - perl-test-simple + - perl-test-warn + - perl-text-parsewords + - perl-tie-cacher + - perl-time-hires + - perl-tree-dag_node + - perl-uri +# - perl-www-mechanize - perl-xml-dom - perl-xml-dom-xpath + - perl-xml-libxml + - perl-xml-parser + - perl-xml-sax >=0.15 - perl-xml-sax-writer - perl-xml-simple - perl-xml-twig - - perl-xml-writer + - perl-xml-writer >=0.4 - perl-yaml # Skipping 'use' tests, which will be done by the 'perl-bioperl' package; done