perl-bioperl-core 1.7.1

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.'

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