printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bioperl-run-pm5123 2>&1 The package 'bioperl-run-pm5123' will be built without being installed. Reading build dependency for bioperl-run-pm5123-1.6.900-1... Reading dependency for bioperl-run-pm5123-1.6.900-1... Reading build conflict for bioperl-run-pm5123-1.6.900-1... The package 'module-build-pm5123' will be installed. Reading dependency for module-build-pm5123-0.42.06-1... Reading runtime dependency for module-build-pm5123-0.42.06-1... The package 'algorithm-diff-pm' will be installed. Reading dependency for algorithm-diff-pm-1.19.02-2... Reading runtime dependency for algorithm-diff-pm-1.19.02-2... The package 'bioperl-pm5123' will be installed. Reading dependency for bioperl-pm5123-1.6.901-2... Reading runtime dependency for bioperl-pm5123-1.6.901-2... fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) soap-lite-ssl-pm5123: Simple Object Access Protocol (SOAP) modules (2) soap-lite-pm5123: Simple Object Access Protocol (SOAP) modules Pick one: [2] (assuming default) The package 'io-string-pm' will be installed. Reading dependency for io-string-pm-1.08-1... Reading runtime dependency for io-string-pm-1.08-1... The package 'ipc-run-pm5123' will be installed. Reading dependency for ipc-run-pm5123-0.92-1... Reading runtime dependency for ipc-run-pm5123-0.92-1... The package 'perl5123-core' will be installed. Reading dependency for perl5123-core-5.12.3-102... Reading runtime dependency for perl5123-core-5.12.3-102... The package 'tree-dag-node-pm' will be installed. Reading dependency for tree-dag-node-pm-1.18-2... Reading runtime dependency for tree-dag-node-pm-1.18-2... The package 'xml-twig-pm5123' will be installed. Reading dependency for xml-twig-pm5123-3.48-1... Reading runtime dependency for xml-twig-pm5123-3.48-1... The package 'cpan-meta-pm5123' will be installed. Reading dependency for cpan-meta-pm5123-2.141520-1... Reading runtime dependency for cpan-meta-pm5123-2.141520-1... The package 'extutils-cbuilder-pm' will be installed. Reading dependency for extutils-cbuilder-pm-0.27.03-2... Reading runtime dependency for extutils-cbuilder-pm-0.27.03-2... The package 'extutils-install-pm' will be installed. Reading dependency for extutils-install-pm-1.54-1... Reading runtime dependency for extutils-install-pm-1.54-1... The package 'extutils-manifest-pm' will be installed. Reading dependency for extutils-manifest-pm-1.63-1... Reading runtime dependency for extutils-manifest-pm-1.63-1... The package 'extutils-parsexs-pm' will be installed. Reading dependency for extutils-parsexs-pm-3.24-1... Reading runtime dependency for extutils-parsexs-pm-3.24-1... The package 'module-metadata-pm5123' will be installed. Reading dependency for module-metadata-pm5123-1.000024-1... Reading runtime dependency for module-metadata-pm5123-1.000024-1... The package 'par-dist-pm' will be installed. Reading dependency for par-dist-pm-0.49-1... Reading runtime dependency for par-dist-pm-0.49-1... The package 'perl-ostype-pm5123' will be installed. Reading dependency for perl-ostype-pm5123-1.007-1... Reading runtime dependency for perl-ostype-pm5123-1.007-1... The package 'pod-readme-pm' will be installed. Reading dependency for pod-readme-pm-0.11-1... Reading runtime dependency for pod-readme-pm-0.11-1... The package 'software-license-pm5123' will be installed. Reading dependency for software-license-pm5123-0.103008-1... Reading runtime dependency for software-license-pm5123-0.103008-1... The package 'test-harness-pm5123' will be installed. Reading dependency for test-harness-pm5123-3.30-1... Reading runtime dependency for test-harness-pm5123-3.30-1... The package 'version-pm5123' will be installed. Reading dependency for version-pm5123-0.99.08-1... Reading runtime dependency for version-pm5123-0.99.08-1... The package 'array-compare-pm5123' will be installed. Reading dependency for array-compare-pm5123-2.02-1... Reading runtime dependency for array-compare-pm5123-2.02-1... The package 'clone-pm5123' will be installed. Reading dependency for clone-pm5123-0.36-1... Reading runtime dependency for clone-pm5123-0.36-1... The package 'data-stag-pm5123' will be installed. Reading dependency for data-stag-pm5123-0.14-1... Reading runtime dependency for data-stag-pm5123-0.14-1... The package 'gd-pm5123' will be installed. Reading dependency for gd-pm5123-2.50-1... Reading runtime dependency for gd-pm5123-2.50-1... The package 'gd-svg-pm5123' will be installed. Reading dependency for gd-svg-pm5123-0.33-1... Reading runtime dependency for gd-svg-pm5123-0.33-1... The package 'graph-pm' will be installed. Reading dependency for graph-pm-0.96-1... Reading runtime dependency for graph-pm-0.96-1... The package 'html-parser-pm5123' will be installed. Reading dependency for html-parser-pm5123-3.71-1... Reading runtime dependency for html-parser-pm5123-3.71-1... The package 'io-stringy-pm' will be installed. Reading dependency for io-stringy-pm-2.110-1022... Reading runtime dependency for io-stringy-pm-2.110-1022... The package 'libwww-pm5123' will be installed. Reading dependency for libwww-pm5123-6.07-1... Reading runtime dependency for libwww-pm5123-6.07-1... The package 'libxml-pm5123' will be installed. Reading dependency for libxml-pm5123-0.08-2... Reading runtime dependency for libxml-pm5123-0.08-2... The package 'set-scalar-pm' will be installed. Reading dependency for set-scalar-pm-1.27-1... Reading runtime dependency for set-scalar-pm-1.27-1... The package 'soap-lite-pm5123' will be installed. Reading dependency for soap-lite-pm5123-0.712-6... Reading runtime dependency for soap-lite-pm5123-0.712-6... The package 'spreadsheet-parseexcel-pm5123' will be installed. Reading dependency for spreadsheet-parseexcel-pm5123-0.59-1... Reading runtime dependency for spreadsheet-parseexcel-pm5123-0.59-1... The package 'spreadsheet-writeexcel-pm' will be installed. Reading dependency for spreadsheet-writeexcel-pm-2.40-1... Reading runtime dependency for spreadsheet-writeexcel-pm-2.40-1... The package 'svg-pm' will be installed. Reading dependency for svg-pm-2.59-2... Reading runtime dependency for svg-pm-2.59-2... The package 'text-shellwords-pm' will be installed. Reading dependency for text-shellwords-pm-1.08-1... Reading runtime dependency for text-shellwords-pm-1.08-1... The package 'uri-pm5123' will be installed. Reading dependency for uri-pm5123-1.64-1... Reading runtime dependency for uri-pm5123-1.64-1... The package 'xml-dom-pm5123' will be installed. Reading dependency for xml-dom-pm5123-1.44-2... Reading runtime dependency for xml-dom-pm5123-1.44-2... The package 'xml-node-pm5123' will be installed. Reading dependency for xml-node-pm5123-0.11-104... Reading runtime dependency for xml-node-pm5123-0.11-104... The package 'xml-parser-pm5123' will be installed. Reading dependency for xml-parser-pm5123-2.41-2... Reading runtime dependency for xml-parser-pm5123-2.41-2... The package 'xml-sax-pm5123' will be installed. Reading dependency for xml-sax-pm5123-0.99-3... Reading runtime dependency for xml-sax-pm5123-0.99-3... The package 'xml-sax-writer-pm5123' will be installed. Reading dependency for xml-sax-writer-pm5123-0.54-1... Reading runtime dependency for xml-sax-writer-pm5123-0.54-1... The package 'xml-writer-pm' will be installed. Reading dependency for xml-writer-pm-0.624-1... Reading runtime dependency for xml-writer-pm-0.624-1... The package 'io-tty-pm5123' will be installed. Reading dependency for io-tty-pm5123-1.10-1... Reading runtime dependency for io-tty-pm5123-1.10-1... The package 'file-slurp-pm' will be installed. Reading dependency for file-slurp-pm-9999.19-2... Reading runtime dependency for file-slurp-pm-9999.19-2... The package 'encode-pm5123' will be installed. Reading dependency for encode-pm5123-2.60-1... Reading runtime dependency for encode-pm5123-2.60-1... The package 'html-entities-numbered-pm' will be installed. Reading dependency for html-entities-numbered-pm-0.04-1... Reading runtime dependency for html-entities-numbered-pm-0.04-1... The package 'html-tree-pm5123' will be installed. Reading dependency for html-tree-pm5123-5.03-1... Reading runtime dependency for html-tree-pm5123-5.03-1... The package 'html-tidy-pm5123' will be installed. Reading dependency for html-tidy-pm5123-1.56-1... Reading runtime dependency for html-tidy-pm5123-1.56-1... The package 'scalar-list-utils-pm5123' will be installed. Reading dependency for scalar-list-utils-pm5123-1.35-1... Reading runtime dependency for scalar-list-utils-pm5123-1.35-1... The package 'text-iconv-pm5123' will be installed. Reading dependency for text-iconv-pm5123-1.7-3... Reading runtime dependency for text-iconv-pm5123-1.7-3... The package 'tie-ixhash-pm' will be installed. Reading dependency for tie-ixhash-pm-1.23-1... Reading runtime dependency for tie-ixhash-pm-1.23-1... The package 'xml-xpathengine-pm' will be installed. Reading dependency for xml-xpathengine-pm-0.14-1... Reading runtime dependency for xml-xpathengine-pm-0.14-1... The package 'cpan-meta-requirements-pm5123' will be installed. Reading dependency for cpan-meta-requirements-pm5123-2.125-1... Reading runtime dependency for cpan-meta-requirements-pm5123-2.125-1... The package 'cpan-meta-yaml-pm' will be installed. Reading dependency for cpan-meta-yaml-pm-0.012-1... Reading runtime dependency for cpan-meta-yaml-pm-0.012-1... The package 'json-pp-pm' will be installed. Reading dependency for json-pp-pm-2.27.203-2... Reading runtime dependency for json-pp-pm-2.27.203-2... The package 'parse-cpan-meta-pm' will be installed. Reading dependency for parse-cpan-meta-pm-1.44.14-1... Reading runtime dependency for parse-cpan-meta-pm-1.44.14-1... The package 'podlators-pm' will be installed. Reading dependency for podlators-pm-2.5.3-1... Reading runtime dependency for podlators-pm-2.5.3-1... The package 'regexp-common-pm' will be installed. Reading dependency for regexp-common-pm-2013031301-1... Reading runtime dependency for regexp-common-pm-2013031301-1... The package 'moose-pm5123' will be installed. Reading dependency for moose-pm5123-2.1209-1... Reading runtime dependency for moose-pm5123-2.1209-1... The package 'json-pm5123' will be installed. Reading dependency for json-pm5123-2.90-1... Reading runtime dependency for json-pm5123-2.90-1... The package 'mldbm-pm' will be installed. Reading dependency for mldbm-pm-2.01-4... Reading runtime dependency for mldbm-pm-2.01-4... The package 'tk-pm5123' will be installed. Reading dependency for tk-pm5123-804.031-2... Reading runtime dependency for tk-pm5123-804.031-2... The package 'xml-libxslt-pm5123' will be installed. Reading dependency for xml-libxslt-pm5123-1.89-1... Reading runtime dependency for xml-libxslt-pm5123-1.89-1... The package 'gd3-shlibs' will be installed. Reading dependency for gd3-shlibs-2.1.0-1... Reading runtime dependency for gd3-shlibs-2.1.0-1... The package 'heap-pm' will be installed. Reading dependency for heap-pm-0.80-1... Reading runtime dependency for heap-pm-0.80-1... The package 'html-tagset-pm' will be installed. Reading dependency for html-tagset-pm-3.20-1... Reading runtime dependency for html-tagset-pm-3.20-1... The package 'authen-ntlm-pm5123' will be installed. Reading dependency for authen-ntlm-pm5123-1.09-1... Reading runtime dependency for authen-ntlm-pm5123-1.09-1... The package 'encode-locale-pm5123' will be installed. Reading dependency for encode-locale-pm5123-1.03-1... Reading runtime dependency for encode-locale-pm5123-1.03-1... The package 'file-listing-pm5123' will be installed. Reading dependency for file-listing-pm5123-6.04-1... Reading runtime dependency for file-listing-pm5123-6.04-1... The package 'http-cookies-pm5123' will be installed. Reading dependency for http-cookies-pm5123-6.01-1... Reading runtime dependency for http-cookies-pm5123-6.01-1... The package 'http-daemon-pm5123' will be installed. Reading dependency for http-daemon-pm5123-6.01-1... Reading runtime dependency for http-daemon-pm5123-6.01-1... The package 'http-date-pm5123' will be installed. Reading dependency for http-date-pm5123-6.02-1... Reading runtime dependency for http-date-pm5123-6.02-1... The package 'http-message-pm5123' will be installed. Reading dependency for http-message-pm5123-6.06-1... Reading runtime dependency for http-message-pm5123-6.06-1... The package 'http-negotiate-pm5123' will be installed. Reading dependency for http-negotiate-pm5123-6.01-1... Reading runtime dependency for http-negotiate-pm5123-6.01-1... The package 'lwp-mediatypes-pm5123' will be installed. Reading dependency for lwp-mediatypes-pm5123-6.02-1... Reading runtime dependency for lwp-mediatypes-pm5123-6.02-1... The package 'net-http-pm5123' will be installed. Reading dependency for net-http-pm5123-6.06-1... Reading runtime dependency for net-http-pm5123-6.06-1... The package 'www-robotrules-pm5123' will be installed. Reading dependency for www-robotrules-pm5123-6.02-1... Reading runtime dependency for www-robotrules-pm5123-6.02-1... The package 'class-inspector-pm5123' will be installed. Reading dependency for class-inspector-pm5123-1.28-1... Reading runtime dependency for class-inspector-pm5123-1.28-1... The package 'constant-pm' will be installed. Reading dependency for constant-pm-1.27-1... Reading runtime dependency for constant-pm-1.27-1... The package 'data-uuid-pm5123' will be installed. Reading dependency for data-uuid-pm5123-1.219-1... Reading runtime dependency for data-uuid-pm5123-1.219-1... The package 'dime-tools-pm5123' will be installed. Reading dependency for dime-tools-pm5123-0.03-1... Reading runtime dependency for dime-tools-pm5123-0.03-1... The package 'fcgi-pm5123' will be installed. Reading dependency for fcgi-pm5123-0.74-1... Reading runtime dependency for fcgi-pm5123-0.74-1... The package 'io-compress-pm5123' will be installed. Reading dependency for io-compress-pm5123-2.063-1... Reading runtime dependency for io-compress-pm5123-2.063-1... The package 'mime-lite-pm5123' will be installed. Reading dependency for mime-lite-pm5123-3.030-2... Reading runtime dependency for mime-lite-pm5123-3.030-2... The package 'mime-tools-pm5123' will be installed. Reading dependency for mime-tools-pm5123-5.505-1... Reading runtime dependency for mime-tools-pm5123-5.505-1... The package 'task-weaken-pm5123' will be installed. Reading dependency for task-weaken-pm5123-1.04-1... Reading runtime dependency for task-weaken-pm5123-1.04-1... The package 'crypt-rc4-pm' will be installed. Reading dependency for crypt-rc4-pm-2.02-1... Reading runtime dependency for crypt-rc4-pm-2.02-1... The package 'digest-perl-md5-pm' will be installed. Reading dependency for digest-perl-md5-pm-1.9-1... Reading runtime dependency for digest-perl-md5-pm-1.9-1... The package 'ole-storagelite-pm' will be installed. Reading dependency for ole-storagelite-pm-0.19-1... Reading runtime dependency for ole-storagelite-pm-0.19-1... The package 'unicode-map-pm5123' will be installed. Reading dependency for unicode-map-pm5123-0.112-16... Reading runtime dependency for unicode-map-pm5123-0.112-16... The package 'rec-descent-pm' will be installed. Reading dependency for rec-descent-pm-1.96.7009-1... Reading runtime dependency for rec-descent-pm-1.96.7009-1... The package 'xml-regexp-pm' will be installed. Reading dependency for xml-regexp-pm-0.04-1... Reading runtime dependency for xml-regexp-pm-0.04-1... The package 'expat1-shlibs' will be installed. Reading dependency for expat1-shlibs-2.1.0-1... Reading runtime dependency for expat1-shlibs-2.1.0-1... The package 'xml-namespacesupport-pm' will be installed. Reading dependency for xml-namespacesupport-pm-1.11-1... Reading runtime dependency for xml-namespacesupport-pm-1.11-1... The package 'xml-sax-base-pm' will be installed. Reading dependency for xml-sax-base-pm-1.08-1... Reading runtime dependency for xml-sax-base-pm-1.08-1... The package 'xml-filter-buffertext-pm5123' will be installed. Reading dependency for xml-filter-buffertext-pm5123-1.01-4... Reading runtime dependency for xml-filter-buffertext-pm5123-1.01-4... The package 'exporter-pm' will be installed. Reading dependency for exporter-pm-5.68-1... Reading runtime dependency for exporter-pm-5.68-1... The package 'libtidyp-shlibs' will be installed. Reading dependency for libtidyp-shlibs-1.04-1... Reading runtime dependency for libtidyp-shlibs-1.04-1... The package 'class-load-pm5123' will be installed. Reading dependency for class-load-pm5123-0.20-1... Reading runtime dependency for class-load-pm5123-0.20-1... The package 'class-load-xs-pm5123' will be installed. Reading dependency for class-load-xs-pm5123-0.06-1... Reading runtime dependency for class-load-xs-pm5123-0.06-1... The package 'data-optlist-pm5123' will be installed. Reading dependency for data-optlist-pm5123-0.109-1... Reading runtime dependency for data-optlist-pm5123-0.109-1... The package 'devel-globaldestruction-pm5123' will be installed. Reading dependency for devel-globaldestruction-pm5123-0.12-1... Reading runtime dependency for devel-globaldestruction-pm5123-0.12-1... The package 'eval-closure-pm5123' will be installed. Reading dependency for eval-closure-pm5123-0.11-1... Reading runtime dependency for eval-closure-pm5123-0.11-1... The package 'list-moreutils-pm5123' will be installed. Reading dependency for list-moreutils-pm5123-0.33-1... Reading runtime dependency for list-moreutils-pm5123-0.33-1... The package 'module-runtime-pm5123' will be installed. Reading dependency for module-runtime-pm5123-0.014-1... Reading runtime dependency for module-runtime-pm5123-0.014-1... The package 'mro-compat-pm5123' will be installed. Reading dependency for mro-compat-pm5123-0.12-1... Reading runtime dependency for mro-compat-pm5123-0.12-1... The package 'package-deprecationmanager-pm5123' will be installed. Reading dependency for package-deprecationmanager-pm5123-0.13-1... Reading runtime dependency for package-deprecationmanager-pm5123-0.13-1... The package 'package-stash-pm5123' will be installed. Reading dependency for package-stash-pm5123-0.36-1... Reading runtime dependency for package-stash-pm5123-0.36-1... The package 'package-stash-xs-pm5123' will be installed. Reading dependency for package-stash-xs-pm5123-0.28-1... Reading runtime dependency for package-stash-xs-pm5123-0.28-1... The package 'params-util-pm5123' will be installed. Reading dependency for params-util-pm5123-1.07-1... Reading runtime dependency for params-util-pm5123-1.07-1... The package 'sub-exporter-pm5123' will be installed. Reading dependency for sub-exporter-pm5123-0.987-1... Reading runtime dependency for sub-exporter-pm5123-0.987-1... The package 'sub-name-pm5123' will be installed. Reading dependency for sub-name-pm5123-0.05-1... Reading runtime dependency for sub-name-pm5123-0.05-1... The package 'try-tiny-pm' will be installed. Reading dependency for try-tiny-pm-0.22-1... Reading runtime dependency for try-tiny-pm-0.22-1... The package 'json-xs-pm5123' will be installed. Reading dependency for json-xs-pm5123-3.01-1... Reading runtime dependency for json-xs-pm5123-3.01-1... The package 'freezethaw-pm' will be installed. Reading dependency for freezethaw-pm-0.5001-1... Reading runtime dependency for freezethaw-pm-0.5001-1... The package 'fontconfig2-shlibs' will be installed. Reading dependency for fontconfig2-shlibs-2.10.2-1... Reading runtime dependency for fontconfig2-shlibs-2.10.2-1... The package 'libjpeg9-shlibs' will be installed. Reading dependency for libjpeg9-shlibs-9a-1... Reading runtime dependency for libjpeg9-shlibs-9a-1... The package 'libpng16-shlibs' will be installed. Reading dependency for libpng16-shlibs-1.6.12-1... Reading runtime dependency for libpng16-shlibs-1.6.12-1... The package 'xft2-shlibs' will be installed. Reading dependency for xft2-shlibs-2.2.0-3... Reading runtime dependency for xft2-shlibs-2.2.0-3... The package 'libxml2-shlibs' will be installed. Reading dependency for libxml2-shlibs-2.9.1-3... Reading runtime dependency for libxml2-shlibs-2.9.1-3... The package 'libxslt-shlibs' will be installed. Reading dependency for libxslt-shlibs-1.1.28-2... Reading runtime dependency for libxslt-shlibs-1.1.28-2... The package 'xml-libxml-pm5123' will be installed. Reading dependency for xml-libxml-pm5123-2.0111-1... Reading runtime dependency for xml-libxml-pm5123-2.0111-1... The package 'freetype219-shlibs' will be installed. Reading dependency for freetype219-shlibs-2.4.12-1... Reading runtime dependency for freetype219-shlibs-2.4.12-1... The package 'libtiff5-shlibs' will be installed. Reading dependency for libtiff5-shlibs-4.0.3-5... Reading runtime dependency for libtiff5-shlibs-4.0.3-5... The package 'digest-hmac-pm' will be installed. Reading dependency for digest-hmac-pm-1.03-1... Reading runtime dependency for digest-hmac-pm-1.03-1... The package 'time-date-pm' will be installed. Reading dependency for time-date-pm-1.16-1... Reading runtime dependency for time-date-pm-1.16-1... The package 'io-html-pm5123' will be installed. Reading dependency for io-html-pm5123-1.001-1... Reading runtime dependency for io-html-pm5123-1.001-1... The package 'io-socket-ssl-pm5123' will be installed. Reading dependency for io-socket-ssl-pm5123-1.997-1... Reading runtime dependency for io-socket-ssl-pm5123-1.997-1... The package 'compress-raw-bzip2-pm5123' will be installed. Reading dependency for compress-raw-bzip2-pm5123-2.063-1... Reading runtime dependency for compress-raw-bzip2-pm5123-2.063-1... The package 'compress-raw-zlib-pm5123' will be installed. Reading dependency for compress-raw-zlib-pm5123-2.063-1... Reading runtime dependency for compress-raw-zlib-pm5123-2.063-1... The package 'email-date-format-pm' will be installed. Reading dependency for email-date-format-pm-1.004-1... Reading runtime dependency for email-date-format-pm-1.004-1... The package 'mailtools-pm5123' will be installed. Reading dependency for mailtools-pm5123-2.13-1... Reading runtime dependency for mailtools-pm5123-2.13-1... The package 'mime-types-pm' will be installed. Reading dependency for mime-types-pm-2.04-2... Reading runtime dependency for mime-types-pm-2.04-2... The package 'unicode-string-pm5123' will be installed. Reading dependency for unicode-string-pm5123-2.09-11... Reading runtime dependency for unicode-string-pm5123-2.09-11... The package 'text-balanced-pm' will be installed. Reading dependency for text-balanced-pm-2.02-2... Reading runtime dependency for text-balanced-pm-2.02-2... The package 'module-implementation-pm5123' will be installed. Reading dependency for module-implementation-pm5123-0.06-1... Reading runtime dependency for module-implementation-pm5123-0.06-1... The package 'sub-install-pm5123' will be installed. Reading dependency for sub-install-pm5123-0.927-1... Reading runtime dependency for sub-install-pm5123-0.927-1... The package 'devel-globaldestruction-xs-pm5123' will be installed. Reading dependency for devel-globaldestruction-xs-pm5123-0.01-1... Reading runtime dependency for devel-globaldestruction-xs-pm5123-0.01-1... The package 'sub-exporter-progressive-pm5123' will be installed. Reading dependency for sub-exporter-progressive-pm5123-0.001011-1... Reading runtime dependency for sub-exporter-progressive-pm5123-0.001011-1... The package 'params-classify-pm5123' will be installed. Reading dependency for params-classify-pm5123-0.013-4... Reading runtime dependency for params-classify-pm5123-0.013-4... The package 'class-c3-pm5123' will be installed. Reading dependency for class-c3-pm5123-0.25-1... Reading runtime dependency for class-c3-pm5123-0.25-1... The package 'dist-checkconflicts-pm5123' will be installed. Reading dependency for dist-checkconflicts-pm5123-0.09-1... Reading runtime dependency for dist-checkconflicts-pm5123-0.09-1... The package 'package-generator-pm' will be installed. Reading dependency for package-generator-pm-1.106-1... Reading runtime dependency for package-generator-pm-1.106-1... The package 'common-sense-pm' will be installed. Reading dependency for common-sense-pm-3.72-1... Reading runtime dependency for common-sense-pm-3.72-1... The package 'types-serialiser-pm' will be installed. Reading dependency for types-serialiser-pm-0.03-1... Reading runtime dependency for types-serialiser-pm-0.03-1... The package 'fontconfig-config' will be installed. Reading dependency for fontconfig-config-2.10.2-1... Reading runtime dependency for fontconfig-config-2.10.2-1... The package 'liblzma5-shlibs' will be installed. Reading dependency for liblzma5-shlibs-5.0.5-2... Reading runtime dependency for liblzma5-shlibs-5.0.5-2... The package 'libjbig-shlibs' will be installed. Reading dependency for libjbig-shlibs-2.0-1... Reading runtime dependency for libjbig-shlibs-2.0-1... The package 'net-ssleay-pm5123' will be installed. Reading dependency for net-ssleay-pm5123-1.65-1... Reading runtime dependency for net-ssleay-pm5123-1.65-1... The package 'net-idn-encode-pm5123' will be installed. Reading dependency for net-idn-encode-pm5123-2.004-1... Reading runtime dependency for net-idn-encode-pm5123-2.004-1... The package 'mozilla-ca-pm' will be installed. Reading dependency for mozilla-ca-pm-20130114-1... Reading runtime dependency for mozilla-ca-pm-20130114-1... The package 'algorithm-c3-pm5123' will be installed. Reading dependency for algorithm-c3-pm5123-0.08-3... Reading runtime dependency for algorithm-c3-pm5123-0.08-3... The package 'openssl100-shlibs' will be installed. Reading dependency for openssl100-shlibs-1.0.1h-1... Reading runtime dependency for openssl100-shlibs-1.0.1h-1... The package 'unicode-normalize-pm5123' will be installed. Reading dependency for unicode-normalize-pm5123-1.18-1... Reading runtime dependency for unicode-normalize-pm5123-1.18-1... The following package will be rebuilt: bioperl-run-pm5123 The following 155 additional packages will be installed: algorithm-c3-pm5123 algorithm-diff-pm array-compare-pm5123 authen-ntlm-pm5123 bioperl-pm5123 class-c3-pm5123 class-inspector-pm5123 class-load-pm5123 class-load-xs-pm5123 clone-pm5123 common-sense-pm compress-raw-bzip2-pm5123 compress-raw-zlib-pm5123 constant-pm cpan-meta-pm5123 cpan-meta-requirements-pm5123 cpan-meta-yaml-pm crypt-rc4-pm data-optlist-pm5123 data-stag-pm5123 data-uuid-pm5123 devel-globaldestruction-pm5123 devel-globaldestruction-xs-pm5123 digest-hmac-pm digest-perl-md5-pm dime-tools-pm5123 dist-checkconflicts-pm5123 email-date-format-pm encode-locale-pm5123 encode-pm5123 eval-closure-pm5123 expat1-shlibs exporter-pm extutils-cbuilder-pm extutils-install-pm extutils-manifest-pm extutils-parsexs-pm fcgi-pm5123 file-listing-pm5123 file-slurp-pm fontconfig-config fontconfig2-shlibs freetype219-shlibs freezethaw-pm gd-pm5123 gd-svg-pm5123 gd3-shlibs graph-pm heap-pm html-entities-numbered-pm html-parser-pm5123 html-tagset-pm html-tidy-pm5123 html-tree-pm5123 http-cookies-pm5123 http-daemon-pm5123 http-date-pm5123 http-message-pm5123 http-negotiate-pm5123 io-compress-pm5123 io-html-pm5123 io-socket-ssl-pm5123 io-string-pm io-stringy-pm io-tty-pm5123 ipc-run-pm5123 json-pm5123 json-pp-pm json-xs-pm5123 libjbig-shlibs libjpeg9-shlibs liblzma5-shlibs libpng16-shlibs libtidyp-shlibs libtiff5-shlibs libwww-pm5123 libxml-pm5123 libxml2-shlibs libxslt-shlibs list-moreutils-pm5123 lwp-mediatypes-pm5123 mailtools-pm5123 mime-lite-pm5123 mime-tools-pm5123 mime-types-pm mldbm-pm module-build-pm5123 module-implementation-pm5123 module-metadata-pm5123 module-runtime-pm5123 moose-pm5123 mozilla-ca-pm mro-compat-pm5123 net-http-pm5123 net-idn-encode-pm5123 net-ssleay-pm5123 ole-storagelite-pm openssl100-shlibs package-deprecationmanager-pm5123 package-generator-pm package-stash-pm5123 package-stash-xs-pm5123 par-dist-pm params-classify-pm5123 params-util-pm5123 parse-cpan-meta-pm perl-ostype-pm5123 perl5123-core pod-readme-pm podlators-pm rec-descent-pm regexp-common-pm scalar-list-utils-pm5123 set-scalar-pm soap-lite-pm5123 software-license-pm5123 spreadsheet-parseexcel-pm5123 spreadsheet-writeexcel-pm sub-exporter-pm5123 sub-exporter-progressive-pm5123 sub-install-pm5123 sub-name-pm5123 svg-pm task-weaken-pm5123 test-harness-pm5123 text-balanced-pm text-iconv-pm5123 text-shellwords-pm tie-ixhash-pm time-date-pm tk-pm5123 tree-dag-node-pm try-tiny-pm types-serialiser-pm unicode-map-pm5123 unicode-normalize-pm5123 unicode-string-pm5123 uri-pm5123 version-pm5123 www-robotrules-pm5123 xft2-shlibs xml-dom-pm5123 xml-filter-buffertext-pm5123 xml-libxml-pm5123 xml-libxslt-pm5123 xml-namespacesupport-pm xml-node-pm5123 xml-parser-pm5123 xml-regexp-pm xml-sax-base-pm xml-sax-pm5123 xml-sax-writer-pm5123 xml-twig-pm5123 xml-writer-pm xml-xpathengine-pm Do you want to continue? [Y/n] (assuming default) Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/algorithm-diff-pm_1.19.02-2_darwin-x86_64.deb Selecting previously deselected package algorithm-diff-pm. (Reading database ... 4740 files and directories currently installed.) Unpacking algorithm-diff-pm (from .../algorithm-diff-pm_1.19.02-2_darwin-x86_64.deb) ... Setting up algorithm-diff-pm (1.19.02-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/common-sense-pm_3.72-1_darwin-x86_64.deb Selecting previously deselected package common-sense-pm. (Reading database ... 4759 files and directories currently installed.) Unpacking common-sense-pm (from .../common-sense-pm_3.72-1_darwin-x86_64.deb) ... Setting up common-sense-pm (3.72-1) ... Reading buildlock packages... 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All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/class-load-xs-pm5123_0.06-1_darwin-x86_64.deb Selecting previously deselected package class-load-xs-pm5123. (Reading database ... 11948 files and directories currently installed.) Unpacking class-load-xs-pm5123 (from .../class-load-xs-pm5123_0.06-1_darwin-x86_64.deb) ... Setting up class-load-xs-pm5123 (0.06-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/html-tidy-pm5123_1.56-1_darwin-x86_64.deb Selecting previously deselected package html-tidy-pm5123. (Reading database ... 11960 files and directories currently installed.) Unpacking html-tidy-pm5123 (from .../html-tidy-pm5123_1.56-1_darwin-x86_64.deb) ... Setting up html-tidy-pm5123 (1.56-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/moose-pm5123_2.1209-1_darwin-x86_64.deb Selecting previously deselected package moose-pm5123. (Reading database ... 11974 files and directories currently installed.) Unpacking moose-pm5123 (from .../moose-pm5123_2.1209-1_darwin-x86_64.deb) ... Setting up moose-pm5123 (2.1209-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/xml-twig-pm5123_3.48-1_darwin-x86_64.deb Selecting previously deselected package xml-twig-pm5123. (Reading database ... 12586 files and directories currently installed.) Unpacking xml-twig-pm5123 (from .../xml-twig-pm5123_3.48-1_darwin-x86_64.deb) ... Setting up xml-twig-pm5123 (3.48-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/array-compare-pm5123_2.02-1_darwin-x86_64.deb Selecting previously deselected package array-compare-pm5123. (Reading database ... 12606 files and directories currently installed.) Unpacking array-compare-pm5123 (from .../array-compare-pm5123_2.02-1_darwin-x86_64.deb) ... Setting up array-compare-pm5123 (2.02-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioperl-pm5123_1.6.901-2_darwin-x86_64.deb Selecting previously deselected package bioperl-pm5123. (Reading database ... 12616 files and directories currently installed.) Unpacking bioperl-pm5123 (from .../bioperl-pm5123_1.6.901-2_darwin-x86_64.deb) ... Setting up bioperl-pm5123 (1.6.901-2) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioperl-run-pm5123-1.6.900-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bioperl-run-pm5123-1.6.900-1' in `/sw/build.build/fink-buildlock-bioperl-run-pm5123-1.6.900-1_2014.08.04-23.10.07_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioperl-run-pm5123-1.6.900-1_2014.08.04-23.10.07_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioperl-run-pm5123-1.6.900-1. (Reading database ... 15607 files and directories currently installed.) Unpacking fink-buildlock-bioperl-run-pm5123-1.6.900-1 (from .../fink-buildlock-bioperl-run-pm5123-1.6.900-1_2014.08.04-23.10.07_darwin-x86_64.deb) ... Setting up fink-buildlock-bioperl-run-pm5123-1.6.900-1 (2014.08.04-23.10.07) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.JyBSK env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/BioPerl-Run-1.006900.tar.gz BioPerl-Run-1.006900 BioPerl-Run-1.006900/Build.PL BioPerl-Run-1.006900/AUTHORS BioPerl-Run-1.006900/META.json BioPerl-Run-1.006900/INSTALL.PROGRAMS BioPerl-Run-1.006900/DEPENDENCIES BioPerl-Run-1.006900/INSTALL.SKIP BioPerl-Run-1.006900/INSTALL BioPerl-Run-1.006900/LICENSE BioPerl-Run-1.006900/README BioPerl-Run-1.006900/Changes BioPerl-Run-1.006900/MANIFEST BioPerl-Run-1.006900/META.yml BioPerl-Run-1.006900/lib BioPerl-Run-1.006900/lib/Bio BioPerl-Run-1.006900/lib/Bio/Factory BioPerl-Run-1.006900/lib/Bio/Factory/EMBOSS.pm BioPerl-Run-1.006900/lib/Bio/Tools BioPerl-Run-1.006900/lib/Bio/Tools/Run BioPerl-Run-1.006900/lib/Bio/Tools/Run/Analysis.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/AssemblerBase.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Genewise.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/FootPrinter.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/StandAloneBlastPlus.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Hmmer.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Coil.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/MCS.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Bowtie.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/tRNAscanSE.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Prints.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Genemark.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/TigrAssembler.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/EMBOSSacd.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Meme.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Primate.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/ERPIN.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Primer3.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/BWA.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phrap.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Cap3.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/TribeMCL.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/RNAMotif.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Samtools.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Eponine.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Profile.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Glimmer.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/AnalysisFactory.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Seg.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/BEDTools.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Maq.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Ensembl.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Minimo.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Genscan.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Newbler.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Simprot.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Match.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Infernal.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/RepeatMasker.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Signalp.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Promoterwise.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/EMBOSSApplication.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Tmhmm.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/BlastPlus.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Vista.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Pseudowise.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Mdust.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/BEDTools BioPerl-Run-1.006900/lib/Bio/Tools/Run/BEDTools/Config.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Analysis BioPerl-Run-1.006900/lib/Bio/Tools/Run/Analysis/soap.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/BlastPlus BioPerl-Run-1.006900/lib/Bio/Tools/Run/BlastPlus/Config.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/BWA BioPerl-Run-1.006900/lib/Bio/Tools/Run/BWA/Config.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Blat.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Muscle.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Lagan.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Proda.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Probcons.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/DBA.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Exonerate.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Sim4.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Gmap.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/TCoffee.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Clustalw.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/MAFFT.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Kalign.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Probalign.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Alignment/Amap.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/AnalysisFactory BioPerl-Run-1.006900/lib/Bio/Tools/Run/AnalysisFactory/soap.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Maq BioPerl-Run-1.006900/lib/Bio/Tools/Run/Maq/Config.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Bowtie BioPerl-Run-1.006900/lib/Bio/Tools/Run/Bowtie/Config.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Samtools BioPerl-Run-1.006900/lib/Bio/Tools/Run/Samtools/Config.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/StandAloneBlastPlus BioPerl-Run-1.006900/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Gumby.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/LVB.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Semphy.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/SLR.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phyml.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Gerp.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/QuickTree.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/PhyloBase.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Molphy BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Njtree BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Hyphy BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phast BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/PAML BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm BioPerl-Run-1.006900/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm BioPerl-Run-1.006900/lib/Bio/DB BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities.pm BioPerl-Run-1.006900/lib/Bio/DB/ESoap.pm BioPerl-Run-1.006900/lib/Bio/DB/ESoap BioPerl-Run-1.006900/lib/Bio/DB/ESoap/WSDL.pm BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/LinkAdaptor.pm BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/GQueryAdaptor.pm BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/Result.pm BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/FetchAdaptor BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm BioPerl-Run-1.006900/lib/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm BioPerl-Run-1.006900/lib/Bio/Installer BioPerl-Run-1.006900/lib/Bio/Installer/Muscle.pm BioPerl-Run-1.006900/lib/Bio/Installer/Generic.pm BioPerl-Run-1.006900/lib/Bio/Installer/EMBOSS.pm BioPerl-Run-1.006900/lib/Bio/Installer/Probcons.pm BioPerl-Run-1.006900/lib/Bio/Installer/SLR.pm BioPerl-Run-1.006900/lib/Bio/Installer/PAML.pm BioPerl-Run-1.006900/lib/Bio/Installer/TCoffee.pm BioPerl-Run-1.006900/lib/Bio/Installer/Clustalw.pm BioPerl-Run-1.006900/lib/Bio/Installer/Hyphy.pm BioPerl-Run-1.006900/t BioPerl-Run-1.006900/t/Probalign.t BioPerl-Run-1.006900/t/EMBOSS.t BioPerl-Run-1.006900/t/DBA.t BioPerl-Run-1.006900/t/Infernal.t BioPerl-Run-1.006900/t/Gumby.t BioPerl-Run-1.006900/t/Tmhmm.t BioPerl-Run-1.006900/t/ProtDist.t BioPerl-Run-1.006900/t/Glimmer3.t BioPerl-Run-1.006900/t/tRNAscanSE.t BioPerl-Run-1.006900/t/RepeatMasker.t BioPerl-Run-1.006900/t/DrawTree.t BioPerl-Run-1.006900/t/Bowtie.t BioPerl-Run-1.006900/t/Molphy.t BioPerl-Run-1.006900/t/Njtree.t BioPerl-Run-1.006900/t/MAFFT.t BioPerl-Run-1.006900/t/Genewise.t BioPerl-Run-1.006900/t/Semphy.t BioPerl-Run-1.006900/t/Profile.t BioPerl-Run-1.006900/t/Meme.t BioPerl-Run-1.006900/t/Probcons.t BioPerl-Run-1.006900/t/Simprot.t BioPerl-Run-1.006900/t/BWA.t BioPerl-Run-1.006900/t/PAML.t BioPerl-Run-1.006900/t/Ensembl.t BioPerl-Run-1.006900/t/Genemark.hmm.prokaryotic.t BioPerl-Run-1.006900/t/Phrap.t BioPerl-Run-1.006900/t/Newbler.t BioPerl-Run-1.006900/t/MCS.t BioPerl-Run-1.006900/t/gmap-run.t BioPerl-Run-1.006900/t/StandAloneFasta.t BioPerl-Run-1.006900/t/DrawGram.t BioPerl-Run-1.006900/t/FootPrinter.t BioPerl-Run-1.006900/t/Coil.t BioPerl-Run-1.006900/t/Primate.t BioPerl-Run-1.006900/t/Blat.t BioPerl-Run-1.006900/t/BEDTools.t BioPerl-Run-1.006900/t/TCoffee.t BioPerl-Run-1.006900/t/Minimo.t BioPerl-Run-1.006900/t/Seg.t BioPerl-Run-1.006900/t/Match.t BioPerl-Run-1.006900/t/SLR.t BioPerl-Run-1.006900/t/Sim4.t BioPerl-Run-1.006900/t/Clustalw.t BioPerl-Run-1.006900/t/Cap3.t BioPerl-Run-1.006900/t/TigrAssembler.t BioPerl-Run-1.006900/t/Muscle.t BioPerl-Run-1.006900/t/ProtPars.t BioPerl-Run-1.006900/t/Mdust.t BioPerl-Run-1.006900/t/Signalp.t BioPerl-Run-1.006900/t/Genscan.t BioPerl-Run-1.006900/t/Kalign.t BioPerl-Run-1.006900/t/Lagan.t BioPerl-Run-1.006900/t/Glimmer2.t BioPerl-Run-1.006900/t/Prints.t BioPerl-Run-1.006900/t/SoapEU-function.t BioPerl-Run-1.006900/t/Samtools.t BioPerl-Run-1.006900/t/Promoterwise.t BioPerl-Run-1.006900/t/Exonerate.t BioPerl-Run-1.006900/t/Pal2Nal.t BioPerl-Run-1.006900/t/PhastCons.t BioPerl-Run-1.006900/t/LVB.t BioPerl-Run-1.006900/t/Hmmer.t BioPerl-Run-1.006900/t/Neighbor.t BioPerl-Run-1.006900/t/SoapEU-unit.t BioPerl-Run-1.006900/t/Vista.t BioPerl-Run-1.006900/t/Consense.t BioPerl-Run-1.006900/t/Eponine.t BioPerl-Run-1.006900/t/SeqBoot.t BioPerl-Run-1.006900/t/Maq.t BioPerl-Run-1.006900/t/Hyphy.t BioPerl-Run-1.006900/t/Amap.t BioPerl-Run-1.006900/t/Primer3.t BioPerl-Run-1.006900/t/TribeMCL.t BioPerl-Run-1.006900/t/SABlastPlus.t BioPerl-Run-1.006900/t/Phyml.t BioPerl-Run-1.006900/t/QuickTree.t BioPerl-Run-1.006900/t/Pseudowise.t BioPerl-Run-1.006900/t/Gerp.t BioPerl-Run-1.006900/t/AnalysisFactory_soap.t BioPerl-Run-1.006900/t/Analysis_soap.t BioPerl-Run-1.006900/t/lib BioPerl-Run-1.006900/t/lib/Test BioPerl-Run-1.006900/t/lib/Test/Simple.pm BioPerl-Run-1.006900/t/lib/Test/Exception.pm BioPerl-Run-1.006900/t/lib/Test/Tutorial.pod BioPerl-Run-1.006900/t/lib/Test/More.pm BioPerl-Run-1.006900/t/lib/Test/Builder.pm BioPerl-Run-1.006900/t/lib/Test/Harness.pm BioPerl-Run-1.006900/t/lib/Test/Warn.pm 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BioPerl-Run-1.006900/t/data/cysprot1a.fa BioPerl-Run-1.006900/t/data/ps1.fa BioPerl-Run-1.006900/t/data/hmmpfam_protein_input BioPerl-Run-1.006900/t/data/simprot_tree.nh BioPerl-Run-1.006900/t/data/purine.1.sto BioPerl-Run-1.006900/t/data/NM_002254.tfa BioPerl-Run-1.006900/t/data/Ft.bam BioPerl-Run-1.006900/t/data/dba2.fa BioPerl-Run-1.006900/t/data/cysprot1b.fa BioPerl-Run-1.006900/t/data/2.bg BioPerl-Run-1.006900/t/data/apes.newick BioPerl-Run-1.006900/t/data/e_coli.bed3 BioPerl-Run-1.006900/t/data/r2.fq BioPerl-Run-1.006900/t/data/e_coli_1.bedpe BioPerl-Run-1.006900/t/data/neighbor.dist BioPerl-Run-1.006900/t/data/test.txt BioPerl-Run-1.006900/t/data/sim4_genomic.fa BioPerl-Run-1.006900/t/data/purine.cm BioPerl-Run-1.006900/t/data/test-spa.fas BioPerl-Run-1.006900/t/data/codeml.mlc BioPerl-Run-1.006900/t/data/cysprot.msf BioPerl-Run-1.006900/t/data/transfac.dat BioPerl-Run-1.006900/t/data/sample_dataset_1.fa BioPerl-Run-1.006900/t/data/signalp_input_protein BioPerl-Run-1.006900/t/data/amino.fa BioPerl-Run-1.006900/t/data/Ft.bed BioPerl-Run-1.006900/t/data/gb_result.xml BioPerl-Run-1.006900/t/data/dba1b.fa BioPerl-Run-1.006900/t/data/pal2nal.aln BioPerl-Run-1.006900/t/data/sample_dataset_1.qual BioPerl-Run-1.006900/t/data/purine.c.cm BioPerl-Run-1.006900/t/data/exonerate_cdna_rev.fa BioPerl-Run-1.006900/t/data/species_tree_njtree.nh BioPerl-Run-1.006900/t/data/H_pylori_J99.glimmer2.icm BioPerl-Run-1.006900/t/data/exonerate_cdna.fa BioPerl-Run-1.006900/t/data/vista.gff BioPerl-Run-1.006900/t/data/277523.cdna.fasta BioPerl-Run-1.006900/t/data/cysprot1b.msf BioPerl-Run-1.006900/t/data/Primer3.fa BioPerl-Run-1.006900/t/data/dna_seqs1.phy BioPerl-Run-1.006900/t/data/semphy.seq BioPerl-Run-1.006900/t/data/test-spa-p.fas BioPerl-Run-1.006900/t/data/H_pylori_J99.fasta BioPerl-Run-1.006900/t/data/sim4_cdna.fa BioPerl-Run-1.006900/t/data/lagan_dna.fa BioPerl-Run-1.006900/t/data/njtree_aln2.nucl.mfa BioPerl-Run-1.006900/t/data/gf-s85.phylip BioPerl-Run-1.006900/t/data/her2-edited.fasta BioPerl-Run-1.006900/t/data/dna1.fa BioPerl-Run-1.006900/t/data/NM_002254.gb BioPerl-Run-1.006900/t/data/r1.fq BioPerl-Run-1.006900/t/data/semphy.tree BioPerl-Run-1.006900/t/data/profile_prot.FastA BioPerl-Run-1.006900/t/data/apes.multi_fasta BioPerl-Run-1.006900/t/data/vista.cls BioPerl-Run-1.006900/t/data/primate_query.fa BioPerl-Run-1.006900/t/data/219877.tree BioPerl-Run-1.006900/t/data/fontfile BioPerl-Run-1.006900/t/data/r1bwa.fq BioPerl-Run-1.006900/t/data/277523.tree BioPerl-Run-1.006900/t/data/hyphy1.fasta BioPerl-Run-1.006900/t/data/FootPrinter.seq.fa BioPerl-Run-1.006900/t/data/esearch_result.xml BioPerl-Run-1.006900/t/data/lvb_sequential.phy BioPerl-Run-1.006900/t/data/esum_result.xml BioPerl-Run-1.006900/t/data/H_pylori_J99.glimmer3.icm BioPerl-Run-1.006900/t/data/fasta.fa BioPerl-Run-1.006900/t/data/TribeMCL.desc BioPerl-Run-1.006900/t/data/gerp BioPerl-Run-1.006900/t/data/gerp/ENr111.mfa.gz BioPerl-Run-1.006900/t/data/gerp/ENr111.gerp.tree BioPerl-Run-1.006900/t/data/bowtie BioPerl-Run-1.006900/t/data/bowtie/indexes BioPerl-Run-1.006900/t/data/bowtie/indexes/e_coli.rev.1.ebwt BioPerl-Run-1.006900/t/data/bowtie/indexes/e_coli.2.ebwt BioPerl-Run-1.006900/t/data/bowtie/indexes/e_coli.4.ebwt BioPerl-Run-1.006900/t/data/bowtie/indexes/e_coli.rev.2.ebwt BioPerl-Run-1.006900/t/data/bowtie/indexes/e_coli.3.ebwt BioPerl-Run-1.006900/t/data/bowtie/indexes/e_coli.1.ebwt BioPerl-Run-1.006900/t/data/bowtie/reads BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_1000_1.fa BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_1000.raw BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli.cb BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_10000snp.fa BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_1000_1.fq BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_1000.fa BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_1000.fq BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_1000_2.fq BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_10000snp.fq BioPerl-Run-1.006900/t/data/bowtie/reads/e_coli_1000_2.fa BioPerl-Run-1.006900/t/data/taxdump BioPerl-Run-1.006900/t/data/taxdump/nodes.dmp BioPerl-Run-1.006900/t/data/taxdump/names.dmp BioPerl-Run-1.006900/t/data/gumby BioPerl-Run-1.006900/t/data/gumby/readme.txt BioPerl-Run-1.006900/t/data/gumby/hmrd.mfa BioPerl-Run-1.006900/t/data/gumby/human.gff BioPerl-Run-1.006900/t/data/gumby/hmrd.tree BioPerl-Run-1.006900/scripts BioPerl-Run-1.006900/scripts/run_neighbor.PLS BioPerl-Run-1.006900/scripts/papplmaker.PLS BioPerl-Run-1.006900/scripts/bioperl_application_installer.PLS BioPerl-Run-1.006900/scripts/multi_hmmsearch.PLS BioPerl-Run-1.006900/scripts/panalysis.PLS BioPerl-Run-1.006900/scripts/run_protdist.PLS sudo -u fink-bld [ENV] sh -c /tmp/fink.35dfg [ -r /sw/fink/dists/stable/main/finkinfo/libs/perlmods/bioperl-run-pm.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.xs27o patch -p1 < /sw/fink/dists/stable/main/finkinfo/libs/perlmods/bioperl-run-pm.patch patching file Build.PL sudo -u fink-bld [ENV] sh -c /tmp/fink.xSJTT ARCHFLAGS="" /usr/bin/arch -x86_64 perl5.12.3 Build.PL --install_base /sw --install_path bin=/sw/bin --install_path lib=/sw/lib/perl5/5.12.3 --install_path arch=/sw/lib/perl5/5.12.3/darwin-thread-multi-2level --install_path bindoc=/sw/share/man/man1 --install_path libdoc=/sw/share/man/man3 --install_path script=/sw/bin --destdir /sw/build.build/root-bioperl-run-pm5123-1.6.900-1 --accept - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.006900' ARCHFLAGS="" ./Build Building BioPerl-Run /bin/rm -rf /sw/build.build/root-bioperl-run-pm5123-1.6.900-1 /bin/mkdir -p /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw /bin/mkdir -p /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioperl-run-pm5123-1.6.900-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.7CVzl ./Build install Building BioPerl-Run Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/ESoap.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/ESoap/WSDL.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities/Result.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Factory/EMBOSS.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/Clustalw.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/EMBOSS.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/Generic.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/Hyphy.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/Muscle.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/PAML.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/Probcons.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/SLR.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Installer/TCoffee.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Tools/Run/Analysis.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Tools/Run/AnalysisFactory.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Tools/Run/AssemblerBase.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Tools/Run/BEDTools.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Tools/Run/BlastPlus.pm Installing /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/lib/perl5/5.12.3/Bio/Tools/Run/Bowtie.pm Installing 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/sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/bioperl-run-pm5123/scripts install scripts/* /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/bioperl-run-pm5123/scripts/ sudo -u fink-bld [ENV] sh -c /tmp/fink.KZBpQ /usr/bin/install -d -m 700 /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123 /bin/cp -r Changes /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123/ /bin/cp -r INSTALL /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123/ /bin/cp -r INSTALL.PROGRAMS /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123/ /bin/cp -r MANIFEST /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123/ /bin/cp -r README /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123/ /bin/cp -r AUTHORS /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123/ /bin/chmod -R go=u-w /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/doc/bioperl-run-pm5123 /bin/rm -f /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/info/dir /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/info/dir.old /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/info/dir /sw/build.build/root-bioperl-run-pm5123-1.6.900-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bioperl-run-pm5123-1.6.900-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/perlmods dpkg-deb: building package `bioperl-run-pm5123' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/perlmods/bioperl-run-pm5123_1.6.900-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bioperl-run-pm5123-1.6.900-1 (Reading database ... 15608 files and directories currently installed.) Removing fink-buildlock-bioperl-run-pm5123-1.6.900-1 ...