printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bioperl-run-pm5124 2>&1 The package 'bioperl-run-pm5124' will be built without being installed. Reading build dependency for bioperl-run-pm5124-1.6.900-1... Reading dependency for bioperl-run-pm5124-1.6.900-1... Reading build conflict for bioperl-run-pm5124-1.6.900-1... The package 'module-build-pm5124' will be installed. Reading dependency for module-build-pm5124-0.42.06-1... Reading runtime dependency for module-build-pm5124-0.42.06-1... 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-pm5124' will be installed. Reading dependency for bioperl-pm5124-1.6.901-2... Reading runtime dependency for bioperl-pm5124-1.6.901-2... fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) soap-lite-ssl-pm5124: Simple Object Access Protocol (SOAP) modules (2) soap-lite-pm5124: 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-pm5124' will be installed. Reading dependency for ipc-run-pm5124-0.92-1... Reading runtime dependency for ipc-run-pm5124-0.92-1... The package 'perl5124-core' will be installed. Reading dependency for perl5124-core-5.12.4-103... Reading runtime dependency for perl5124-core-5.12.4-103... 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-pm5124' will be installed. Reading dependency for xml-twig-pm5124-3.48-1... Reading runtime dependency for xml-twig-pm5124-3.48-1... The package 'cpan-meta-pm5124' will be installed. Reading dependency for cpan-meta-pm5124-2.141520-1... Reading runtime dependency for cpan-meta-pm5124-2.141520-1... 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-pm5124' will be installed. Reading dependency for module-metadata-pm5124-1.000024-1... Reading runtime dependency for module-metadata-pm5124-1.000024-1... 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-pm5124' will be installed. Reading dependency for perl-ostype-pm5124-1.007-1... Reading runtime dependency for perl-ostype-pm5124-1.007-1... 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-pm5124' will be installed. Reading dependency for software-license-pm5124-0.103008-1... Reading runtime dependency for software-license-pm5124-0.103008-1... The package 'test-harness-pm5124' will be installed. Reading dependency for test-harness-pm5124-3.30-1... Reading runtime dependency for test-harness-pm5124-3.30-1... The package 'version-pm5124' will be installed. Reading dependency for version-pm5124-0.99.08-1... Reading runtime dependency for version-pm5124-0.99.08-1... The package 'array-compare-pm5124' will be installed. Reading dependency for array-compare-pm5124-2.02-1... Reading runtime dependency for array-compare-pm5124-2.02-1... The package 'clone-pm5124' will be installed. Reading dependency for clone-pm5124-0.36-1... Reading runtime dependency for clone-pm5124-0.36-1... The package 'data-stag-pm5124' will be installed. Reading dependency for data-stag-pm5124-0.14-1... Reading runtime dependency for data-stag-pm5124-0.14-1... The package 'gd-pm5124' will be installed. Reading dependency for gd-pm5124-2.50-1... Reading runtime dependency for gd-pm5124-2.50-1... The package 'gd-svg-pm5124' will be installed. Reading dependency for gd-svg-pm5124-0.33-1... Reading runtime dependency for gd-svg-pm5124-0.33-1... 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-pm5124' will be installed. Reading dependency for html-parser-pm5124-3.71-1... Reading runtime dependency for html-parser-pm5124-3.71-1... 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-pm5124' will be installed. Reading dependency for libwww-pm5124-6.07-1... Reading runtime dependency for libwww-pm5124-6.07-1... The package 'libxml-pm5124' will be installed. Reading dependency for libxml-pm5124-0.08-2... Reading runtime dependency for libxml-pm5124-0.08-2... 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-pm5124' will be installed. Reading dependency for soap-lite-pm5124-0.712-6... Reading runtime dependency for soap-lite-pm5124-0.712-6... The package 'spreadsheet-parseexcel-pm5124' will be installed. Reading dependency for spreadsheet-parseexcel-pm5124-0.59-1... Reading runtime dependency for spreadsheet-parseexcel-pm5124-0.59-1... 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-pm5124' will be installed. Reading dependency for uri-pm5124-1.64-1... Reading runtime dependency for uri-pm5124-1.64-1... The package 'xml-dom-pm5124' will be installed. Reading dependency for xml-dom-pm5124-1.44-2... Reading runtime dependency for xml-dom-pm5124-1.44-2... The package 'xml-node-pm5124' will be installed. Reading dependency for xml-node-pm5124-0.11-104... Reading runtime dependency for xml-node-pm5124-0.11-104... The package 'xml-parser-pm5124' will be installed. Reading dependency for xml-parser-pm5124-2.41-2... Reading runtime dependency for xml-parser-pm5124-2.41-2... The package 'xml-sax-pm5124' will be installed. Reading dependency for xml-sax-pm5124-0.99-3... Reading runtime dependency for xml-sax-pm5124-0.99-3... The package 'xml-sax-writer-pm5124' will be installed. Reading dependency for xml-sax-writer-pm5124-0.54-1... Reading runtime dependency for xml-sax-writer-pm5124-0.54-1... 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-pm5124' will be installed. Reading dependency for io-tty-pm5124-1.10-1... Reading runtime dependency for io-tty-pm5124-1.10-1... 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-pm5124' will be installed. Reading dependency for encode-pm5124-2.60-1... Reading runtime dependency for encode-pm5124-2.60-1... 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-pm5124' will be installed. Reading dependency for html-tree-pm5124-5.03-1... Reading runtime dependency for html-tree-pm5124-5.03-1... The package 'html-tidy-pm5124' will be installed. Reading dependency for html-tidy-pm5124-1.56-1... Reading runtime dependency for html-tidy-pm5124-1.56-1... The package 'scalar-list-utils-pm5124' will be installed. Reading dependency for scalar-list-utils-pm5124-1.35-1... Reading runtime dependency for scalar-list-utils-pm5124-1.35-1... The package 'text-iconv-pm5124' will be installed. Reading dependency for text-iconv-pm5124-1.7-3... Reading runtime dependency for text-iconv-pm5124-1.7-3... 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-pm5124' will be installed. Reading dependency for cpan-meta-requirements-pm5124-2.125-1... Reading runtime dependency for cpan-meta-requirements-pm5124-2.125-1... 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-pm5124' will be installed. Reading dependency for moose-pm5124-2.1209-1... Reading runtime dependency for moose-pm5124-2.1209-1... The package 'json-pm5124' will be installed. Reading dependency for json-pm5124-2.90-1... Reading runtime dependency for json-pm5124-2.90-1... 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-pm5124' will be installed. Reading dependency for tk-pm5124-804.031-2... Reading runtime dependency for tk-pm5124-804.031-2... The package 'xml-libxslt-pm5124' will be installed. Reading dependency for xml-libxslt-pm5124-1.89-1... Reading runtime dependency for xml-libxslt-pm5124-1.89-1... 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-pm5124' will be installed. Reading dependency for authen-ntlm-pm5124-1.09-1... Reading runtime dependency for authen-ntlm-pm5124-1.09-1... The package 'encode-locale-pm5124' will be installed. Reading dependency for encode-locale-pm5124-1.03-1... Reading runtime dependency for encode-locale-pm5124-1.03-1... The package 'file-listing-pm5124' will be installed. Reading dependency for file-listing-pm5124-6.04-1... Reading runtime dependency for file-listing-pm5124-6.04-1... The package 'http-cookies-pm5124' will be installed. Reading dependency for http-cookies-pm5124-6.01-1... Reading runtime dependency for http-cookies-pm5124-6.01-1... The package 'http-daemon-pm5124' will be installed. Reading dependency for http-daemon-pm5124-6.01-1... Reading runtime dependency for http-daemon-pm5124-6.01-1... The package 'http-date-pm5124' will be installed. Reading dependency for http-date-pm5124-6.02-1... Reading runtime dependency for http-date-pm5124-6.02-1... The package 'http-message-pm5124' will be installed. Reading dependency for http-message-pm5124-6.06-1... Reading runtime dependency for http-message-pm5124-6.06-1... The package 'http-negotiate-pm5124' will be installed. Reading dependency for http-negotiate-pm5124-6.01-1... Reading runtime dependency for http-negotiate-pm5124-6.01-1... The package 'lwp-mediatypes-pm5124' will be installed. Reading dependency for lwp-mediatypes-pm5124-6.02-1... Reading runtime dependency for lwp-mediatypes-pm5124-6.02-1... The package 'net-http-pm5124' will be installed. Reading dependency for net-http-pm5124-6.06-1... Reading runtime dependency for net-http-pm5124-6.06-1... The package 'www-robotrules-pm5124' will be installed. Reading dependency for www-robotrules-pm5124-6.02-1... Reading runtime dependency for www-robotrules-pm5124-6.02-1... The package 'class-inspector-pm5124' will be installed. Reading dependency for class-inspector-pm5124-1.28-1... Reading runtime dependency for class-inspector-pm5124-1.28-1... 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-pm5124' will be installed. Reading dependency for data-uuid-pm5124-1.219-1... Reading runtime dependency for data-uuid-pm5124-1.219-1... The package 'dime-tools-pm5124' will be installed. Reading dependency for dime-tools-pm5124-0.03-1... Reading runtime dependency for dime-tools-pm5124-0.03-1... The package 'fcgi-pm5124' will be installed. Reading dependency for fcgi-pm5124-0.74-1... Reading runtime dependency for fcgi-pm5124-0.74-1... The package 'io-compress-pm5124' will be installed. Reading dependency for io-compress-pm5124-2.063-1... Reading runtime dependency for io-compress-pm5124-2.063-1... The package 'mime-lite-pm5124' will be installed. Reading dependency for mime-lite-pm5124-3.030-2... Reading runtime dependency for mime-lite-pm5124-3.030-2... The package 'mime-tools-pm5124' will be installed. Reading dependency for mime-tools-pm5124-5.505-1... Reading runtime dependency for mime-tools-pm5124-5.505-1... The package 'task-weaken-pm5124' will be installed. Reading dependency for task-weaken-pm5124-1.04-1... Reading runtime dependency for task-weaken-pm5124-1.04-1... 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-pm5124' will be installed. Reading dependency for unicode-map-pm5124-0.112-16... Reading runtime dependency for unicode-map-pm5124-0.112-16... 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-pm5124' will be installed. Reading dependency for xml-filter-buffertext-pm5124-1.01-4... Reading runtime dependency for xml-filter-buffertext-pm5124-1.01-4... 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-pm5124' will be installed. Reading dependency for class-load-pm5124-0.20-1... Reading runtime dependency for class-load-pm5124-0.20-1... The package 'class-load-xs-pm5124' will be installed. Reading dependency for class-load-xs-pm5124-0.06-1... Reading runtime dependency for class-load-xs-pm5124-0.06-1... The package 'data-optlist-pm5124' will be installed. Reading dependency for data-optlist-pm5124-0.109-1... Reading runtime dependency for data-optlist-pm5124-0.109-1... The package 'devel-globaldestruction-pm5124' will be installed. Reading dependency for devel-globaldestruction-pm5124-0.12-1... Reading runtime dependency for devel-globaldestruction-pm5124-0.12-1... The package 'eval-closure-pm5124' will be installed. Reading dependency for eval-closure-pm5124-0.11-1... Reading runtime dependency for eval-closure-pm5124-0.11-1... The package 'list-moreutils-pm5124' will be installed. Reading dependency for list-moreutils-pm5124-0.33-1... Reading runtime dependency for list-moreutils-pm5124-0.33-1... The package 'module-runtime-pm5124' will be installed. Reading dependency for module-runtime-pm5124-0.014-1... Reading runtime dependency for module-runtime-pm5124-0.014-1... The package 'mro-compat-pm5124' will be installed. Reading dependency for mro-compat-pm5124-0.12-1... Reading runtime dependency for mro-compat-pm5124-0.12-1... The package 'package-deprecationmanager-pm5124' will be installed. Reading dependency for package-deprecationmanager-pm5124-0.13-1... Reading runtime dependency for package-deprecationmanager-pm5124-0.13-1... The package 'package-stash-pm5124' will be installed. Reading dependency for package-stash-pm5124-0.36-1... Reading runtime dependency for package-stash-pm5124-0.36-1... The package 'package-stash-xs-pm5124' will be installed. Reading dependency for package-stash-xs-pm5124-0.28-1... Reading runtime dependency for package-stash-xs-pm5124-0.28-1... The package 'params-util-pm5124' will be installed. Reading dependency for params-util-pm5124-1.07-1... Reading runtime dependency for params-util-pm5124-1.07-1... The package 'sub-exporter-pm5124' will be installed. Reading dependency for sub-exporter-pm5124-0.987-1... Reading runtime dependency for sub-exporter-pm5124-0.987-1... The package 'sub-name-pm5124' will be installed. Reading dependency for sub-name-pm5124-0.05-1... Reading runtime dependency for sub-name-pm5124-0.05-1... 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-pm5124' will be installed. Reading dependency for json-xs-pm5124-3.01-1... Reading runtime dependency for json-xs-pm5124-3.01-1... 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-pm5124' will be installed. Reading dependency for xml-libxml-pm5124-2.0111-1... Reading runtime dependency for xml-libxml-pm5124-2.0111-1... 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-pm5124' will be installed. Reading dependency for io-html-pm5124-1.001-1... Reading runtime dependency for io-html-pm5124-1.001-1... The package 'io-socket-ssl-pm5124' will be installed. Reading dependency for io-socket-ssl-pm5124-1.997-1... Reading runtime dependency for io-socket-ssl-pm5124-1.997-1... The package 'compress-raw-bzip2-pm5124' will be installed. Reading dependency for compress-raw-bzip2-pm5124-2.063-1... Reading runtime dependency for compress-raw-bzip2-pm5124-2.063-1... The package 'compress-raw-zlib-pm5124' will be installed. Reading dependency for compress-raw-zlib-pm5124-2.063-1... Reading runtime dependency for compress-raw-zlib-pm5124-2.063-1... 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-pm5124' will be installed. Reading dependency for mailtools-pm5124-2.13-1... Reading runtime dependency for mailtools-pm5124-2.13-1... 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-pm5124' will be installed. Reading dependency for unicode-string-pm5124-2.09-11... Reading runtime dependency for unicode-string-pm5124-2.09-11... 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-pm5124' will be installed. Reading dependency for module-implementation-pm5124-0.06-1... Reading runtime dependency for module-implementation-pm5124-0.06-1... The package 'sub-install-pm5124' will be installed. Reading dependency for sub-install-pm5124-0.927-1... Reading runtime dependency for sub-install-pm5124-0.927-1... The package 'devel-globaldestruction-xs-pm5124' will be installed. Reading dependency for devel-globaldestruction-xs-pm5124-0.01-1... Reading runtime dependency for devel-globaldestruction-xs-pm5124-0.01-1... The package 'sub-exporter-progressive-pm5124' will be installed. Reading dependency for sub-exporter-progressive-pm5124-0.001011-1... Reading runtime dependency for sub-exporter-progressive-pm5124-0.001011-1... The package 'params-classify-pm5124' will be installed. Reading dependency for params-classify-pm5124-0.013-4... Reading runtime dependency for params-classify-pm5124-0.013-4... The package 'class-c3-pm5124' will be installed. Reading dependency for class-c3-pm5124-0.25-1... Reading runtime dependency for class-c3-pm5124-0.25-1... The package 'dist-checkconflicts-pm5124' will be installed. Reading dependency for dist-checkconflicts-pm5124-0.09-1... Reading runtime dependency for dist-checkconflicts-pm5124-0.09-1... 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-pm5124' will be installed. Reading dependency for net-ssleay-pm5124-1.65-1... Reading runtime dependency for net-ssleay-pm5124-1.65-1... The package 'net-idn-encode-pm5124' will be installed. Reading dependency for net-idn-encode-pm5124-2.004-1... Reading runtime dependency for net-idn-encode-pm5124-2.004-1... 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-pm5124' will be installed. Reading dependency for algorithm-c3-pm5124-0.08-3... Reading runtime dependency for algorithm-c3-pm5124-0.08-3... 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-pm5124' will be installed. Reading dependency for unicode-normalize-pm5124-1.18-1... Reading runtime dependency for unicode-normalize-pm5124-1.18-1... The following package will be rebuilt: bioperl-run-pm5124 The following 155 additional packages will be installed: algorithm-c3-pm5124 algorithm-diff-pm array-compare-pm5124 authen-ntlm-pm5124 bioperl-pm5124 class-c3-pm5124 class-inspector-pm5124 class-load-pm5124 class-load-xs-pm5124 clone-pm5124 common-sense-pm compress-raw-bzip2-pm5124 compress-raw-zlib-pm5124 constant-pm cpan-meta-pm5124 cpan-meta-requirements-pm5124 cpan-meta-yaml-pm crypt-rc4-pm data-optlist-pm5124 data-stag-pm5124 data-uuid-pm5124 devel-globaldestruction-pm5124 devel-globaldestruction-xs-pm5124 digest-hmac-pm digest-perl-md5-pm dime-tools-pm5124 dist-checkconflicts-pm5124 email-date-format-pm encode-locale-pm5124 encode-pm5124 eval-closure-pm5124 expat1-shlibs exporter-pm extutils-cbuilder-pm extutils-install-pm extutils-manifest-pm extutils-parsexs-pm fcgi-pm5124 file-listing-pm5124 file-slurp-pm fontconfig-config fontconfig2-shlibs freetype219-shlibs freezethaw-pm gd-pm5124 gd-svg-pm5124 gd3-shlibs graph-pm heap-pm html-entities-numbered-pm html-parser-pm5124 html-tagset-pm html-tidy-pm5124 html-tree-pm5124 http-cookies-pm5124 http-daemon-pm5124 http-date-pm5124 http-message-pm5124 http-negotiate-pm5124 io-compress-pm5124 io-html-pm5124 io-socket-ssl-pm5124 io-string-pm io-stringy-pm io-tty-pm5124 ipc-run-pm5124 json-pm5124 json-pp-pm json-xs-pm5124 libjbig-shlibs libjpeg9-shlibs liblzma5-shlibs libpng16-shlibs libtidyp-shlibs libtiff5-shlibs libwww-pm5124 libxml-pm5124 libxml2-shlibs libxslt-shlibs list-moreutils-pm5124 lwp-mediatypes-pm5124 mailtools-pm5124 mime-lite-pm5124 mime-tools-pm5124 mime-types-pm mldbm-pm module-build-pm5124 module-implementation-pm5124 module-metadata-pm5124 module-runtime-pm5124 moose-pm5124 mozilla-ca-pm mro-compat-pm5124 net-http-pm5124 net-idn-encode-pm5124 net-ssleay-pm5124 ole-storagelite-pm openssl100-shlibs package-deprecationmanager-pm5124 package-generator-pm package-stash-pm5124 package-stash-xs-pm5124 par-dist-pm params-classify-pm5124 params-util-pm5124 parse-cpan-meta-pm perl-ostype-pm5124 perl5124-core pod-readme-pm podlators-pm rec-descent-pm regexp-common-pm scalar-list-utils-pm5124 set-scalar-pm soap-lite-pm5124 software-license-pm5124 spreadsheet-parseexcel-pm5124 spreadsheet-writeexcel-pm sub-exporter-pm5124 sub-exporter-progressive-pm5124 sub-install-pm5124 sub-name-pm5124 svg-pm task-weaken-pm5124 test-harness-pm5124 text-balanced-pm text-iconv-pm5124 text-shellwords-pm tie-ixhash-pm time-date-pm tk-pm5124 tree-dag-node-pm try-tiny-pm types-serialiser-pm unicode-map-pm5124 unicode-normalize-pm5124 unicode-string-pm5124 uri-pm5124 version-pm5124 www-robotrules-pm5124 xft2-shlibs xml-dom-pm5124 xml-filter-buffertext-pm5124 xml-libxml-pm5124 xml-libxslt-pm5124 xml-namespacesupport-pm xml-node-pm5124 xml-parser-pm5124 xml-regexp-pm xml-sax-base-pm xml-sax-pm5124 xml-sax-writer-pm5124 xml-twig-pm5124 xml-writer-pm xml-xpathengine-pm Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/BioPerl-Run-1.006900.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 13.8M 0 30163 0 0 29270 0 0:08:16 0:00:01 0:08:15 29256 0 13.8M 0 92427 0 0 45493 0 0:05:19 0:00:02 0:05:17 45485 2 13.8M 2 375k 0 0 124k 0 0:01:53 0:00:03 0:01:50 124k 4 13.8M 4 637k 0 0 159k 0 0:01:29 0:00:04 0:01:25 159k 6 13.8M 6 896k 0 0 175k 0 0:01:20 0:00:05 0:01:15 182k 6 13.8M 6 917k 0 0 140k 0 0:01:40 0:00:06 0:01:34 161k 6 13.8M 6 918k 0 0 123k 0 0:01:55 0:00:07 0:01:48 152k 7 13.8M 7 1000k 0 0 123k 0 0:01:54 0:00:08 0:01:46 123k 7 13.8M 7 1101k 0 0 122k 0 0:01:56 0:00:09 0:01:47 95007 9 13.8M 9 1395k 0 0 139k 0 0:01:41 0:00:10 0:01:31 101k 12 13.8M 12 1722k 0 0 155k 0 0:01:31 0:00:11 0:01:20 177k 13 13.8M 13 1881k 0 0 156k 0 0:01:30 0:00:12 0:01:18 211k 15 13.8M 15 2204k 0 0 168k 0 0:01:24 0:00:13 0:01:11 241k 19 13.8M 19 2765k 0 0 197k 0 0:01:11 0:00:14 0:00:57 332k 23 13.8M 23 3278k 0 0 218k 0 0:01:05 0:00:15 0:00:50 375k 23 13.8M 23 3383k 0 0 211k 0 0:01:07 0:00:16 0:00:51 333k 24 13.8M 24 3434k 0 0 201k 0 0:01:10 0:00:17 0:00:53 310k 25 13.8M 25 3566k 0 0 197k 0 0:01:11 0:00:18 0:00:53 274k 29 13.8M 29 4137k 0 0 217k 0 0:01:05 0:00:19 0:00:46 273k 32 13.8M 32 4557k 0 0 227k 0 0:01:02 0:00:20 0:00:42 256k 38 13.8M 38 5434k 0 0 258k 0 0:00:54 0:00:21 0:00:33 411k 39 13.8M 39 5585k 0 0 253k 0 0:00:56 0:00:22 0:00:34 428k 40 13.8M 40 5769k 0 0 250k 0 0:00:56 0:00:23 0:00:33 439k 42 13.8M 42 5989k 0 0 249k 0 0:00:57 0:00:24 0:00:33 368k 43 13.8M 43 6153k 0 0 237k 0 0:00:59 0:00:25 0:00:34 272k 43 13.8M 43 6155k 0 0 234k 0 0:01:00 0:00:26 0:00:34 136k 47 13.8M 47 6739k 0 0 249k 0 0:00:57 0:00:27 0:00:30 229k 48 13.8M 48 6870k 0 0 244k 0 0:00:57 0:00:28 0:00:29 219k 48 13.8M 48 6897k 0 0 233k 0 0:01:00 0:00:29 0:00:31 164k 48 13.8M 48 6897k 0 0 225k 0 0:01:02 0:00:30 0:00:32 158k 48 13.8M 48 6898k 0 0 219k 0 0:01:04 0:00:31 0:00:33 143k 50 13.8M 50 7200k 0 0 224k 0 0:01:03 0:00:32 0:00:31 94581 54 13.8M 54 7720k 0 0 233k 0 0:01:00 0:00:33 0:00:27 171k 57 13.8M 57 8124k 0 0 238k 0 0:00:59 0:00:34 0:00:25 275k 62 13.8M 62 8905k 0 0 254k 0 0:00:55 0:00:35 0:00:20 449k 64 13.8M 64 9203k 0 0 252k 0 0:00:56 0:00:36 0:00:20 461k 65 13.8M 65 9267k 0 0 246k 0 0:00:57 0:00:37 0:00:20 374k 68 13.8M 68 9735k 0 0 256k 0 0:00:55 0:00:38 0:00:17 403k 73 13.8M 73 10.1M 0 0 267k 0 0:00:53 0:00:39 0:00:14 462k 79 13.8M 79 10.9M 0 0 281k 0 0:00:50 0:00:40 0:00:10 473k 79 13.8M 79 11.0M 0 0 275k 0 0:00:51 0:00:41 0:00:10 454k 84 13.8M 84 11.7M 0 0 286k 0 0:00:49 0:00:42 0:00:07 618k 90 13.8M 90 12.5M 0 0 297k 0 0:00:47 0:00:43 0:00:04 610k 90 13.8M 90 12.5M 0 0 292k 0 0:00:48 0:00:44 0:00:04 481k 90 13.8M 90 12.6M 0 0 286k 0 0:00:49 0:00:45 0:00:04 322k 91 13.8M 91 12.6M 0 0 282k 0 0:00:50 0:00:46 0:00:04 341k 94 13.8M 94 13.1M 0 0 285k 0 0:00:49 0:00:47 0:00:02 281k 97 13.8M 97 13.5M 0 0 288k 0 0:00:49 0:00:48 0:00:01 203k 100 13.8M 100 13.8M 0 0 293k 0 0:00:48 0:00:48 --:--:-- 303k 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 ... 4296 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 ... 4315 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... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/constant-pm_1.27-1_darwin-x86_64.deb Selecting previously deselected package constant-pm. 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All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/expat1-shlibs_2.1.0-1_darwin-x86_64.deb Selecting previously deselected package expat1-shlibs. (Reading database ... 4382 files and directories currently installed.) Unpacking expat1-shlibs (from .../expat1-shlibs_2.1.0-1_darwin-x86_64.deb) ... Setting up expat1-shlibs (2.1.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/exporter-pm_5.68-1_darwin-x86_64.deb Selecting previously deselected package exporter-pm. (Reading database ... 4387 files and directories currently installed.) Unpacking exporter-pm (from .../exporter-pm_5.68-1_darwin-x86_64.deb) ... Setting up exporter-pm (5.68-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/extutils-cbuilder-pm_0.27.03-2_darwin-x86_64.deb Selecting previously deselected package extutils-cbuilder-pm. 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(Reading database ... 11531 files and directories currently installed.) Unpacking moose-pm5124 (from .../moose-pm5124_2.1209-1_darwin-x86_64.deb) ... Setting up moose-pm5124 (2.1209-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/xml-twig-pm5124_3.48-1_darwin-x86_64.deb Selecting previously deselected package xml-twig-pm5124. (Reading database ... 12143 files and directories currently installed.) Unpacking xml-twig-pm5124 (from .../xml-twig-pm5124_3.48-1_darwin-x86_64.deb) ... Setting up xml-twig-pm5124 (3.48-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/array-compare-pm5124_2.02-1_darwin-x86_64.deb Selecting previously deselected package array-compare-pm5124. (Reading database ... 12163 files and directories currently installed.) Unpacking array-compare-pm5124 (from .../array-compare-pm5124_2.02-1_darwin-x86_64.deb) ... Setting up array-compare-pm5124 (2.02-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioperl-pm5124_1.6.901-2_darwin-x86_64.deb Selecting previously deselected package bioperl-pm5124. (Reading database ... 12173 files and directories currently installed.) Unpacking bioperl-pm5124 (from .../bioperl-pm5124_1.6.901-2_darwin-x86_64.deb) ... Setting up bioperl-pm5124 (1.6.901-2) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioperl-run-pm5124-1.6.900-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bioperl-run-pm5124-1.6.900-1' in `/sw/build.build/fink-buildlock-bioperl-run-pm5124-1.6.900-1_2014.07.27-14.40.25_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioperl-run-pm5124-1.6.900-1_2014.07.27-14.40.25_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioperl-run-pm5124-1.6.900-1. (Reading database ... 15164 files and directories currently installed.) Unpacking fink-buildlock-bioperl-run-pm5124-1.6.900-1 (from .../fink-buildlock-bioperl-run-pm5124-1.6.900-1_2014.07.27-14.40.25_darwin-x86_64.deb) ... Setting up fink-buildlock-bioperl-run-pm5124-1.6.900-1 (2014.07.27-14.40.25) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.4SrcZ 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 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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 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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 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BioPerl-Run-1.006900/t/lib/Test/Builder BioPerl-Run-1.006900/t/lib/Test/Builder/Module.pm BioPerl-Run-1.006900/t/lib/Test/Builder/Tester.pm BioPerl-Run-1.006900/t/lib/Test/Harness BioPerl-Run-1.006900/t/lib/Test/Harness/Results.pm BioPerl-Run-1.006900/t/lib/Test/Harness/Point.pm BioPerl-Run-1.006900/t/lib/Test/Harness/Iterator.pm BioPerl-Run-1.006900/t/lib/Test/Harness/TAP.pod BioPerl-Run-1.006900/t/lib/Test/Harness/Assert.pm BioPerl-Run-1.006900/t/lib/Test/Harness/Util.pm BioPerl-Run-1.006900/t/lib/Test/Harness/Straps.pm BioPerl-Run-1.006900/t/lib/Sub BioPerl-Run-1.006900/t/lib/Sub/Uplevel.pm BioPerl-Run-1.006900/t/data BioPerl-Run-1.006900/t/data/eponine.fa BioPerl-Run-1.006900/t/data/prosite.dat BioPerl-Run-1.006900/t/data/new_pep.fa BioPerl-Run-1.006900/t/data/e_coli_2.bedpe BioPerl-Run-1.006900/t/data/hyphy1.tree BioPerl-Run-1.006900/t/data/purine.all.fa BioPerl-Run-1.006900/t/data/r2bwa.fq BioPerl-Run-1.006900/t/data/Ft.bed12 BioPerl-Run-1.006900/t/data/Prints_prot.FastA 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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 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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._xXTf [ -r /sw/fink/dists/stable/main/finkinfo/libs/perlmods/bioperl-run-pm.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.7oKZR 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.t9E3Z ARCHFLAGS="" /usr/bin/arch -x86_64 perl5.12.4 Build.PL --install_base /sw --install_path bin=/sw/bin --install_path lib=/sw/lib/perl5/5.12.4 --install_path arch=/sw/lib/perl5/5.12.4/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-pm5124-1.6.900-1 --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-pm5124-1.6.900-1 /bin/mkdir -p /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw /bin/mkdir -p /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioperl-run-pm5124-1.6.900-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.TR8ix ./Build install Building BioPerl-Run Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/ESoap.pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/SoapEUtilities.pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/ESoap/WSDL.pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4/Bio/DB/SoapEUtilities/Result.pm Installing 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Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Promoterwise.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Pseudowise.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::RNAMotif.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Samtools.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Seg.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Signalp.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Simprot.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::TigrAssembler.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Tmhmm.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::TribeMCL.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man/man3/Bio::Tools::Run::Vista.3pm mv /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/man /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/lib/perl5/5.12.4 mkdir -p /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/bioperl-run-pm5124/scripts install scripts/* /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/bioperl-run-pm5124/scripts/ sudo -u fink-bld [ENV] sh -c /tmp/fink.PFObl /usr/bin/install -d -m 700 /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124 /bin/cp -r Changes /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124/ /bin/cp -r INSTALL /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124/ /bin/cp -r INSTALL.PROGRAMS /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124/ /bin/cp -r MANIFEST /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124/ /bin/cp -r README /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124/ /bin/cp -r AUTHORS /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124/ /bin/chmod -R go=u-w /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/doc/bioperl-run-pm5124 /bin/rm -f /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/info/dir /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/info/dir.old /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/sw/share/info/dir /sw/build.build/root-bioperl-run-pm5124-1.6.900-1/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-pm5124-1.6.900-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/perlmods dpkg-deb: building package `bioperl-run-pm5124' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/perlmods/bioperl-run-pm5124_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-pm5124-1.6.900-1 (Reading database ... 15165 files and directories currently installed.) Removing fink-buildlock-bioperl-run-pm5124-1.6.900-1 ...