** Bio::GMOD::Monitor Tests ** Do you want to run the Bio::GMOD::Monitor::* tests (further configuration follows) y/n [n] n ---------------------------------------------- Bio::GMOD File Paths BIN /usr/local/bin NONROOT MOD CGIBIN (Run perl Makefile.PL -h for help on changing) ---------------------------------------------- Checking if your kit is complete... Looks good Writing Makefile for Bio::GMOD cp GMOD/Admin/Archive/WormBase.pm blib/lib/Bio/GMOD/Admin/Archive/WormBase.pm cp GMOD/Admin/Monitor/WormBase.pm blib/lib/Bio/GMOD/Admin/Monitor/WormBase.pm cp GMOD/Admin/Monitor/httpd.pm blib/lib/Bio/GMOD/Admin/Monitor/httpd.pm cp GMOD/Adaptor.pm blib/lib/Bio/GMOD/Adaptor.pm cp GMOD/Admin/Monitor/mysqld.pm blib/lib/Bio/GMOD/Admin/Monitor/mysqld.pm cp GMOD/Admin/Update.pm blib/lib/Bio/GMOD/Admin/Update.pm cp GMOD/Adaptor/FlyBase.pm blib/lib/Bio/GMOD/Adaptor/FlyBase.pm cp GMOD/Adaptor/SGD.pm blib/lib/Bio/GMOD/Adaptor/SGD.pm cp GMOD/Util/CheckVersions/WormBase.pm blib/lib/Bio/GMOD/Util/CheckVersions/WormBase.pm cp GMOD/Admin/Update/WormBase.pm blib/lib/Bio/GMOD/Admin/Update/WormBase.pm cp GMOD/Util/Status.pm blib/lib/Bio/GMOD/Util/Status.pm cp GMOD/Query.pm blib/lib/Bio/GMOD/Query.pm cp GMOD/Util/Mirror.pm blib/lib/Bio/GMOD/Util/Mirror.pm cp GMOD/Adaptor/WormBase.pm blib/lib/Bio/GMOD/Adaptor/WormBase.pm cp GMOD/Util/CheckVersions.pm blib/lib/Bio/GMOD/Util/CheckVersions.pm cp GMOD/Admin/Monitor/blat.pm blib/lib/Bio/GMOD/Admin/Monitor/blat.pm cp GMOD/Query/FlyBase.pm blib/lib/Bio/GMOD/Query/FlyBase.pm cp GMOD/Util/Rearrange.pm blib/lib/Bio/GMOD/Util/Rearrange.pm cp GMOD/Query/WormBase.pm blib/lib/Bio/GMOD/Query/WormBase.pm cp GMOD/Adaptor/generic.pm blib/lib/Bio/GMOD/Adaptor/generic.pm cp GMOD/Admin/Monitor/acedb.pm blib/lib/Bio/GMOD/Admin/Monitor/acedb.pm cp GMOD/Admin/Archive.pm blib/lib/Bio/GMOD/Admin/Archive.pm cp GMOD/Admin/Monitor.pm blib/lib/Bio/GMOD/Admin/Monitor.pm cp GMOD.pm blib/lib/Bio/GMOD.pm cp GMOD/StandardURLs.pm blib/lib/Bio/GMOD/StandardURLs.pm /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_fetch_genes.PLS bin/gmod_fetch_genes.pl Extracting gmod_fetch_genes.pl (with variable substitutions) cp bin/gmod_fetch_genes.pl blib/script/gmod_fetch_genes.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_fetch_genes.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_update_installation.PLS bin/gmod_update_installation.pl Extracting gmod_update_installation.pl (with variable substitutions) cp bin/gmod_update_installation.pl blib/script/gmod_update_installation.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_check_versions.PLS bin/gmod_check_versions.pl Extracting gmod_check_versions.pl (with variable substitutions) cp bin/gmod_check_versions.pl blib/script/gmod_check_versions.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_check_versions.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_monitor_installation-wormbase.PLS bin/gmod_monitor_installation-wormbase.pl Extracting gmod_monitor_installation-wormbase.pl (with variable substitutions) cp bin/gmod_monitor_installation-wormbase.pl blib/script/gmod_monitor_installation-wormbase.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation-wormbase.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_monitor_installation.PLS bin/gmod_monitor_installation.pl Extracting gmod_monitor_installation.pl (with variable substitutions) cp bin/gmod_monitor_installation.pl blib/script/gmod_monitor_installation.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_update_installation-wormbase.PLS bin/gmod_update_installation-wormbase.pl Extracting gmod_update_installation-wormbase.pl (with variable substitutions) cp bin/gmod_update_installation-wormbase.pl blib/script/gmod_update_installation-wormbase.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation-wormbase.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_standard_urls.PLS bin/gmod_standard_urls.pl Extracting gmod_standard_urls.pl (with variable substitutions) cp bin/gmod_standard_urls.pl blib/script/gmod_standard_urls.pl /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_standard_urls.pl Manifying blib/man1/gmod_fetch_genes.pl.1 Manifying blib/man1/gmod_update_installation.pl.1 Manifying blib/man1/gmod_check_versions.pl.1 Manifying blib/man1/gmod_monitor_installation-wormbase.pl.1 Manifying blib/man1/gmod_monitor_installation.pl.1 Manifying blib/man1/gmod_update_installation-wormbase.pl.1 Manifying blib/man1/gmod_standard_urls.pl.1 Manifying blib/man3/Bio::GMOD::Admin::Monitor::WormBase.3 Manifying blib/man3/Bio::GMOD::Admin::Archive::WormBase.3 Manifying blib/man3/Bio::GMOD::Admin::Monitor::httpd.3 Manifying blib/man3/Bio::GMOD::Adaptor.3 Manifying blib/man3/Bio::GMOD::Admin::Monitor::mysqld.3 Manifying blib/man3/Bio::GMOD::Admin::Update.3 Manifying blib/man3/Bio::GMOD::Adaptor::FlyBase.3 Manifying blib/man3/Bio::GMOD::Adaptor::SGD.3 Manifying blib/man3/Bio::GMOD::Util::CheckVersions::WormBase.3 Manifying blib/man3/Bio::GMOD::Admin::Update::WormBase.3 Manifying blib/man3/Bio::GMOD::Util::Status.3 Manifying blib/man3/Bio::GMOD::Query.3 Manifying blib/man3/Bio::GMOD::Util::Mirror.3 Manifying blib/man3/Bio::GMOD::Adaptor::WormBase.3 Manifying blib/man3/Bio::GMOD::Util::CheckVersions.3 Manifying blib/man3/Bio::GMOD::Admin::Monitor::blat.3 Manifying blib/man3/Bio::GMOD::Util::Rearrange.3 Manifying blib/man3/Bio::GMOD::Query::FlyBase.3 Manifying blib/man3/Bio::GMOD::Query::WormBase.3 Manifying blib/man3/Bio::GMOD::Adaptor::generic.3 Manifying blib/man3/Bio::GMOD::Admin::Monitor::acedb.3 Manifying blib/man3/Bio::GMOD::Admin::Archive.3 Manifying blib/man3/Bio::GMOD.3 Manifying blib/man3/Bio::GMOD::Admin::Monitor.3 Manifying blib/man3/Bio::GMOD::StandardURLs.3 /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/defaults.wormbase.PLS cgi-bin/defaults.wormbase Extracting defaults.wormbase (with variable substitutions) /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/version.wormbase.PLS cgi-bin/version.wormbase Extracting version.wormbase (with variable substitutions) /Users/cpanrun/pristine/5.8.7/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl Extracting cgi_install.pl (with variable substitutions) PERL_DL_NONLAZY=1 /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/acedb....................Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at blib/lib/Bio/GMOD/Admin/Monitor/acedb.pm line 7. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at (eval 3) line 2. ok t/Adaptor..................Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok t/Archive..................Subroutine create_archive redefined at blib/lib/Bio/GMOD/Admin/Archive.pm line 128. ok t/BioGMOD..................Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok t/CheckVersions............Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok t/CheckVersionsWormBase....Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok t/httpd....................Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at blib/lib/Bio/GMOD/Admin/Monitor/httpd.pm line 7. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at (eval 3) line 2. ok t/Mirror...................[2006 Jun 27 20:02] Downloading file README... ok t/mysqld...................Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at blib/lib/Bio/GMOD/Admin/Monitor/mysqld.pm line 6. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at (eval 3) line 2. ok t/Query....................Useless use of string in void context at blib/lib/Bio/GMOD/Query.pm line 29. ok t/QueryWormBase............ok t/Rearrange................ok t/StandardURLs.............Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok t/Status...................ok t/Update...................Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. [2006 Jun 27 20:02] Creating temporary directory at t/tmpdir/WS159... [2006 Jun 27 20:02] Successfully created temporary directory... [2006 Jun 27 20:02] Sufficient space to install test (0.01 GB required; 14.22 GB available)... ok t/UpdateWormBase...........ok All tests successful. Files=16, Tests=60, 10 wallclock secs ( 3.05 cusr + 1.05 csys = 4.10 CPU) Warning: You do not have permissions to install into /usr/local/bin at /Users/cpanrun/pristine/5.8.7/lib/5.8.7/ExtUtils/Install.pm line 114. Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Adaptor.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Query.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/StandardURLs.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Adaptor/FlyBase.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Adaptor/generic.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Adaptor/SGD.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Adaptor/WormBase.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Archive.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Monitor.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Update.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Archive/WormBase.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Monitor/acedb.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Monitor/blat.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Monitor/httpd.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Monitor/mysqld.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Monitor/WormBase.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Admin/Update/WormBase.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Query/FlyBase.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Query/WormBase.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Util/CheckVersions.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Util/Mirror.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Util/Rearrange.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Util/Status.pm Installing /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/Bio/GMOD/Util/CheckVersions/WormBase.pm Installing /Users/cpanrun/pristine/5.8.7/man/man1/gmod_check_versions.pl.1 Installing /Users/cpanrun/pristine/5.8.7/man/man1/gmod_fetch_genes.pl.1 Installing /Users/cpanrun/pristine/5.8.7/man/man1/gmod_monitor_installation-wormbase.pl.1 Installing /Users/cpanrun/pristine/5.8.7/man/man1/gmod_monitor_installation.pl.1 Installing /Users/cpanrun/pristine/5.8.7/man/man1/gmod_standard_urls.pl.1 Installing /Users/cpanrun/pristine/5.8.7/man/man1/gmod_update_installation-wormbase.pl.1 Installing /Users/cpanrun/pristine/5.8.7/man/man1/gmod_update_installation.pl.1 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Adaptor.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Adaptor::FlyBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Adaptor::generic.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Adaptor::SGD.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Adaptor::WormBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Archive.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Archive::WormBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Monitor.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Monitor::acedb.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Monitor::blat.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Monitor::httpd.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Monitor::mysqld.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Monitor::WormBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Update.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Admin::Update::WormBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Query.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Query::FlyBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Query::WormBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::StandardURLs.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Util::CheckVersions.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Util::CheckVersions::WormBase.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Util::Mirror.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Util::Rearrange.3 Installing /Users/cpanrun/pristine/5.8.7/man/man3/Bio::GMOD::Util::Status.3 Installing /usr/local/bin/gmod_check_versions.pl Installing /usr/local/bin/gmod_fetch_genes.pl Installing /usr/local/bin/gmod_monitor_installation-wormbase.pl Installing /usr/local/bin/gmod_monitor_installation.pl Installing /usr/local/bin/gmod_standard_urls.pl Installing /usr/local/bin/gmod_update_installation-wormbase.pl Installing /usr/local/bin/gmod_update_installation.pl Appending installation info to /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level/perllocal.pod /Users/cpanrun/pristine/5.8.7/bin/perl "/Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-GMOD/install_util/cgi_install.pl" 'BIN=/usr/local/bin' Can't locate Bio/Root/IO.pm in @INC (@INC contains: /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-GMOD/install_util/cgi_install.pl line 4. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-GMOD/install_util/cgi_install.pl line 4. make: *** [cgi_install] Error 2