** 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 /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_fetch_genes.pl /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation.pl /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_check_versions.pl /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation-wormbase.pl /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation.pl /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation-wormbase.pl /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/defaults.wormbase.PLS cgi-bin/defaults.wormbase Extracting defaults.wormbase (with variable substitutions) /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/version.wormbase.PLS cgi-bin/version.wormbase Extracting version.wormbase (with variable substitutions) /home/cpanrun/pa-risc1.1/build/5.8.2/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 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/acedb....................1..1 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 1) line 3. ok 1 - use Bio::GMOD::Admin::Monitor::acedb; ok t/Adaptor..................1..3 ok 1 - use Bio::GMOD::Adaptor; Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok 2 - generic parameter loading: test_value ok 3 - generic parameter loading: value2 ok t/Archive..................1..1 Subroutine create_archive redefined at blib/lib/Bio/GMOD/Admin/Archive.pm line 128. ok 1 - use Bio::GMOD::Admin::Archive; ok t/BioGMOD..................1..13 ok 1 - use Bio::GMOD; Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok 2 - new constructor ok 3 - accessor adaptor() ok 4 - accessor mod() ok 5 - new constructor via organism: nematode ok 6 - accessor adaptor() ok 7 - accessor mod() ok 8 - new constructor via species: briggsae ok 9 - accessor adaptor() ok 10 - accessor mod() ok 11 - new constructor via species: C. remanei ok 12 - accessor adaptor() ok 13 - accessor mod() ok t/CheckVersions............1..4 ok 1 - use Bio::GMOD::Util::CheckVersions; Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok 2 - new constructor via Bio::GMOD ok 3 - live_version() ok 4 - dev_version() ok t/CheckVersionsWormBase....1..4 ok 1 - use Bio::GMOD::Util::CheckVersions::WormBase; Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok 2 - new constructor via Bio::GMOD ok 3 - live_version() ok 4 - dev_version() ok t/httpd....................1..1 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 1) line 3. ok 1 - use Bio::GMOD::Admin::Monitor::httpd; ok t/Mirror...................1..2 ok 1 - use Bio::GMOD::Util::Mirror; [2007 Jun 28 07:03] Downloading file README... ok 2 - mirroring a file ok t/mysqld...................1..1 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. # Failed test (t/mysqld.t at line 45) # Tried to use 'Bio::GMOD::Admin::Monitor::mysqld'. # Error: Can't locate DBI.pm in @INC (@INC contains: t .. . ./blib/lib /home/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-GMOD/blib/lib /home/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-GMOD/blib/arch /home/cpanrun/pa-risc1.1/build/5.8.2/lib/5.8.2/PA-RISC1.1-thread-multi /home/cpanrun/pa-risc1.1/build/5.8.2/lib/5.8.2 /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/PA-RISC1.1-thread-multi /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2 /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl) at blib/lib/Bio/GMOD/Admin/Monitor/mysqld.pm line 8. # BEGIN failed--compilation aborted at blib/lib/Bio/GMOD/Admin/Monitor/mysqld.pm line 8. # Compilation failed in require at (eval 1) line 2. not ok 1 - use Bio::GMOD::Admin::Monitor::mysqld; # Looks like you failed 1 tests of 1. dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay t/Query....................1..1 Useless use of string in void context at blib/lib/Bio/GMOD/Query.pm line 29. ok 1 - use Bio::GMOD::Query; ok t/QueryWormBase............1..1 ok 1 - use Bio::GMOD::Query::WormBase; ok t/Rearrange................1..4 ok 1 - use Bio::GMOD::Util::Rearrange; ok 2 - rearrange(), scalar ok 3 - rearrange(), scalar ok 4 - rearrange(), array ok t/StandardURLs.............1..8 ok 1 - use Bio::GMOD::StandardURLs; Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok 2 - new constructor via Bio::GMOD ok 3 - fetching available species: C_briggsae C_elegans ok 4 - fetching available releases: WS100 WS110 WS120 WS130 WS140 WS150 WS160 WS175 WS176 ok 5 - fetching available releases: WS100 WS110 WS120 WS130 WS140 WS150 WS160 WS175 WS176 ok 6 - fetching available datasets: dna, protein, feature, ncrna, mrna ok 7 - fetching current release: WS176 ok 8 - fetching supported datasets: feature protein dna ncrna mrna ok t/Status...................1..1 ok 1 - use Bio::GMOD::Util::Status; ok t/Update...................1..8 ok 1 - use Bio::GMOD::Admin::Update; Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. ok 2 - new constructor: Bio::GMOD::Admin::Update::WormBase=HASH(0x40656b28) ok 3 - accessor, adaptor(): Bio::GMOD::Adaptor::WormBase=HASH(0x4018573c) ok 4 - accessor, mod(): WormBase ok 5 - generic parameter loading: test_value [2007 Jun 28 07:03] Creating temporary directory at t/tmpdir/WS176... [2007 Jun 28 07:03] Successfully created temporary directory... ok 6 - temp dir creation Argument ":" isn't numeric in division (/) at blib/lib/Bio/GMOD/Admin/Update.pm line 106, line 1. ok 7 - check of available space Argument ":" isn't numeric in division (/) at blib/lib/Bio/GMOD/Admin/Update.pm line 106, line 5. [2007 Jun 28 07:03] Insufficient space to install test (0.01 GB required; 0.00 GB available)... Died at blib/lib/Bio/GMOD/Util/Status.pm line 36, line 8. # Looks like you planned 8 tests but only ran 7. # Looks like your test died just after 7. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED test 8 Failed 1/8 tests, 87.50% okay t/UpdateWormBase...........1..7 ok 1 - use Bio::GMOD::Admin::Update::WormBase; ok 2 - Bio::GMOD::Admin::Update::WormBase->can('update') ok 3 - Bio::GMOD::Admin::Update::WormBase->can('fetch_acedb') ok 4 - Bio::GMOD::Admin::Update::WormBase->can('fetch_elegans_gff') ok 5 - Bio::GMOD::Admin::Update::WormBase->can('fetch_briggsae_gff') ok 6 - Bio::GMOD::Admin::Update::WormBase->can('fetch_blast_blat') ok 7 - Bio::GMOD::Admin::Update::WormBase->can('analyze_logs') ok Failed 2/16 test scripts, 87.50% okay. 2/60 subtests failed, 96.67% okay. Failed Test Stat Wstat Total Fail Failed List of Failed --------------------------------------------------------------------------------------------------------------------------- t/Update.t 255 65280 8 2 25.00% 8 t/mysqld.t 1 256 1 1 100.00% 1 make: *** [test_dynamic] Error 25