Set up gcc environment - 3.3 ** 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 /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_fetch_genes.pl Set up gcc environment - 3.3 /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation.pl Set up gcc environment - 3.3 /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_check_versions.pl Set up gcc environment - 3.3 /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation-wormbase.pl Set up gcc environment - 3.3 /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation.pl Set up gcc environment - 3.3 /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation-wormbase.pl Set up gcc environment - 3.3 /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_standard_urls.pl Set up gcc environment - 3.3 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 /export/home/cpanrun/build/5.10.0/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/defaults.wormbase.PLS cgi-bin/defaults.wormbase Extracting defaults.wormbase (with variable substitutions) /export/home/cpanrun/build/5.10.0/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/version.wormbase.PLS cgi-bin/version.wormbase Extracting version.wormbase (with variable substitutions) /export/home/cpanrun/build/5.10.0/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 /export/home/cpanrun/build/5.10.0/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, '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. 1..1 Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::acedb::ISA at (eval 3) line 2. 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::httpd::ISA at (eval 3) line 2. ok 1 - use Bio::GMOD::Admin::Monitor::httpd; ok t/Mirror...................1..2 ok 1 - use Bio::GMOD::Util::Mirror; Can't connect: Net::FTP: connect: Connection refused at t/Mirror.t line 49 # Looks like you planned 2 tests but only ran 1. # Looks like your test died just after 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED test 2 Failed 1/2 tests, 50.00% okay 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. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::mysqld::ISA at (eval 3) line 2. ok 1 - use Bio::GMOD::Admin::Monitor::mysqld; ok 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 not ok 1 - use Bio::GMOD::Query::WormBase; # Failed test 'use Bio::GMOD::Query::WormBase;' # at t/QueryWormBase.t line 33. # Tried to use 'Bio::GMOD::Query::WormBase'. # Error: Can't locate Ace.pm in @INC (@INC contains: t .. . ./blib/lib /export/home/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-GMOD/blib/lib /export/home/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-GMOD/blib/arch /export/home/cpanrun/build/5.10.0/site/lib /export/home/cpanrun/build/5.10.0/lib) at blib/lib/Bio/GMOD/Query/WormBase.pm line 5. # BEGIN failed--compilation aborted at t/QueryWormBase.t line 33. # Compilation failed in require at (eval 3) line 2. # BEGIN failed--compilation aborted at (eval 3) line 2. # Looks like you failed 1 test of 1. dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay 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 WS143 WS144 WS145 WS146 WS147 WS148 WS149 WS150 WS151 WS152 WS153 WS154 WS155 WS156 WS157 WS158 WS159 WS160 WS161 WS162 WS163 WS164 WS165 WS166 WS167 WS168 WS169 WS170 WS171 WS172 WS173 WS174 WS175 WS176 WS177 WS178 WS179 WS180 WS181 WS182 WS183 ok 5 - fetching available releases: WS100 WS110 WS120 WS130 WS140 WS143 WS144 WS145 WS146 WS147 WS148 WS149 WS150 WS151 WS152 WS153 WS154 WS155 WS156 WS157 WS158 WS159 WS160 WS161 WS162 WS163 WS164 WS165 WS166 WS167 WS168 WS169 WS170 WS171 WS172 WS173 WS174 WS175 WS176 WS177 WS178 WS179 WS180 WS181 WS182 WS183 ok 6 - fetching available datasets: dna, protein, feature, ncrna, mrna ok 7 - fetching current release: WS183 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(0x879768) ok 3 - accessor, adaptor(): Bio::GMOD::Adaptor::WormBase=HASH(0x26a2f8) ok 4 - accessor, mod(): WormBase ok 5 - generic parameter loading: test_value [2007 Nov 27 12:25] Creating temporary directory at t/tmpdir/WS183... [2007 Nov 27 12:25] Successfully created temporary directory... ok 6 - temp dir creation ok 7 - check of available space [2007 Nov 27 12:25] Sufficient space to install test (0.01 GB required; 0.48 GB available)... ok 8 - fetching disk space ok 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 Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/Mirror.t 255 65280 2 2 2 t/QueryWormBase.t 1 256 1 1 1 Failed 2/16 test scripts. 2/60 subtests failed. Files=16, Tests=60, 26 wallclock secs (12.62 cusr + 1.78 csys = 14.40 CPU) Failed 2/16 test programs. 2/60 subtests failed. make: *** [test_dynamic] Error 255