=~=~=~=~=~=~=~=~=~=~=~= PuTTY log 2006.05.24 11:29:00 =~=~=~=~=~=~=~=~=~=~=~= perl Makefile.PL Should I use your previous settings to set the file paths and options (y/n) [y]? n ** Bio::GMOD::Monitor Tests ** Do you want to run the Bio::GMOD::Monitor::* tests (further configuration follows) y/n [n] y Do you want to run the httpd tests (httpd will be restarted; may need su privs) y/n: [n] y Full path to apachectl: [/usr/local/apache/bin/apachectl] /usr/local/sbin/apachectl Do you want to run the acedb tests (acedb will be restarted; may need su privs) y/n: [n] y Do you want to run the mysqld tests (mysqld will be restarted; may need su privs) y/n: [n] y Full path to mysql init script: [/etc/rc.d/init.d/mysqld] /usr/local/etc/rc.d/mysql-server.sh ---------------------------------------------- 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 moondance# make 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 /usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_fetch_genes.PLS bin/gmod_fetch_genes.pl Extracting gmod_fetch_genes.pl (with variable substitutions) /usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_update_installation.PLS bin/gmod_update_installation.pl Extracting gmod_update_installation.pl (with variable substitutions) /usr/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) /usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/gmod_monitor_installation.PLS bin/gmod_monitor_installation.pl Extracting gmod_monitor_installation.pl (with variable substitutions) /usr/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) /usr/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_fetch_genes.pl blib/script/gmod_fetch_genes.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_fetch_genes.pl cp bin/gmod_update_installation.pl blib/script/gmod_update_installation.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation.pl /usr/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 /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_check_versions.pl cp bin/gmod_monitor_installation-wormbase.pl blib/script/gmod_monitor_installation-wormbase.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation-wormbase.pl cp bin/gmod_monitor_installation.pl blib/script/gmod_monitor_installation.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_monitor_installation.pl cp bin/gmod_update_installation-wormbase.pl blib/script/gmod_update_installation-wormbase.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_update_installation-wormbase.pl cp bin/gmod_standard_urls.pl blib/script/gmod_standard_urls.pl /usr/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_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 /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/defaults.wormbase.PLS cgi-bin/defaults.wormbase Extracting defaults.wormbase (with variable substitutions) /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/version.wormbase.PLS cgi-bin/version.wormbase Extracting version.wormbase (with variable substitutions) /usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl Extracting cgi_install.pl (with variable substitutions) moondance# make test PERL_DL_NONLAZY=1 /usr/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, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at (eval 5) line 2, line 1. t/acedb....................ok 1/4/usr/local/acedb/bin/ace.pl: not found Can't exec "/etc/rc.d/init.d/xinetd": No such file or directory at blib/lib/Bio/GMOD/Admin/Monitor/acedb.pm line 41, line 1. No matching processes were found Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA, line 1. t/acedb....................ok t/Adaptor.................. t/Adaptor..................ok 1/3Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. t/Adaptor..................ok 2/3 t/Adaptor..................ok t/Archive..................Subroutine create_archive redefined at blib/lib/Bio/GMOD/Admin/Archive.pm line 128. t/Archive..................ok 1/1 t/Archive..................ok t/BioGMOD.................. t/BioGMOD..................ok 1/13Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. t/BioGMOD..................ok 2/13 t/BioGMOD..................ok 8/13 t/BioGMOD..................ok t/CheckVersions............ t/CheckVersions............ok 1/4Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. t/CheckVersions............ok 2/4 t/CheckVersions............ok 3/4 t/CheckVersions............ok t/CheckVersionsWormBase.... t/CheckVersionsWormBase....ok 1/4Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. t/CheckVersionsWormBase....ok 2/4 t/CheckVersionsWormBase....ok 3/4 t/CheckVersionsWormBase....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, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at (eval 5) line 2, line 1. t/httpd....................ok 1/4Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at blib/lib/Bio/GMOD/Admin/Monitor.pm line 20, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at blib/lib/Bio/GMOD/Admin/Monitor.pm line 20, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA at blib/lib/Bio/GMOD/Admin/Monitor.pm line 20, line 1. t/httpd....................ok 3/4 t/httpd....................ok 4/4Argument "restarting httpd" isn't numeric in foreach loop entry at /usr/local/lib/perl5/site_perl/5.8.8/Test/More.pm line 1079, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA, line 1. Can't locate package Bio::GMOD::Util::Email for @Bio::GMOD::Admin::Monitor::ISA, line 1. t/httpd....................ok t/Mirror................... t/Mirror...................ok 1/2Use of uninitialized value in pattern match (m//) at blib/lib/Bio/GMOD/Util/Mirror.pm line 186. [2006 May 24 11:28] Downloading file README... ----> Failed to establish connection. t/Mirror...................NOK 2 # Failed test 'mirroring a file' # in t/Mirror.t at line 54. # Looks like you failed 1 test of 2. t/Mirror...................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 2 Failed 1/2 tests, 50.00% okay 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 5) line 2. t/mysqld...................ok 1/4DBI connect('test','nobody',...) failed: Access denied for user 'nobody'@'localhost' (using password: NO) at blib/lib/Bio/GMOD/Admin/Monitor/mysqld.pm line 20 /usr/local/etc/rc.d/mysql-server.sh: unknown directive 'condrestart'. Usage: /usr/local/etc/rc.d/mysql-server.sh [fast|force|one](start stop restart rcvar status poll) DBI connect('test','nobody',...) failed: Access denied for user 'nobody'@'localhost' (using password: NO) at blib/lib/Bio/GMOD/Admin/Monitor/mysqld.pm line 45 t/mysqld...................NOK 4 # Failed test '[2006 May 24 11:29] Restarting mysqld via /usr/local/etc/rc.d/mysql-server.sh . [failed]' # in t/mysqld.t at line 82. # Looks like you failed 1 test of 4. t/mysqld...................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 4 Failed 1/4 tests, 75.00% okay t/Query....................Useless use of string in void context at blib/lib/Bio/GMOD/Query.pm line 29. t/Query....................ok 1/1 t/Query....................ok t/QueryWormBase............ t/QueryWormBase............NOK 1 # Failed test 'use Bio::GMOD::Query::WormBase;' # in t/QueryWormBase.t at line 33. # Tried to use 'Bio::GMOD::Query::WormBase'. # Error: Can't locate Ace.pm in @INC (@INC contains: t .. . ./blib/lib /home/aaron/BSD/p5-Bio-GMOD/work/Bio-GMOD-0.028/blib/lib /home/aaron/BSD/p5-Bio-GMOD/work/Bio-GMOD-0.028/blib/arch /usr/local/lib/perl5/5.8.8/BSDPAN /usr/local/lib/perl5/site_perl/5.8.8/mach /usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.8.8/mach /usr/local/lib/perl5/5.8.8) 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 5) line 2. # BEGIN failed--compilation aborted at (eval 5) line 2. # Looks like you failed 1 test of 1. t/QueryWormBase............dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay t/Rearrange................ t/Rearrange................ok 1/4 t/Rearrange................ok t/StandardURLs............. t/StandardURLs.............ok 1/8Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. t/StandardURLs.............ok 2/8 t/StandardURLs.............ok 3/8 t/StandardURLs.............ok t/Status................... t/Status...................ok 1/1 t/Status...................ok t/Update................... t/Update...................ok 1/8Use of uninitialized value in concatenation (.) or string at blib/lib/Bio/GMOD/Adaptor/WormBase.pm line 15. [2006 May 24 11:30] Creating temporary directory at t/tmpdir/WS157... [2006 May 24 11:30] Successfully created temporary directory... t/Update...................ok 6/8[2006 May 24 11:30] Sufficient space to install test (0.01 GB required; 0.85 GB available)... t/Update...................ok t/UpdateWormBase........... t/UpdateWormBase...........ok 1/7 t/UpdateWormBase...........ok Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/Mirror.t 1 256 2 1 2 Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/QueryWormBase.t 1 256 1 1 1 Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/mysqld.t 1 256 4 1 4 Failed 3/16 test scripts. 3/69 subtests failed. Files=16, Tests=69, 145 wallclock secs (13.94 cusr + 1.95 csys = 15.88 CPU) moondance#