Attachment 214127 Details for Bug 298326 – Build log

Build log

bioperl-network-1.6.0:20091225-044351.log (text/plain), 9.20 KB, created by Diego Elio Pettenò (RETIRED) on 2009-12-25 14:50:43 UTC

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Creator: Diego Elio Pettenò (RETIRED)

Created: 2009-12-25 14:50:43 UTC

Size: 9.20 KB

patch

obsolete

> * CPV:  sci-biology/bioperl-network-1.6.0
> * REPO: gentoo
> * USE:  elibc_glibc kernel_linux test userland_GNU x86
>>>> Unpacking source...
>>>> Unpacking BioPerl-network-1.6.0.tar.bz2 to /var/tmp/portage/sci-biology/bioperl-network-1.6.0/work
>>>> Source unpacked in /var/tmp/portage/sci-biology/bioperl-network-1.6.0/work
>>>> Preparing source in /var/tmp/portage/sci-biology/bioperl-network-1.6.0/work/BioPerl-network-1.6.0 ...
>>>> Source prepared.
>>>> Configuring source in /var/tmp/portage/sci-biology/bioperl-network-1.6.0/work/BioPerl-network-1.6.0 ...
> * Using Module::Build
>Checking whether your kit is complete...
>Looks good
>
>Checking prerequisites...
>Looks good
>
>Creating new 'Build' script for 'BioPerl-network' version '1.006000'
>>>> Source configured.
>>>> Compiling source in /var/tmp/portage/sci-biology/bioperl-network-1.6.0/work/BioPerl-network-1.6.0 ...
>Copying Bio/Network/IO/psi25.pm -> blib/lib/Bio/Network/IO/psi25.pm
>Copying Bio/Network/Edge.pm -> blib/lib/Bio/Network/Edge.pm
>Copying Bio/Network/ProteinNet.pm -> blib/lib/Bio/Network/ProteinNet.pm
>Copying Bio/Network/IO/psi10.pm -> blib/lib/Bio/Network/IO/psi10.pm
>Copying Bio/Network/Node.pm -> blib/lib/Bio/Network/Node.pm
>Copying Bio/Network/IO/psi/intact.pm -> blib/lib/Bio/Network/IO/psi/intact.pm
>Copying Bio/Network/IO.pm -> blib/lib/Bio/Network/IO.pm
>Copying Bio/Network/IO/dip_tab.pm -> blib/lib/Bio/Network/IO/dip_tab.pm
>Copying Bio/Network/Interaction.pm -> blib/lib/Bio/Network/Interaction.pm
>Manifying blib/lib/Bio/Network/IO/dip_tab.pm -> blib/libdoc/Bio::Network::IO::dip_tab.3pm
>Manifying blib/lib/Bio/Network/IO/psi10.pm -> blib/libdoc/Bio::Network::IO::psi10.3pm
>Manifying blib/lib/Bio/Network/Edge.pm -> blib/libdoc/Bio::Network::Edge.3pm
>Manifying blib/lib/Bio/Network/IO.pm -> blib/libdoc/Bio::Network::IO.3pm
>Manifying blib/lib/Bio/Network/ProteinNet.pm -> blib/libdoc/Bio::Network::ProteinNet.3pm
>Manifying blib/lib/Bio/Network/IO/psi25.pm -> blib/libdoc/Bio::Network::IO::psi25.3pm
>Manifying blib/lib/Bio/Network/IO/psi/intact.pm -> blib/libdoc/Bio::Network::IO::psi::intact.3pm
>Manifying blib/lib/Bio/Network/Node.pm -> blib/libdoc/Bio::Network::Node.3pm
>Manifying blib/lib/Bio/Network/Interaction.pm -> blib/libdoc/Bio::Network::Interaction.3pm
>>>> Source compiled.
>t/Edge.t ......... 
>1..10
>ok 1 - use Bio::Network::ProteinNet;
>ok 2 - use Bio::Network::Edge;
>ok 3 - use Bio::Network::Node;
>ok 4 - use Bio::Seq;
>ok 5 - The object isa Bio::Network::Edge
>ok 6
>ok 7
>ok 8 - The object isa Bio::Network::Edge
>ok 9
>ok 10
>ok
>t/Graph-MD5.t .... 
>1..23
>ok 1 - use Graph::Undirected;
>ok 2
>ok 3
>ok 4
>ok 5
>ok 6
>ok 7
>ok 8
>ok 9
>ok 10
>ok 11
>ok 12
>ok 13
>ok 14
>ok 15
>ok 16
>ok 17
>ok 18
>ok 19
>ok 20
>ok 21
>ok 22
>ok 23
>ok
>t/Graph-Seq.t .... 
>1..21
>ok 1 - use Graph::Undirected;
>ok 2 - use Graph::Traversal::DFS;
>ok 3 - use Bio::Seq;
>ok 4
>ok 5
>ok 6
>ok 7
>ok 8
>ok 9
>ok 10
>ok 11
>ok 12
>ok 13
>ok 14
>ok 15
>ok 16
>ok 17
>ok 18
>ok 19
>ok 20
>ok 21
>ok
>t/IO_dip_tab.t ... 
>1..19
>ok 1 - use Bio::Network::IO;
>ok 2 - use Bio::Network::Edge;
>ok 3 - use Bio::Network::Node;
>ok 4 - use Bio::Seq;
>ok 5
>ok 6
>ok 7
>ok 8
>ok 9
>ok 10 - PIR:A64696
>ok 11
>ok 12
>ok 13
>ok 14
>ok 15
>ok 16
>ok 17
>ok 18
>ok 19
>ok
>t/IO_psi10.t ..... 
>1..22
>ok 1 - use Bio::Network::IO;
>ok 2 - use Bio::Network::Node;
>ok 3
>ok 4
>ok 5
>ok 6
>ok 7
>ok 8
>ok 9
>ok 10
>ok 11
>ok 12
>ok 13
>ok 14
>ok 15
>ok 16
>ok 17
>ok 18
>ok 19
>ok 20
>Can't locate object method "proteins" via package "Bio::Network::Node=HASH(0xa3d3d44)" (perhaps you forgot to load "Bio::Network::Node=HASH(0xa3d3d44)"?) at t/IO_psi10.t line 63.
># Looks like you planned 22 tests but ran 20.
># Looks like your test exited with 255 just after 20.
>Dubious, test returned 255 (wstat 65280, 0xff00)
>Failed 2/22 subtests 
>t/IO_psi25.t ..... 
>1..9
>ok 1 - use Bio::Network::IO;
>ok 2
>ok 3
>ok 4
>ok 5
>ok 6
>ok 7
>ok 8
>ok 9
>ok
>t/Interaction.t .. 
>1..23
>ok 1 - use Bio::Network::ProteinNet;
>ok 2 - use Bio::Network::Interaction;
>ok 3 - use Bio::Network::Node;
>ok 4 - use Bio::Seq;
>ok 5 - use Bio::Annotation::Comment;
>ok 6 - use Bio::Annotation::Collection;
>ok 7 - use Bio::Annotation::OntologyTerm;
>ok 8
>ok 9
>ok 10
>ok 11
>ok 12
>ok 13
>ok 14
>ok 15
>ok 16
>ok 17
>ok 18
>ok 19
>ok 20 - Comment: Reliable
>ok 21
>ok 22
>ok 23
>ok
>t/Node.t ......... 
>1..32
>ok 1 - use Bio::Network::ProteinNet;
>ok 2 - use Bio::Network::Node;
>ok 3 - use Bio::Seq;
>ok 4
>ok 5
>ok 6
>ok 7
>ok 8
>ok 9
>ok 10
>ok 11
>ok 12
>ok 13
>ok 14
>ok 15
>ok 16
>ok 17
>ok 18
>ok 19
>ok 20
>ok 21
>ok 22
>ok 23
>ok 24
>ok 25
>ok 26
>ok 27
>ok 28
>ok 29
>ok 30
>ok 31
>ok 32
>ok
>t/ProteinNet.t ... 
>1..171
>ok 1 - use Bio::Network::ProteinNet;
>ok 2 - use Bio::Network::IO;
>ok 3
>ok 4
>ok 5
>ok 6
>ok 7
>ok 8
>ok 9
>ok 10
>ok 11
>ok 12
>ok 13
>ok 14
>ok 15
>ok 16
>ok 17
>ok 18
>ok 19
>ok 20
>ok 21 - 0.028
>ok 22
>ok 23
>ok 24
>ok 25
>ok 26
>ok 27
>ok 28
>ok 29
>ok 30
>ok 31
>ok 32
>ok 33
>ok 34
>ok 35
>ok 36
>ok 37
>ok 38
>ok 39
>ok 40
>ok 41
>ok 42
>ok 43
>ok 44
>ok 45
>ok 46
>ok 47
>ok 48
>ok 49
>ok 50
>ok 51
>ok 52
>ok 53
>ok 54
>ok 55
>ok 56
>ok 57
>ok 58
>ok 59
>ok 60
>ok 61
>ok 62
>ok 63
>ok 64
>ok 65
>ok 66
>ok 67
>ok 68
>ok 69
>ok 70
>ok 71
>ok 72
>ok 73
>ok 74
>ok 75
>ok 76
>ok 77
>ok 78
>ok 79
>ok 80
>ok 81
>ok 82
>ok 83
>ok 84
>ok 85
>ok 86
>ok 87
>ok 88
>ok 89
>ok 90
>ok 91
>ok 92
>ok 93
>ok 94
>ok 95
>ok 96
>ok 97
>ok 98
>ok 99
>ok 100
>ok 101
>ok 102
>ok 103
>ok 104
>ok 105
>ok 106
>ok 107
>ok 108
>ok 109
>ok 110
>ok 111
>ok 112
>ok 113
>ok 114
>ok 115
>ok 116
>ok 117
>ok 118
>ok 119
>ok 120
>ok 121
>ok 122
>ok 123
>ok 124
>ok 125
>ok 126
>ok 127
>ok 128
>ok 129
>ok 130
>ok 131
>ok 132
>ok 133
>ok 134
>ok 135
>ok 136
>ok 137
>ok 138
>ok 139
>ok 140
>ok 141
>ok 142
>ok 143
>ok 144
>ok 145
>ok 146
>ok 147
>ok 148
>ok 149
>ok 150
>ok 151
>ok 152
>ok 153
>ok 154
>ok 155
>ok 156
>ok 157
>ok 158
>ok 159
>ok 160
>ok 161
>ok 162
>ok 163
>ok 164
>ok 165
>ok 166
>ok 167
>ok 168
>ok 169
>ok 170 - The object isa Bio::Network::Node
>ok 171 - The object isa Bio::Network::Node
>ok
>
>Test Summary Report
>-------------------
>t/IO_psi10.t   (Wstat: 65280 Tests: 20 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 22 tests but ran 20.
>Files=9, Tests=328, 40 wallclock secs ( 0.10 usr  0.03 sys + 38.83 cusr  0.56 csys = 39.52 CPU)
>Result: FAIL
>Failed 1/9 test programs. 0/328 subtests failed.
> * ERROR: sci-biology/bioperl-network-1.6.0 failed:
> *   test failed
> * 
> * Call stack:
> *     ebuild.sh, line   61:  Called src_test
> *   environment, line 2807:  Called perl-module_src_test
> *   environment, line 2595:  Called die
> * The specific snippet of code:
> *               ./Build test verbose=${TEST_VERBOSE:-0} || die "test failed";
> * 
> * If you need support, post the output of 'emerge --info =sci-biology/bioperl-network-1.6.0',
> * the complete build log and the output of 'emerge -pqv =sci-biology/bioperl-network-1.6.0'.
> * The complete build log is located at '/var/log/portage/build/sci-biology/bioperl-network-1.6.0:20091225-044351.log'.
> * The ebuild environment file is located at '/var/tmp/portage/sci-biology/bioperl-network-1.6.0/temp/environment'.
> * S: '/var/tmp/portage/sci-biology/bioperl-network-1.6.0/work/BioPerl-network-1.6.0'
>
>>>> Install bioperl-network-1.6.0 into /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/ category sci-biology
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/IO.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/ProteinNet.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/Interaction.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/Node.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/Edge.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/IO/psi25.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/IO/dip_tab.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/IO/psi10.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/lib/perl5/vendor_perl/5.8.8/Bio/Network/IO/psi/intact.pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::IO::psi::intact.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::IO::psi25.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::IO::dip_tab.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::Edge.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::Node.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::IO::psi10.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::IO.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::Interaction.3pm
>Installing /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/usr/share/man/man3/Bio::Network::ProteinNet.3pm
>>>> Completed installing bioperl-network-1.6.0 into /var/tmp/portage/sci-biology/bioperl-network-1.6.0/image/
>
> * Removing /usr/share/doc
> * Removing /usr/share/info
>Merge of sci-biology/bioperl-network-1.6.0 at 2009-12-25T04:43:51+00:00
>failed

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Attachments on bug 298326: 214127