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yeban/jb_pl_test_output

Created November 21, 2014 16:13
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jb_pl_test_output
# Failed test 'bin/draw-basepair-track.pl compiled ok'
# at tests/perl_tests/00.compile.t line 45.
# stdout:
# stderr: Can't locate GD/Image.pm in @INC (you may need to install the GD::Image module) (@INC contains: /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5 /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/lib /Users/priyam/jbrowse/src/perl5 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
# BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
# Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
# BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
# Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
# BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
# Compilation failed in require at bin/draw-basepair-track.pl line 82.
# BEGIN failed--compilation aborted at bin/draw-basepair-track.pl line 82.
# Looks like you failed 1 test of 44.
tests/perl_tests/00.compile.t .....................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/44 subtests
tests/perl_tests/add-json.pl.t .................... ok
# using temp dir /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/tDho95noju
tests/perl_tests/bam-to-json.pl.t ................. ok
# writing output to /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/koENVNZ5dU
# writing output to /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/pnWxAFa2aL
tests/perl_tests/biodb-to-json.pl.t ............... ok
tests/perl_tests/conf_format.t .................... ok
# using temp dir /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/rMNPgkI6H_
Can't locate GD/Image.pm in @INC (you may need to install the GD::Image module) (@INC contains: /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5 /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/lib /Users/priyam/jbrowse/src/perl5 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TiledImage.pm line 71.
Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/TrackImage.pm line 23.
Compilation failed in require at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
BEGIN failed--compilation aborted at /Users/priyam/jbrowse/bin/../src/perl5/ImageTrackRenderer.pm line 58.
Compilation failed in require at bin/draw-basepair-track.pl line 82.
BEGIN failed--compilation aborted at bin/draw-basepair-track.pl line 82.
# Failed test 'script ran ok'
# at tests/perl_tests/draw-basepair-track.pl.t line 32.
# Failed test 'made some pngs'
# at tests/perl_tests/draw-basepair-track.pl.t line 36.
# Failed test 'made trackData'
# at tests/perl_tests/draw-basepair-track.pl.t line 38.
No such file or directory reading /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/rMNPgkI6H_/tracks/foo/mahoney/trackData.json at tests/perl_tests/lib/FileSlurping.pm line 99.
# Tests were run but no plan was declared and done_testing() was not seen.
tests/perl_tests/draw-basepair-track.pl.t .........
Dubious, test returned 2 (wstat 512, 0x200)
Failed 3/3 subtests
tests/perl_tests/fakefasta.t ...................... ok
tests/perl_tests/featurestream.t .................. ok
# Failed test 'got the right number of classes'
# at tests/perl_tests/flatfile-to-json.pl.t line 339.
# got: '334'
# expected: '5'
# [
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# 'Id',
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# 'isArrayAttr' => {
# 'Subfeatures' => 1
# }
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# 'isArrayAttr' => {}
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# 'isArrayAttr' => {}
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# 'Type',
# 'Name',
# 'Subfeatures',
# 'Score'
# ],
# 'isArrayAttr' => {
# 'Subfeatures' => 1
# }
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# {
# 'attributes' => [
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# {
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# Failed test 'got the right number of classes'
# at tests/perl_tests/flatfile-to-json.pl.t line 339.
# got: '333'
# expected: '5'
# [
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# 'isArrayAttr' => {
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# Failed test at tests/perl_tests/flatfile-to-json.pl.t line 386.
# Structures begin differing at:
# $got->{attributes}[3] = 'Score'
# $expected->{attributes}[3] = 'Seq_id'
# {
# 'featureCount' => 20,
# 'formatVersion' => 1,
# 'histograms' => {
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# Failed test at tests/perl_tests/flatfile-to-json.pl.t line 424.
# Structures begin differing at:
# $got->{attributes}[3] = 'Name'
# $expected->{attributes}[3] = 'Source'
# {
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# 'urlTemplate' => 'lf-{Chunk}.jsonz'
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# Looks like you failed 4 tests of 37.
tests/perl_tests/flatfile-to-json.pl.t ............
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/37 subtests
tests/perl_tests/genbank.t ........................ ok
tests/perl_tests/generate-names-incremental.pl.t .. ok
# Failed test 'got right data from volvox test data run'
# at tests/perl_tests/generate-names.pl.t line 39.
# Structures begin differing at:
# $got->{c00/f.json}{rs17883998}{exact}[0][1] = '12'
# $expected->{c00/f.json}{rs17883998}{exact}[0][1] = '11'
# Failed test 'same data after incremental run with --safeMode'
# at tests/perl_tests/generate-names.pl.t line 58.
# Structures begin differing at:
# $got->{6bf/3.json}{rs112989936}{exact}[0][1] = '12'
# $expected->{6bf/3.json}{rs112989936}{exact}[0][1] = '11'
# Looks like you failed 2 tests of 3.
tests/perl_tests/generate-names.pl.t ..............
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/3 subtests
tests/perl_tests/json.t ........................... ok
# loaded 2559 test features
tests/perl_tests/lazy_nclist.t .................... ok
tests/perl_tests/maker2jbrowse.t .................. ok
tests/perl_tests/nclist.t ......................... ok
WARNING: multiple reference sequences found named 'NC_001133', using only the first one.
# Failed test 'see 12 uncompressed seq chunks'
# at tests/perl_tests/prepare-refseqs.pl.t line 59.
# got: '0'
# expected: '12'
# []
# Failed test 'see 12 uncompressed seq chunks'
# at tests/perl_tests/prepare-refseqs.pl.t line 73.
# got: '0'
# expected: '12'
# []
WARNING: multiple reference sequences found named 'NC_001133', using only the first one.
# Failed test 'see 3 COMPRESSED seq chunks'
# at tests/perl_tests/prepare-refseqs.pl.t line 89.
# got: '0'
# expected: '3'
# /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/UtLONTroDH
# Looks like you failed 3 tests of 13.
tests/perl_tests/prepare-refseqs.pl.t .............
Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/13 subtests
tests/perl_tests/remove-track.pl.t ................ ok
# writing output to /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/08n9Kk20KW
# Track nonExistentTrack not found in the UCSC track database (trackDb.txt.gz) file. Is it a real UCSC track? at bin/ucsc-to-json.pl line 194.
# To format the jaxQtlAsIs track, you must have both files tests/data/hg19/database//jaxQtlAsIs.sql and tests/data/hg19/database//jaxQtlAsIs.txt.gz
tests/perl_tests/ucsc-to-json.pl.t ................ ok
# using temp dir /var/folders/62/zdks231968z8fkbbrghvz7gh0000gn/T/mYJ1oU9krD
tests/perl_tests/wig-to-json.pl.t ................. ok
Test Summary Report
-------------------
tests/perl_tests/00.compile.t (Wstat: 256 Tests: 44 Failed: 1)
Failed test: 19
Non-zero exit status: 1
tests/perl_tests/draw-basepair-track.pl.t (Wstat: 512 Tests: 3 Failed: 3)
Failed tests: 1-3
Non-zero exit status: 2
Parse errors: No plan found in TAP output
tests/perl_tests/flatfile-to-json.pl.t (Wstat: 1024 Tests: 37 Failed: 4)
Failed tests: 30, 32, 35, 37
Non-zero exit status: 4
tests/perl_tests/generate-names.pl.t (Wstat: 512 Tests: 3 Failed: 2)
Failed tests: 1-2
Non-zero exit status: 2
tests/perl_tests/prepare-refseqs.pl.t (Wstat: 768 Tests: 13 Failed: 3)
Failed tests: 5, 7, 9
Non-zero exit status: 3
Files=20, Tests=224, 15 wallclock secs ( 0.07 usr 0.03 sys + 12.41 cusr 1.59 csys = 14.10 CPU)
Result: FAIL
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