[Debian-med-packaging] Bug#954511: bioperl-run: FTBFS: dh_auto_test: error: perl Build test --verbose 1 returned exit code 255
Lucas Nussbaum
lucas at debian.org
Sun Mar 22 08:14:39 GMT 2020
Source: bioperl-run
Version: 1.7.3-3
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200321 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> mkdir t.skip
> for t in Blat Eponine Glimmer2 Gumby RepeatMasker Phyml Hyphy BWA MCS ; do mv t/${t}.t t.skip ; done
> mv: cannot stat 't/Gumby.t': No such file or directory
> mv: cannot stat 't/BWA.t': No such file or directory
> PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \
> HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \
> dh_auto_test --no-parallel
> perl Build test --verbose 1
>
> AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output
> PROBCONS Written by Chuong Do
> AMAP algorithm implemented by Ariel Schwartz
>
> Using parameter set:
> initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 }
> gapOpen[] = { 0.01993141696 0.01993141696 }
> gapExtend[] = { 0.7943345308 0.7943345308 }
>
> Loading sequence file: t/data/cysprot.fa
> Computing posterior matrices
> Building DAG
> Starting the sequence annealing process
> Creating candidate edge list
> Adding edges to the DAG
>
> AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output
> PROBCONS Written by Chuong Do
> AMAP algorithm implemented by Ariel Schwartz
>
> Using parameter set:
> initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 }
> gapOpen[] = { 0.01993141696 0.01993141696 }
> gapExtend[] = { 0.7943345308 0.7943345308 }
>
> Loading sequence file: /tmp/ftWO42xDDD
> Computing posterior matrices
> Building DAG
> Starting the sequence annealing process
> Creating candidate edge list
> Adding edges to the DAG
> t/Amap.t ......................
> 1..18
> ok 1 - use Bio::Tools::Run::Alignment::Amap;
> ok 2 - use Bio::SeqIO;
> ok 3 - use File::Spec;
> ok 4 - Found input file
> ok 5 - An object of class 'Bio::Tools::Run::Alignment::Amap' isa 'Bio::Tools::Run::Alignment::Amap'
> ok 6 - program_dir returned correct default
> ok 7 - error_string returned correct default
> ok 8 - aformat returned correct default
> ok 9 - outfile_name returned correct default
> ok 10 - Correct exe default name
> ok 11 - Correct minimum program version
> ok 12 - No error occured
> ok 13 - outfile_name returned something
> ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
> ok 15 - Correct number of seqs returned
> ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
> ok 17 - Correct number of seqs returned
> ok 18 - Got the correct ave % identity
> ok
> t/BEDTools.t .................. skipped: The optional module Bio::Tools::Run::BEDTools (or dependencies thereof) was not installed
> # You named your test '71'. You shouldn't use numbers for your test names.
> # Very confusing.
> # You named your test '91'. You shouldn't use numbers for your test names.
> # Very confusing.
> t/Coil.t ......................
> 1..6
> ok 1 - use Bio::Tools::Run::Coil;
> ok 2 - use Bio::SeqIO;
> ok 3
> ok 4
> ok 5 - 71
> ok 6 - 91
> ok
> t/Consense.t ..................
> 1..8
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense;
> ok 2 - use Bio::AlignIO;
> ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::Consense' isa 'Bio::Tools::Run::Phylo::Phylip::Consense'
> ok 4 - could not set rooted option
> [2J[Hconsense: can't find input tree file "intree"
> Please enter a new file name>
> [2J[H
> Consensus tree program, version 3.697
>
> Settings for this run:
> C Consensus type (MRe, strict, MR, Ml): Majority rule (extended)
> O Outgroup root: No, use as outgroup species 1
> R Trees to be treated as Rooted: No
> T Terminal type (IBM PC, ANSI, none): ANSI
> 1 Print out the sets of species: Yes
> 2 Print indications of progress of run: Yes
> 3 Print out tree: Yes
> 4 Write out trees onto tree file: Yes
>
> Are these settings correct? (type Y or the letter for one to change)
> [2J[H
> Consensus tree program, version 3.697
>
> Settings for this run:
> C Consensus type (MRe, strict, MR, Ml): Majority rule (extended)
> R Trees to be treated as Rooted: Yes
> T Terminal type (IBM PC, ANSI, none): ANSI
> 1 Print out the sets of species: Yes
> 2 Print indications of progress of run: Yes
> 3 Print out tree: Yes
> 4 Write out trees onto tree file: Yes
>
> Are these settings correct? (type Y or the letter for one to change)
>
> Consensus tree written to file "outtree"
>
> Output written to file "outfile"
>
> Done.
> ok 5
> ok 6
> ok 7
> ok 8
> ok
> Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,0][0,0] Score 0
> Recovering alignment: [0,0][0,0] Explicit read offWarning Error
> Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0
> no source found!
> Warning Error
> In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read
> off. Problem!
> Warning Error
> In full dc, at 0:0,0:0 got a bad hidden explicit read off...
> Warning Error
> Major problem (!) - in DnaMatchBlock matrix to special read off,
> position 0,0 state 0 no source found!
> Warning Error
> Problem in reading off special state system, hit a non start state
> (or an internal error) in a single alignment mode
> Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 7%] 4000 Cells done [ 9%] 5000 Cells done [12%] 6000 Cells done [14%] 7000 Cells done [17%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [29%] 13000 Cells done [31%] 14000 Cells done [34%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [41%] 18000 Cells done [43%] 19000 Cells done [46%] 20000 Cells done [48%] 21000 Cells done [51%] 22000 Cells done [53%] 23000 Cells done [55%] 24000 Cells done [58%] 25000 Cells done [60%] 26000 Cells done [63%] 27000 Cells done [65%] 28000 Cells done [68%] 29000 Cells done [70%] 30000 Cells done [72%] 31000 Cells done [75%] 32000 Cells done [77%] 33000 Cells done [80%] 34000 Cells done [82%] 35000 Cells done [85%] 36000 Cells done [87%] 37000 Cells done [89%] 38000 Cells done [92%] 39000 Cells done [94%] 40000 Cells done [97%] 41000 Cells done [99%][0,0][0,0] Score 0
> Recovering alignment: [0,0][0,0] Explicit read offWarning Error
> Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0
> no source found!
> Warning Error
> In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read
> off. Problem!
> Warning Error
> In full dc, at 0:0,0:0 got a bad hidden explicit read off...
> Warning Error
> Major problem (!) - in DnaMatchBlock matrix to special read off,
> position 0,0 state 0 no source found!
> Warning Error
> Problem in reading off special state system, hit a non start state
> (or an internal error) in a single alignment mode
> Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,0][0,0] Score 0
> Recovering alignment: [0,0][0,0] Explicit read offWarning Error
> Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0
> no source found!
> Warning Error
> In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read
> off. Problem!
> Warning Error
> In full dc, at 0:0,0:0 got a bad hidden explicit read off...
> Warning Error
> Major problem (!) - in DnaMatchBlock matrix to special read off,
> position 0,0 state 0 no source found!
> Warning Error
> Problem in reading off special state system, hit a non start state
> (or an internal error) in a single alignment mode
> t/DBA.t .......................
> 1..5
> ok 1 - use Bio::Tools::Run::Alignment::DBA;
> ok 2 - use Bio::SimpleAlign;
> ok 3 - use Bio::AlignIO;
> ok 4 - use Bio::SeqIO;
> ok 5 - An object of class 'Bio::Tools::Run::Alignment::DBA' isa 'Bio::Tools::Run::Alignment::DBA'
> ok
> t/DrawGram.t ..................
> 1..6
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram;
> ok 2 - use Bio::TreeIO;
> ok 3
> ok 4
> ok 5
> ok 6
> ok
> t/DrawTree.t ..................
> 1..6
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree;
> ok 2 - use Bio::TreeIO;
> ok 3
> ok 4
> ok 5
> ok 6
> ok
> -- namet is "-sequence" associated seqall qualifiers
>
> -- namet is "-outfile" associated outfile qualifiers
>
> t/EMBOSS.t ....................
> 1..31
> ok 1 - use Bio::Root::IO;
> ok 2 - use Bio::SeqIO;
> ok 3 - use Bio::AlignIO;
> ok 4 - use Bio::Factory::EMBOSS;
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> ok 10
> ok 11
> ok 12
> ok 13
> ok 14 - SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE
> 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
> t/Exonerate.t .................
> 1..89
> ok 1 - use Bio::Tools::Run::Alignment::Exonerate;
> ok 2 - An object of class 'Bio::Tools::Run::Alignment::Exonerate' isa 'Bio::Tools::Run::Alignment::Exonerate'
> ok 3
> ok 4 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO'
> 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 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 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO'
> 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
> # Required executable for Bio::Tools::Run::Phylo::FastTree is not present
> t/FastTree.t ..................
> 1..9
> ok 1 - use Bio::Root::IO;
> ok 2 - use Bio::Tools::Run::Phylo::FastTree;
> ok 3 - use Bio::AlignIO;
> ok 4 - Make the object
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present
> ok
> # Required executable for Bio::Tools::Run::FootPrinter is not present
> t/FootPrinter.t ...............
> 1..24
> ok 1 - use Bio::Tools::Run::FootPrinter;
> ok 2 - use Bio::SeqIO;
> ok 3 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 4 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 5 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 6 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 7 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 8 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 9 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 10 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 11 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 12 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 13 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 14 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 15 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 16 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 17 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 18 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 19 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 20 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 21 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 22 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 23 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok 24 # skip Required executable for Bio::Tools::Run::FootPrinter is not present
> ok
> # Required environment variable $GENEMARK_MODELS is not set
> t/Genemark.hmm.prokaryotic.t ..
> 1..99
> ok 1 - use Bio::Tools::Run::Genemark;
> ok 2 - use Bio::Root::IO;
> ok 3 - use Bio::Seq;
> ok 4 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 5 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 6 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 7 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 8 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 9 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 10 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 11 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 12 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 13 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 14 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 15 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 16 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 17 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 18 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 19 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 20 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 21 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 22 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 23 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 24 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 25 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 26 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 27 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 28 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 29 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 30 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 31 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 32 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 33 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 34 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 35 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 36 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 37 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 38 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 39 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 40 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 41 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 42 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 43 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 44 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 45 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 46 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 47 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 48 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 49 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 50 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 51 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 52 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 53 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 54 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 55 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 56 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 57 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 58 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 59 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 60 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 61 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 62 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 63 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 64 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 65 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 66 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 67 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 68 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 69 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 70 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 71 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 72 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 73 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 74 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 75 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 76 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 77 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 78 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 79 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 80 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 81 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 82 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 83 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 84 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 85 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 86 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 87 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 88 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 89 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 90 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 91 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 92 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 93 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 94 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 95 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 96 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 97 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 98 # skip Required environment variable $GENEMARK_MODELS is not set
> ok 99 # skip Required environment variable $GENEMARK_MODELS is not set
> ok
> These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values
> t/Genewise.t ..................
> 1..17
> ok 1 - use Bio::Tools::Run::Genewise;
> ok 2 - use Bio::Root::IO;
> ok 3 - use Bio::Seq;
> ok 4 - An object of class 'Bio::Tools::Run::Genewise' isa 'Bio::Tools::Run::Genewise'
> 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
> # Required environment variable $GENSCANDIR is not set
> t/Genscan.t ...................
> 1..6
> ok 1 - use Bio::Tools::Run::Genscan;
> ok 2 - use Bio::Root::IO;
> ok 3 # skip Required environment variable $GENSCANDIR is not set
> ok 4 # skip Required environment variable $GENSCANDIR is not set
> ok 5 # skip Required environment variable $GENSCANDIR is not set
> ok 6 # skip Required environment variable $GENSCANDIR is not set
> ok
> # Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> t/Gerp.t ......................
> 1..33
> ok 1 - use Bio::Tools::Run::Phylo::Gerp;
> ok 2 - use Bio::AlignIO;
> ok 3 - use Bio::TreeIO;
> ok 4 - use Bio::Root::Utilities;
> ok 5 - Found input alignment file
> ok 6 - Found input tree file
> ok 7 - An object of class 'Bio::Tools::Run::Phylo::Gerp' isa 'Bio::Tools::Run::Phylo::Gerp'
> ok 8 - has a created method not in args supplied to new
> ok 9 - quiet was set
> ok 10 - program_dir returned correct default
> ok 11 - Correct exe default name
> ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present
> ok
> t/Glimmer3.t ..................
> 1..111
> ok 1 - use Bio::Tools::Run::Glimmer;
> ok 2 - use Bio::Root::IO;
> ok 3 - use Bio::Seq;
> ok 4 - An object of class 'Bio::Tools::Run::Glimmer' isa 'Bio::Tools::Run::Glimmer'
> ok 5 - An object of class 'Bio::Tools::Glimmer' isa 'Bio::Tools::Glimmer'
> ok 6 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 7 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 8 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 9 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 10 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 11 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 12 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 13 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 14 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 15 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 17 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 18 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 19 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 20 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 21 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 22 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 23 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 24 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 25 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 26 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 27 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 28 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 29 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 30 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 31 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 32 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 33 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 34 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 35 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 36 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 37 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 38 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 39 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 40 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 41 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 42 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 43 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 44 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 45 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 46 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 47 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 48 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 49 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 50 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 51 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 52 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 53 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 54 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 55 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 56 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 57 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 58 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 59 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 60 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 61 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 62 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 63 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 64 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 65 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 66 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 67 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 68 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 69 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 70 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 72 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 73 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 74 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 75 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 76 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 77 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 78 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 79 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 80 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 81 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 82 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 83 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 84 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 85 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 86 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 87 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 88 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 89 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 90 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 91 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 92 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 93 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 94 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 95 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 96 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 97 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 98 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 99 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 100 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 101 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 102 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 103 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 104 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 105 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
> ok
> # Required executable for Bio::Tools::Run::Hmmer is not present
> t/Hmmer.t .....................
> 1..27
> ok 1 - use Bio::Tools::Run::Hmmer;
> ok 2 - use Bio::SeqIO;
> ok 3 - use Bio::AlignIO;
> ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer'
> ok 5
> ok 6
> ok 7
> ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present
> ok
> t/Infernal.t ..................
> 1..3
> ok 1 - use Bio::Tools::Run::Infernal;
> ok 2 - use Bio::SeqIO;
> ok 3 - use Bio::AlignIO;
> ok
>
> # Failed test 'Code tested only on kalign versions >= 2'
> # at t/Kalign.t line 23.
> # got: ''
> # expected: '1'
> [2020-03-22 03:18:02] : ERROR : Input alignment format could not be detected. (rwalign.c line 314)
> [2020-03-22 03:18:02] : ERROR : Function "detect_alignment_format(b, &type)" failed. (rwalign.c line 187)
> [2020-03-22 03:18:02] : ERROR : Function "tmp_msa = read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383)
> [2020-03-22 03:18:02] : ERROR : Function "run_kalign(param)" failed. (run_kalign.c line 353)
>
> --------------------- WARNING ---------------------
> MSG: Kalign call crashed: 256 [command /usr/bin/kalign -in t/data/cysprot.fa -out /tmp/ilV8fEWBHj/nJrv_GQaDU]
>
> ---------------------------------------------------
>
> # Failed test at t/Kalign.t line 25.
> Can't call method "num_sequences" on an undefined value at t/Kalign.t line 26.
> # Looks like your test exited with 25 just after 5.
> t/Kalign.t ....................
> 1..8
> ok 1 - use Bio::Tools::Run::Alignment::Kalign;
> ok 2 - use Bio::AlignIO;
> ok 3 - use Bio::SeqIO;
> not ok 4 - Code tested only on kalign versions >= 2
>
> Kalign (3.2.3)
>
> Copyright (C) 2006,2019,2020 Timo Lassmann
>
> This program comes with ABSOLUTELY NO WARRANTY; for details type:
> `kalign -showw'.
> This is free software, and you are welcome to redistribute it
> under certain conditions; consult the COPYING file for details.
>
> Please cite:
> Lassmann, Timo.
> "Kalign 3: multiple sequence alignment of large data sets."
> Bioinformatics (2019)
> https://doi.org/10.1093/bioinformatics/btz795
>
> [2020-03-22 03:18:02] : LOG : /usr/bin/kalign -in t/data/cysprot.fa -out /tmp/ilV8fEWBHj/nJrv_GQaDU
> not ok 5
> Dubious, test returned 25 (wstat 6400, 0x1900)
> Failed 5/8 subtests
> # Required executable for Bio::Tools::Run::Phylo::LVB is not present
> t/LVB.t .......................
> 1..19
> ok 1 - use Bio::Tools::Run::Phylo::LVB;
> ok 2 - use Bio::AlignIO;
> ok 3 - An object of class 'Bio::Tools::Run::Phylo::LVB' isa 'Bio::Tools::Run::Phylo::LVB'
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 16 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok 19 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present
> ok
> # Required executable for Bio::Tools::Run::Alignment::Lagan is not present
> t/Lagan.t .....................
> 1..12
> ok 1 - use Bio::AlignIO;
> ok 2 - use Bio::Tools::Run::Alignment::Lagan;
> ok 3 - use Bio::Root::IO;
> ok 4 - use Bio::SeqIO;
> ok 5 - use Bio::Seq;
> ok 6 - use Bio::Matrix::Mlagan;
> ok 7 - An object of class 'Bio::Tools::Run::Alignment::Lagan' isa 'Bio::Tools::Run::Alignment::Lagan'
> ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present
> ok
> t/MAFFT.t .....................
> 1..23
> ok 1 - use Bio::Tools::Run::Alignment::MAFFT;
> ok 2 - use Bio::AlignIO;
> ok 3 - use Bio::SeqIO;
> ok 4 - An object of class 'Bio::Tools::Run::Alignment::MAFFT' isa 'Bio::Tools::Run::Alignment::MAFFT'
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9 - 42 or 43 expected
> ok 10
> ok 11
> ok 12
> ok 13
> ok 14
> ok 15
> ok 16
> ok 17
> ok 18 # skip Tests require version 6 of MAFFT
> ok 19 # skip Tests require version 6 of MAFFT
> ok 20 # skip Tests require version 6 of MAFFT
> ok 21 # skip Tests require version 6 of MAFFT
> ok 22 # skip Tests require version 6 of MAFFT
> ok 23 # skip Tests require version 6 of MAFFT
> ok
> # Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> t/MSAProbs.t ..................
> 1..19
> ok 1 - use Bio::Tools::Run::Alignment::MSAProbs;
> ok 2 - use Bio::Tools::GuessSeqFormat;
> ok 3 - use Bio::AlignIO;
> ok 4 - use Bio::SeqIO;
> ok 5 - use Bio::Root::IO;
> ok 6 - use POSIX;
> ok 7
> ok 8 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 16 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok 19 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
> ok
> t/Match.t ..................... skipped: The optional module Config::Any (or dependencies thereof) was not installed
> # Required executable for Bio::Tools::Run::Mdust is not present
> t/Mdust.t .....................
> 1..5
> ok 1 - use Bio::Tools::Run::Mdust;
> ok 2 - use Bio::SeqIO;
> ok 3 - An object of class 'Bio::Tools::Run::Mdust' isa 'Bio::Tools::Run::Mdust'
> ok 4 # skip Required executable for Bio::Tools::Run::Mdust is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Mdust is not present
> ok
> # Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> t/Molphy.t ....................
> 1..10
> ok 1 - use Bio::Tools::Phylo::Molphy;
> ok 2 - use Bio::Tools::Run::Phylo::Molphy::ProtML;
> ok 3 - use Bio::AlignIO;
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> ok
> t/Muscle.t ....................
> 1..8
> ok 1 - use Bio::Tools::Run::Alignment::Muscle;
> ok 2 - use Bio::AlignIO;
> ok 3 - use Bio::SeqIO;
> ok 4 - use Bio::Root::IO;
> ok 5 - use POSIX;
> ok 6
> ok 7 - Code tested only on muscle versions > 3.6
> ok 8 - log file
> ok
> t/Neighbor.t ..................
> 1..19
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist;
> ok 2 - use Bio::Tools::Run::Phylo::Phylip::Neighbor;
> ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::Neighbor' isa 'Bio::Tools::Run::Phylo::Phylip::Neighbor'
> ok 4 - couldn't set factory parameter
> ok 5 - couldn't set factory parameter
> ok 6 - couldn't set factory parameter
> ok 7 - couldn't set factory parameter
> ok 8 - couldn't set factory parameter
> ok 9 - couldn't set factory parameter
> ok 10
> ok 11
> ok 12
> ok 13
> ok 14
> ok 15
> ok 16
> ok 17 - failed creating tree by neighbor
> [2J[Hprotdist: can't find input file "infile"
> Please enter a new file name>
> [2J[H
> Protein distance algorithm, version 3.697
>
> Settings for this run:
> P Use JTT, PMB, PAM, Kimura, categories model? Jones-Taylor-Thornton matrix
> G Gamma distribution of rates among positions? No
> C One category of substitution rates? Yes
> W Use weights for positions? No
> M Analyze multiple data sets? No
> I Input sequences interleaved? Yes
> 0 Terminal type (IBM PC, ANSI)? ANSI
> 1 Print out the data at start of run No
> 2 Print indications of progress of run Yes
>
> Are these settings correct? (type Y or the letter for one to change)
>
> Computing distances:
> S01
> S02 .
> S03 ..
> S04 ...
> S05 ....
> S06 .....
> S07 ......
> S08 .......
> S09 ........
> S10 .........
> S11 ..........
> S12 ...........
> S13 ............
> S14 .............
>
> Output written to file "outfile"
>
> Done.
> ok 18 - failed to assign serial names
> ok 19 - failed to restore original names
> ok
> # Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
> t/Njtree.t ....................
> 1..6
> ok 1 - use Bio::Root::IO;
> ok 2 - use Bio::Tools::Run::Phylo::Njtree::Best;
> ok 3 - use Bio::AlignIO;
> ok 4 - use Bio::TreeIO;
> ok 5
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
> ok
> # Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
> t/Pal2Nal.t ...................
> 1..9
> ok 1 - use Bio::Tools::Run::Alignment::Pal2Nal;
> ok 2 - An object of class 'Bio::Tools::Run::Alignment::Pal2Nal' isa 'Bio::Tools::Run::Alignment::Pal2Nal'
> ok 3 - program_dir returned correct default
> ok 4 - Correct exe default name
> ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
> ok
> t/PhastCons.t ................. skipped: The optional module Clone (or dependencies thereof) was not installed
> # Required executable for Bio::Tools::Run::Primate is not present
> t/Primate.t ...................
> 1..8
> ok 1 - use Bio::Tools::Run::Primate;
> ok 2 - use Bio::SeqIO;
> ok 3 # skip Required executable for Bio::Tools::Run::Primate is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Primate is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Primate is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Primate is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Primate is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Primate is not present
> ok
> t/Primer3.t ................... skipped: The optional module Clone (or dependencies thereof) was not installed
> # Required executable for Bio::Tools::Run::Prints is not present
> t/Prints.t ....................
> 1..7
> ok 1 - use Bio::Tools::Run::Prints;
> ok 2 - use Bio::SeqIO;
> ok 3 - use Bio::Seq;
> ok 4 - An object of class 'Bio::Tools::Run::Prints' isa 'Bio::Tools::Run::Prints'
> ok 5 # skip Required executable for Bio::Tools::Run::Prints is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Prints is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Prints is not present
> ok
> # Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> t/Probalign.t .................
> 1..13
> ok 1 - use Bio::Tools::Run::Alignment::Probalign;
> ok 2 - use Bio::AlignIO;
> ok 3 - use Bio::SeqIO;
> ok 4 - use Cwd;
> ok 5 - use POSIX;
> ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present
> ok
>
> PROBCONS version 1.12 - align multiple protein sequences and print to standard output
> Written by Chuong Do
>
> Using parameter set:
> initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 }
> gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 }
> gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 }
>
> Loading sequence file: t/data/cysprot.fa
> Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA))
>
>
>
> PROBCONS version 1.12 - align multiple protein sequences and print to standard output
> Written by Chuong Do
>
> Using parameter set:
> initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 }
> gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 }
> gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 }
>
> Loading sequence file: /tmp/tFK7SHRkaU
> Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA))
>
>
>
> PROBCONS version 1.12 - align multiple protein sequences and print to standard output
> Written by Chuong Do
>
> Using parameter set:
> initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 }
> gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 }
> gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 }
>
> Loading sequence file: /tmp/V9aWT7O_TJ
> Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done.
> Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done.
> Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done.
> Computing posterior matrix: (1) CYS1_DICDI vs. (5) CATL_HUMAN -- done.
> Computing posterior matrix: (1) CYS1_DICDI vs. (6) CATL_RAT -- done.
> Computing posterior matrix: (1) CYS1_DICDI vs. (7) PAPA_CARPA -- done.
> Computing posterior matrix: (2) ALEU_HORVU vs. (3) CATH_HUMAN -- done.
> Computing posterior matrix: (2) ALEU_HORVU vs. (4) CATH_RAT -- done.
> Computing posterior matrix: (2) ALEU_HORVU vs. (5) CATL_HUMAN -- done.
> Computing posterior matrix: (2) ALEU_HORVU vs. (6) CATL_RAT -- done.
> Computing posterior matrix: (2) ALEU_HORVU vs. (7) PAPA_CARPA -- done.
> Computing posterior matrix: (3) CATH_HUMAN vs. (4) CATH_RAT -- done.
> Computing posterior matrix: (3) CATH_HUMAN vs. (5) CATL_HUMAN -- done.
> Computing posterior matrix: (3) CATH_HUMAN vs. (6) CATL_RAT -- done.
> Computing posterior matrix: (3) CATH_HUMAN vs. (7) PAPA_CARPA -- done.
> Computing posterior matrix: (4) CATH_RAT vs. (5) CATL_HUMAN -- done.
> Computing posterior matrix: (4) CATH_RAT vs. (6) CATL_RAT -- done.
> Computing posterior matrix: (4) CATH_RAT vs. (7) PAPA_CARPA -- done.
> Computing posterior matrix: (5) CATL_HUMAN vs. (6) CATL_RAT -- done.
> Computing posterior matrix: (5) CATL_HUMAN vs. (7) PAPA_CARPA -- done.
> Computing posterior matrix: (6) CATL_RAT vs. (7) PAPA_CARPA -- done.
> Trained parameter set:
> initDistrib[] = { 0.8318762183 5.24617426e-05 5.24617426e-05 0.08400939405 0.08400939405 }
> gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 }
> gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 }
>
>
> PROBCONS version 1.12 - align multiple protein sequences and print to standard output
> Written by Chuong Do
>
> Using parameter set:
> initDistrib[] = { 0.8318762183 5.246169894e-05 5.246169894e-05 0.08400939405 0.08400939405 }
> gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 }
> gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 }
>
> Loading sequence file: /tmp/7o03qJ_67y
> Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA))
>
>
> t/Probcons.t ..................
> 1..11
> ok 1 - use Bio::Tools::Run::Alignment::Probcons;
> ok 2 - use Bio::AlignIO;
> ok 3 - use Bio::SeqIO;
> ok 4 - Code tested only on probcons versions > 1.09
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> ok 10
> ok 11
> ok
> # Required executable for Bio::Tools::Run::Profile is not present
> t/Profile.t ...................
> 1..7
> ok 1 - use Bio::Tools::Run::Profile;
> ok 2 - use Bio::SeqIO;
> ok 3 - use Bio::Seq;
> ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile'
> ok 5 # skip Required executable for Bio::Tools::Run::Profile is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Profile is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Profile is not present
> ok
> t/Promoterwise.t ..............
> 1..9
> ok 1 - use Bio::Tools::Run::Promoterwise;
> ok 2 - use Bio::Seq;
> ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise'
> ok 4
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> ok
> t/ProtDist.t ..................
> 1..14
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist;
> ok 2 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 3 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 12 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 13 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 14 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok
> t/ProtPars.t ..................
> 1..11
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtPars;
> ok 2 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtPars' isa 'Bio::Tools::Run::Phylo::Phylip::ProtPars'
> ok 3 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed
> ok
> # Required executable for Bio::Tools::Run::Pseudowise is not present
> t/Pseudowise.t ................
> 1..18
> ok 1 - use Bio::Tools::Run::Pseudowise;
> ok 2 - use Bio::Root::IO;
> ok 3 - use Bio::Seq;
> ok 4
> ok 5 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 16 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Pseudowise is not present
> ok
> # Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> t/QuickTree.t .................
> 1..13
> ok 1 - use Bio::Tools::Run::Phylo::QuickTree;
> ok 2 - use Bio::AlignIO;
> ok 3 - Found input file
> ok 4 - An object of class 'Bio::Tools::Run::Phylo::QuickTree' isa 'Bio::Tools::Run::Phylo::QuickTree'
> ok 5 - program_dir returned correct default
> ok 6 - Correct exe default name
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
> ok
> t/Raxml.t .....................
> 1..12
> ok 1 - use Bio::Root::IO;
> ok 2 - use Bio::Tools::Run::Phylo::Raxml;
> ok 3 - use Bio::AlignIO;
> ok 4 - Make the object
> ok 5 - An object of class 'Bio::Tools::Run::Phylo::Raxml' isa 'Bio::Tools::Run::Phylo::Raxml'
> ok 6 - Tree is defined
> ok 7 - Tree is defined
> ok 8 - File containing best tree exists in tempdir
> ok 9 - Tree is defined
> ok 10 - Tree is defined
> ok 11 - Number of nodes is correct
> ok 12 - Tree is defined
> ok
> # DB and mask make tests
> # run BLAST methods
> t/SABlastPlus.t ...............
> 1..71
> ok 1 - use Bio::Tools::Run::StandAloneBlastPlus;
> ok 2 - use Bio::Tools::Run::WrapperBase;
> ok 3 - use Bio::Tools::Run::WrapperBase::CommandExts;
> ok 4 - BlastPlus factory
> ok 5 - make factory
> ok 6 - test db made with fasta
> ok 7 - temp db
> ok 8 - right type
> ok 9
> ok 10 - named db made
> ok 11 - check_db
> ok 12 - correct name
> ok 13 - dbinfo hash returned
> ok 14 - correct type
> ok 15 - windowmasker mask made
> ok 16 - dustmasker mask made
> ok 17 - check_db with arg
> ok 18 - db_info with arg
> ok 19 - protein db made
> ok 20 - correct type
> ok 21 - segmasker mask made
> ok 22 - segmasker mask made; blastdb as data
> ok 23
> ok 24 - protein db made with pre-built mask
> ok 25 - db_info records mask info
> ok 26
> ok 27 - mask built and db made on construction (windowmasker)
> ok 28
> ok 29 - mask built and db made on construction (segmasker)
> ok 30
> ok 31 - mask built and db made on construction (dustmasker)
> ok 32
> ok 33
> ok 34
> ok 35 - make db from Bio::SeqIO
> ok 36
> ok 37 - make db from Bio::AlignIO
> ok 38
> ok 39 - make db from \@seqs
> ok 40 - dbdir : ./a/b; dbname : test; create
> ok 41 - make db
> ok 42
> ok 43
> ok 44
> ok 45
> ok 46 - run blastn
> ok 47 - default hit limit
> ok 48 - return more alignments (arg spec)
> ok 49 - got more hits
> ok 50 - run blastn with Bio::Seq query
> ok 51 - run tblastn
> ok 52 - tblastn hits
> ok 53 - run tblastx
> ok 54 - tblastx hits
> ok 55
> ok 56 - run blastp
> ok 57 - blastp hits
> ok 58 - bl2seq (blastn)
> ok 59 - got hit
> ok 60 - bl2seq (tblastx)
> ok 61 - got hit
> ok 62 - bl2seq (blastx)
> ok 63 - got hit
> ok 64 - bl2seq (blastp)
> ok 65 - no hit
> ok 66 - bl2seq (blastp)
> ok 67 - got hit
> ok 68 - bl2seq (tblastx) - multiple outfmt options
> ok 69 - bl2seq (tblastx) - multiple outfmt options (use method arg)
> ok 70 - bl2seq (tblastx) - multiple outfmt options (no explict quotes should also work)
> ok 71 - bl2seq (tblastx) - multiple outfmt options (a single format number in quotes
> ok
> # Required executable for Bio::Tools::Run::Phylo::SLR is not present
> t/SLR.t .......................
> 1..7
> ok 1 - use Bio::Root::IO;
> ok 2 - use Bio::Tools::Run::Phylo::SLR;
> ok 3 - use Bio::AlignIO;
> ok 4 - use Bio::TreeIO;
> ok 5
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present
> ok
> t/Samtools.t ..................
> 1..41
> ok 1 - make a factory using command 'pileup'
> ok 2 - parameters changed on construction
> ok 3 - access parameter
> ok 4 - parameters_changed cleared on read
> ok 5 - set a param not set in constructor
> ok 6 - parameters_changed set
> ok 7 - parameter really set
> ok 8 - original parameter unchanged
> ok 9 - parameters_changed cleared on read
> ok 10 - change an original parameter
> ok 11 - parameter really changed
> ok 12 - reset parameters with arg
> ok 13 - original parameters undefined
> ok 14 - parameter really reset via arg
> ok 15 - parameters changed
> ok 16 - all available options
> ok 17 - available parameters
> ok 18 - available switches
> ok 19 - get_parameters correct
> ok 20 - command attribute set
> ok 21 - internal command array set
> ok 22 - internal prefix hash set
> ok 23 - commands filtered by prefix
> ok 24 - translate_params: command correct
> ok 25 - translate_params: options correct
> ok 26 - merge bam factory instantiated
> ok 27 - merged bam file created
> ok 28 - fasta index factory
> ok 29 - make fasta index
> ok 30 - fai file present
> ok 31 - bam -> sam cvt factory
> ok 32 - convert bam -> sam
> ok 33 - sam file present and text
> ok 34 - sam -> bam cvt factory
> ok 35 - convert sam -> bam
> ok 36 - bam file present and binary
> ok 37 - bam sort factory
> ok 38 - sort bam file
> ok 39 - bam index factory
> ok 40 - make bam index
> ok 41 - bai file present and binary
> ok
> # Required executable for Bio::Tools::Run::Seg is not present
> t/Seg.t .......................
> 1..8
> ok 1 - use Bio::Tools::Run::Seg;
> ok 2 - use Bio::SeqIO;
> ok 3 - use Bio::Seq;
> ok 4 - An object of class 'Bio::Tools::Run::Seg' isa 'Bio::Tools::Run::Seg'
> ok 5 # skip Required executable for Bio::Tools::Run::Seg is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Seg is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Seg is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Seg is not present
> ok
> # Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> t/Semphy.t ....................
> 1..19
> ok 1 - use Bio::Tools::Run::Phylo::Semphy;
> ok 2 - An object of class 'Bio::Tools::Run::Phylo::Semphy' isa 'Bio::Tools::Run::Phylo::Semphy'
> ok 3 - has a created method not in args
> ok 4 - ratio param was set via -z
> ok 5 - jtt switch was set
> ok 6 - program_dir returned correct default
> ok 7 - Correct exe default name
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present
> ok
> t/SeqBoot.t ...................
> 1..9
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
> ok 2 - use Bio::AlignIO;
> ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::SeqBoot' isa 'Bio::Tools::Run::Phylo::Phylip::SeqBoot'
> ok 4 - couldn't set datatype parameter
> ok 5 - coludn't set number of replicates
> ok 6
> ok 7
> ok 8 - ailed to assign serial names
> ok 9 - fail to restore original names
> ok
> # Required executable for Bio::Tools::Run::Signalp is not present
> t/Signalp.t ...................
> 1..7
> ok 1 - use Bio::Tools::Run::Signalp;
> ok 2 - use Bio::SeqIO;
> ok 3 - use Bio::Seq;
> ok 4 - An object of class 'Bio::Tools::Run::Signalp' isa 'Bio::Tools::Run::Signalp'
> ok 5 # skip Required executable for Bio::Tools::Run::Signalp is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Signalp is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Signalp is not present
> ok
> t/Sim4.t ......................
> 1..23
> ok 1 - use Bio::Tools::Run::Alignment::Sim4;
> ok 2 - use Bio::SimpleAlign;
> ok 3 - use Bio::AlignIO;
> ok 4 - use Bio::SeqIO;
> ok 5 - An object of class 'Bio::Tools::Run::Alignment::Sim4' isa 'Bio::Tools::Run::Alignment::Sim4'
> 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
> # Required executable for Bio::Tools::Run::Simprot is not present
> t/Simprot.t ...................
> 1..6
> ok 1 - use Bio::Root::IO;
> ok 2 - use Bio::Tools::Run::Simprot;
> ok 3 - use Bio::AlignIO;
> ok 4 - use Bio::TreeIO;
> ok 5
> ok 6 # skip Required executable for Bio::Tools::Run::Simprot is not present
> ok
> t/SoapEU-function.t ........... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed
> t/SoapEU-unit.t ............... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed
> # Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> t/StandAloneFasta.t ...........
> 1..15
> ok 1 - use Bio::Tools::Run::Alignment::StandAloneFasta;
> ok 2 - use Bio::SeqIO;
> ok 3
> ok 4 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
> ok
> # Required executable for Bio::Tools::Run::Tmhmm is not present
> t/Tmhmm.t .....................
> 1..9
> ok 1 - use Bio::Tools::Run::Tmhmm;
> ok 2 - use Bio::SeqIO;
> ok 3 - An object of class 'Bio::Tools::Run::Tmhmm' isa 'Bio::Tools::Run::Tmhmm'
> ok 4 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Tmhmm is not present
> ok
> t/TribeMCL.t .................. skipped: The optional module Bio::Cluster::SequenceFamily (or dependencies thereof) was not installed
> t/Vista.t .....................
> 1..7
> ok 1 - use Bio::Tools::Run::Vista;
> ok 2 - use Bio::AlignIO;
> ok 3 # skip Skipping due to old java version
> ok 4 # skip Skipping due to old java version
> ok 5 # skip Skipping due to old java version
> ok 6 # skip Skipping due to old java version
> ok 7 # skip Skipping due to old java version
> ok
> # Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> t/gmap-run.t ..................
> 1..8
> ok 1 - use Bio::Tools::Run::Alignment::Gmap;
> ok 2 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> ok 3 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present
> ok
> # Required executable for Bio::Tools::Run::tRNAscanSE is not present
> t/tRNAscanSE.t ................
> 1..12
> ok 1 - use Bio::Tools::Run::tRNAscanSE;
> ok 2 - use Bio::Root::IO;
> ok 3 - use Bio::Seq;
> ok 4 - An object of class 'Bio::Tools::Run::tRNAscanSE' isa 'Bio::Tools::Run::tRNAscanSE'
> ok 5 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok 6 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok 7 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok 8 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present
> ok
>
> Test Summary Report
> -------------------
> t/Kalign.t (Wstat: 6400 Tests: 5 Failed: 2)
> Failed tests: 4-5
> Non-zero exit status: 25
> Parse errors: Bad plan. You planned 8 tests but ran 5.
> Files=60, Tests=998, 23 wallclock secs ( 0.17 usr 0.08 sys + 22.74 cusr 2.21 csys = 25.20 CPU)
> Result: FAIL
> Failed 1/60 test programs. 2/998 subtests failed.
> dh_auto_test: error: perl Build test --verbose 1 returned exit code 255
The full build log is available from:
http://qa-logs.debian.net/2020/03/21/bioperl-run_1.7.3-3_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
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