Your message dated Wed, 01 Apr 2020 13:18:33 +0000
with message-id <e1jjdgl-000auy...@fasolo.debian.org>
and subject line Bug#954511: fixed in bioperl-run 1.7.3-4
has caused the Debian Bug report #954511,
regarding bioperl-run: FTBFS: dh_auto_test: error: perl Build test --verbose 1
returned exit code 255
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
954511: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954511
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: bioperl-run
Source-Version: 1.7.3-4
Done: Pranav Ballaney <ballaneypra...@gmail.com>
We believe that the bug you reported is fixed in the latest version of
bioperl-run, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 954...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pranav Ballaney <ballaneypra...@gmail.com> (supplier of updated bioperl-run
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 31 Mar 2020 01:13:25 +0530
Source: bioperl-run
Architecture: source
Version: 1.7.3-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Pranav Ballaney <ballaneypra...@gmail.com>
Closes: 954511
Changes:
bioperl-run (1.7.3-4) unstable; urgency=medium
.
[ Michael R. Crusoe ]
* Team upload.
* Fix the autopkgtests
* Set 'Bio::Factory::EMBOSS' as the main module name for the purpose of
the use.t autopkgtest
* fix hyphympi autopkgtests
* libipc-run-perl is needed for Bio::Tools::Run::BEDTools
* drawgram is pary of the phylip package
.
[ Pranav Ballaney ]
* Change kalign command string to input via stdin It fails to take input
via the -in flag during testing
* Revert changes made outside of debian/
* Update quilt version
* Kalign takes input via a pipe
* Extract Kalign version properly (Closes: #954511)
.
[ Andreas Tille ]
* Standards-Version: 4.5.0 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Wrap long lines in changelog entries: 1.7.2-1.
* Set upstream metadata fields: Bug-Submit.
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bioperl-run_1.7.3-4.debian.tar.xz
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bioperl-run_1.7.3-4_amd64.buildinfo
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55e410fb8eb5e601bf5b1b09a75f79d5 14636 science optional
bioperl-run_1.7.3-4.debian.tar.xz
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bioperl-run_1.7.3-4_amd64.buildinfo
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--- End Message ---
