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.