Your message dated Sun, 01 Dec 2024 10:34:09 +0000
with message-id <[email protected]>
and subject line Bug#1077454: fixed in bioperl-run 1.7.3-13
has caused the Debian Bug report #1077454,
regarding bioperl-run: FTBFS: dh_auto_test: error: /usr/bin/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 [email protected]
immediately.)
--
1077454: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1077454
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: bioperl-run
Version: 1.7.3-11
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-20240728 ftbfs-trixie
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 RepeatMasker Phyml Hyphy MCS ; do mv t/${t}.t
> t.skip ; done
> PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin
> \
> PHYLIPDIR=/usr/lib/phylip/bin HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/
> \
> dh_auto_test --no-parallel
> /usr/bin/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/fX0DPN3b3w
> 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 ..................
> 1..423
> ok 1 - make a default factory
> ok 2 - default to command 'bam_to_bed'
> ok 3 - make a factory using command 'annotate'
> ok 4 - factory command for 'annotate' is correct
> ok 5 - all available options for 'annotate'
> ok 6 - available parameters for 'annotate'
> ok 7 - available switches for 'annotate'
> ok 8 - get version for 'annotate'
> ok 9 - can run command 'annotate'
> ok 10 - result files exists for command 'annotate'
> ok 11 - can return output format for command 'annotate'
> ok 12 - result claims to be in correct format for command 'annotate'
> ok 13 - can return output file for command 'annotate'
> ok 14 - file format of '/tmp/kkC7ThWHQe/wnoZSRbChD.bed' consistent with claim
> for 'annotate'
> ok 15 - can set want to IO object for command 'annotate'
> ok 16 - can get the basic object result for command 'annotate'
> ok 17 - 'returned object is correct for command 'annotate'' isa
> 'Bio::Root::IO'
> ok 18 - can get the specific object result for command 'annotate'
> ok 19 - 'returned object is correct for command 'annotate'' isa
> 'Bio::SeqFeature::Collection'
> ok 20 - correct number of features for command 'annotate' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 21 - make a factory using command 'fasta_from_bed'
> ok 22 - factory command for 'fasta_from_bed' is correct
> ok 23 - all available options for 'fasta_from_bed'
> ok 24 - available parameters for 'fasta_from_bed'
> ok 25 - available switches for 'fasta_from_bed'
> ok 26 - get version for 'fasta_from_bed'
> ok 27 - can run command 'fasta_from_bed'
> ok 28 - result files exists for command 'fasta_from_bed'
> ok 29 - can return output format for command 'fasta_from_bed'
> ok 30 - result claims to be in correct format for command 'fasta_from_bed'
> ok 31 - can return output file for command 'fasta_from_bed'
> ok 32 - file format consistent with claim for 'fasta_from_bed'
> ok 33 - can set want to IO object for command 'fasta_from_bed'
> ok 34 - can get the basic object result for command 'fasta_from_bed'
> ok 35 - 'returned object is correct for command 'fasta_from_bed'' isa
> 'Bio::Root::IO'
> ok 36 - can get the specific object result for command 'fasta_from_bed'
> ok 37 - 'returned object is correct for command 'fasta_from_bed'' isa
> 'Bio::SeqIO'
> ok 38 - correct number of sequences for command 'fasta_from_bed'
> ok 39 - make a factory using command 'overlap'
> ok 40 - factory command for 'overlap' is correct
> ok 41 - all available options for 'overlap'
> ok 42 - available parameters for 'overlap'
> ok 43 - available switches for 'overlap'
> ok 44 - get version for 'overlap'
> ok 45 - can set parameter -columns => '2,3,5,6'
> ok 46 - can run command 'overlap'
> ok 47 - result files exists for command 'overlap'
> ok 48 - can return output format for command 'overlap'
> ok 49 - result claims to be in correct format for command 'overlap'
> ok 50 - can return output file for command 'overlap'
> ok 51 - file format of '/tmp/SUxP03nUzv/Vd4iG3DfxM.bed' consistent with claim
> for 'overlap'
> ok 52 - can set want to IO object for command 'overlap'
> ok 53 - can get the basic object result for command 'overlap'
> ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO'
> ok 55 - can get the specific object result for command 'overlap'
> ok 56 - 'returned object is correct for command 'overlap'' isa
> 'Bio::SeqFeature::Collection'
> ok 57 - correct number of features for command 'overlap' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 58 - make a factory using command 'bam_to_bed'
> ok 59 - factory command for 'bam_to_bed' is correct
> ok 60 - all available options for 'bam_to_bed'
> ok 61 - available parameters for 'bam_to_bed'
> ok 62 - available switches for 'bam_to_bed'
> ok 63 - get version for 'bam_to_bed'
> ok 64 - can run command 'bam_to_bed'
> ok 65 - result files exists for command 'bam_to_bed'
> ok 66 - can return output format for command 'bam_to_bed'
> ok 67 - result claims to be in correct format for command 'bam_to_bed'
> ok 68 - can return output file for command 'bam_to_bed'
> ok 69 - file format of '/tmp/T23LNsl5n4/YTZ5GqMRzu.bed' consistent with claim
> for 'bam_to_bed'
> ok 70 - can set want to IO object for command 'bam_to_bed'
> ok 71 - can get the basic object result for command 'bam_to_bed'
> ok 72 - 'returned object is correct for command 'bam_to_bed'' isa
> 'Bio::Root::IO'
> ok 73 - can get the specific object result for command 'bam_to_bed'
> ok 74 - 'returned object is correct for command 'bam_to_bed'' isa
> 'Bio::SeqFeature::Collection'
> ok 75 - correct number of features for command 'bam_to_bed' # TODO maybe
> adapt reference results to Debian specific dataset
> ok 76 - make a factory using command 'genome_coverage'
> ok 77 - factory command for 'genome_coverage' is correct
> ok 78 - all available options for 'genome_coverage'
> ok 79 - available parameters for 'genome_coverage'
> ok 80 - available switches for 'genome_coverage'
> ok 81 - get version for 'genome_coverage'
> ok 82 - can run command 'genome_coverage'
> ok 83 - result files exists for command 'genome_coverage'
> ok 84 - can return output format for command 'genome_coverage'
> ok 85 - result claims to be in correct format for command 'genome_coverage'
> ok 86 - can return output file for command 'genome_coverage'
> ok 87 - make readable output
> ok 88 - - number of lines # TODO maybe adapt reference results to Debian
> specific dataset
> ok 89 - can set want to IO object for command 'genome_coverage'
> ok 90 - can get the basic object result for command 'genome_coverage'
> ok 91 - 'returned object is correct for command 'genome_coverage'' isa
> 'Bio::Root::IO'
> ok 92 - make a factory using command 'pair_to_pair'
> ok 93 - factory command for 'pair_to_pair' is correct
> ok 94 - all available options for 'pair_to_pair'
> ok 95 - available parameters for 'pair_to_pair'
> ok 96 - available switches for 'pair_to_pair'
> ok 97 - get version for 'pair_to_pair'
> ok 98 - can set parameter -type => 'neither'
> ok 99 - can run command 'pair_to_pair'
> ok 100 - result files exists for command 'pair_to_pair'
> ok 101 - can return output format for command 'pair_to_pair'
> ok 102 - result claims to be in correct format for command 'pair_to_pair'
> ok 103 - can return output file for command 'pair_to_pair'
> ok 104 - file format of '/tmp/JFfFlV2Qiq/NgTB6RnIlB.bedpe' consistent with
> claim for 'pair_to_pair'
> ok 105 - can set want to IO object for command 'pair_to_pair'
> ok 106 - can get the basic object result for command 'pair_to_pair'
> ok 107 - 'returned object is correct for command 'pair_to_pair'' isa
> 'Bio::Root::IO'
> ok 108 - can get the specific object result for command 'pair_to_pair'
> ok 109 - 'returned object is correct for command 'pair_to_pair'' isa
> 'Bio::SeqFeature::Collection'
> ok 110 - correct number of features for command 'pair_to_pair' # TODO maybe
> adapt reference results to Debian specific dataset
> ok 111 - make a factory using command 'bed_to_bam'
> ok 112 - factory command for 'bed_to_bam' is correct
> ok 113 - all available options for 'bed_to_bam'
> ok 114 - available parameters for 'bed_to_bam'
> ok 115 - available switches for 'bed_to_bam'
> ok 116 - get version for 'bed_to_bam'
> ok 117 - can run command 'bed_to_bam'
> ok 118 - result files exists for command 'bed_to_bam'
> ok 119 - can return output format for command 'bed_to_bam'
> ok 120 - result claims to be in correct format for command 'bed_to_bam'
> ok 121 - can return output file for command 'bed_to_bam'
> ok 122 - can set want to IO object for command 'bed_to_bam'
> ok 123 - can get the basic object result for command 'bed_to_bam'
> ok 124 - 'returned object is correct for command 'bed_to_bam'' isa
> 'Bio::Root::IO'
> ok 125 - make a factory using command 'graph_union'
> ok 126 - factory command for 'graph_union' is correct
> ok 127 - all available options for 'graph_union'
> ok 128 - available parameters for 'graph_union'
> ok 129 - available switches for 'graph_union'
> ok 130 - get version for 'graph_union'
> ok 131 - can run command 'graph_union'
> ok 132 - result files exists for command 'graph_union'
> ok 133 - can return output format for command 'graph_union'
> ok 134 - result claims to be in correct format for command 'graph_union'
> ok 135 - can return output file for command 'graph_union'
> ok 136 - can set want to IO object for command 'graph_union'
> ok 137 - can get the basic object result for command 'graph_union'
> ok 138 - 'returned object is correct for command 'graph_union'' isa
> 'Bio::Root::IO'
> ok 139 - make a factory using command 'pair_to_bed'
> ok 140 - factory command for 'pair_to_bed' is correct
> ok 141 - all available options for 'pair_to_bed'
> ok 142 - available parameters for 'pair_to_bed'
> ok 143 - available switches for 'pair_to_bed'
> ok 144 - get version for 'pair_to_bed'
> ok 145 - can run command 'pair_to_bed'
> ok 146 - result files exists for command 'pair_to_bed'
> ok 147 - can return output format for command 'pair_to_bed'
> ok 148 - result claims to be in correct format for command 'pair_to_bed'
> ok 149 - can return output file for command 'pair_to_bed'
> ok 150 - can set want to IO object for command 'pair_to_bed'
> ok 151 - can get the basic object result for command 'pair_to_bed'
> ok 152 - 'returned object is correct for command 'pair_to_bed'' isa
> 'Bio::Root::IO'
> ok 153 - can get the specific object result for command 'pair_to_bed'
> ok 154 - 'returned object is correct for command 'pair_to_bed'' isa
> 'Bio::SeqFeature::Collection'
> ok 155 - correct number of features for command 'pair_to_bed' # TODO maybe
> adapt reference results to Debian specific dataset
> ok 156 - make a factory using command 'bed_to_IGV'
> ok 157 - factory command for 'bed_to_IGV' is correct
> ok 158 - all available options for 'bed_to_IGV'
> ok 159 - available parameters for 'bed_to_IGV'
> ok 160 - available switches for 'bed_to_IGV'
> ok 161 - get version for 'bed_to_IGV'
> ok 162 - can run command 'bed_to_IGV'
> ok 163 - result files exists for command 'bed_to_IGV'
> ok 164 - can return output format for command 'bed_to_IGV'
> ok 165 - result claims to be in correct format for command 'bed_to_IGV'
> ok 166 - can return output file for command 'bed_to_IGV'
> ok 167 - can set want to IO object for command 'bed_to_IGV'
> ok 168 - can get the basic object result for command 'bed_to_IGV'
> ok 169 - 'returned object is correct for command 'bed_to_IGV'' isa
> 'Bio::Root::IO'
> ok 170 - make a factory using command 'group_by'
> ok 171 - factory command for 'group_by' is correct
> ok 172 - all available options for 'group_by'
> ok 173 - available parameters for 'group_by'
> ok 174 - available switches for 'group_by'
> ok 175 - get version for 'group_by'
> ok 176 - can set parameter -group => 1
> ok 177 - can set parameter -columns => '2,2,3,3'
> ok 178 - can set parameter -operations => 'min,max,min,max'
> ok 179 - can run command 'group_by'
> ok 180 - result files exists for command 'group_by'
> ok 181 - can return output format for command 'group_by'
> ok 182 - result claims to be in correct format for command 'group_by'
> ok 183 - can return output file for command 'group_by'
> ok 184 - file format of '/tmp/o0tYeyHwCy/EPCpWUxQoR.bed' consistent with
> claim for 'group_by'
> ok 185 - can set want to IO object for command 'group_by'
> ok 186 - can get the basic object result for command 'group_by'
> ok 187 - 'returned object is correct for command 'group_by'' isa
> 'Bio::Root::IO'
> ok 188 - can get the specific object result for command 'group_by'
> ok 189 - 'returned object is correct for command 'group_by'' isa
> 'Bio::SeqFeature::Collection'
> ok 190 - correct number of features for command 'group_by' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 191 - make a factory using command 'shuffle'
> ok 192 - factory command for 'shuffle' is correct
> ok 193 - all available options for 'shuffle'
> ok 194 - available parameters for 'shuffle'
> ok 195 - available switches for 'shuffle'
> ok 196 - get version for 'shuffle'
> ok 197 - can run command 'shuffle'
> ok 198 - result files exists for command 'shuffle'
> ok 199 - can return output format for command 'shuffle'
> ok 200 - result claims to be in correct format for command 'shuffle'
> ok 201 - can return output file for command 'shuffle'
> ok 202 - file format of '/tmp/QHEQsFSmzs/P8ifTUhWsb.bed' consistent with
> claim for 'shuffle'
> ok 203 - can set want to IO object for command 'shuffle'
> ok 204 - can get the basic object result for command 'shuffle'
> ok 205 - 'returned object is correct for command 'shuffle'' isa
> 'Bio::Root::IO'
> ok 206 - can get the specific object result for command 'shuffle'
> ok 207 - 'returned object is correct for command 'shuffle'' isa
> 'Bio::SeqFeature::Collection'
> ok 208 - correct number of features for command 'shuffle' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 209 - make a factory using command 'b12_to_b6'
> ok 210 - factory command for 'b12_to_b6' is correct
> ok 211 - all available options for 'b12_to_b6'
> ok 212 - available parameters for 'b12_to_b6'
> ok 213 - available switches for 'b12_to_b6'
> ok 214 - get version for 'b12_to_b6'
> ok 215 - can run command 'b12_to_b6'
> ok 216 - result files exists for command 'b12_to_b6'
> ok 217 - can return output format for command 'b12_to_b6'
> ok 218 - result claims to be in correct format for command 'b12_to_b6'
> ok 219 - can return output file for command 'b12_to_b6'
> ok 220 - file format of '/tmp/WJDM_snXJN/uhCPinlTbh.bed' consistent with
> claim for 'b12_to_b6'
> ok 221 - can set want to IO object for command 'b12_to_b6'
> ok 222 - can get the basic object result for command 'b12_to_b6'
> ok 223 - 'returned object is correct for command 'b12_to_b6'' isa
> 'Bio::Root::IO'
> ok 224 - can get the specific object result for command 'b12_to_b6'
> ok 225 - 'returned object is correct for command 'b12_to_b6'' isa
> 'Bio::SeqFeature::Collection'
> ok 226 - correct number of features for command 'b12_to_b6' # TODO maybe
> adapt reference results to Debian specific dataset
> ok 227 - make a factory using command 'intersect'
> ok 228 - factory command for 'intersect' is correct
> ok 229 - all available options for 'intersect'
> ok 230 - available parameters for 'intersect'
> ok 231 - available switches for 'intersect'
> ok 232 - get version for 'intersect'
> ok 233 - can run command 'intersect'
> ok 234 - result files exists for command 'intersect'
> ok 235 - can return output format for command 'intersect'
> ok 236 - result claims to be in correct format for command 'intersect'
> ok 237 - can return output file for command 'intersect'
> ok 238 - can set want to IO object for command 'intersect'
> ok 239 - can get the basic object result for command 'intersect'
> ok 240 - 'returned object is correct for command 'intersect'' isa
> 'Bio::Root::IO'
> ok 241 - can get the specific object result for command 'intersect'
> ok 242 - 'returned object is correct for command 'intersect'' isa
> 'Bio::SeqFeature::Collection'
> not ok 243 - correct number of features for command 'intersect' # TODO maybe
> adapt reference results to Debian specific dataset
> # Failed (TODO) test 'correct number of features for command 'intersect''
> # at t/BEDTools.t line 364.
> # got: '1305'
> # expected: '72534'
> ok 244 - make a factory using command 'slop'
> ok 245 - factory command for 'slop' is correct
> ok 246 - all available options for 'slop'
> ok 247 - available parameters for 'slop'
> ok 248 - available switches for 'slop'
> ok 249 - get version for 'slop'
> ok 250 - can set parameter -add_bidirectional => 100
> ok 251 - can run command 'slop'
> ok 252 - result files exists for command 'slop'
> ok 253 - can return output format for command 'slop'
> ok 254 - result claims to be in correct format for command 'slop'
> ok 255 - can return output file for command 'slop'
> ok 256 - file format of '/tmp/iPzkxglpxF/mJRv8Iex3_.bed' consistent with
> claim for 'slop'
> ok 257 - can set want to IO object for command 'slop'
> ok 258 - can get the basic object result for command 'slop'
> ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO'
> ok 260 - can get the specific object result for command 'slop'
> ok 261 - 'returned object is correct for command 'slop'' isa
> 'Bio::SeqFeature::Collection'
> ok 262 - correct number of features for command 'slop' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 263 - make a factory using command 'closest'
> ok 264 - factory command for 'closest' is correct
> ok 265 - all available options for 'closest'
> ok 266 - available parameters for 'closest'
> ok 267 - available switches for 'closest'
> ok 268 - get version for 'closest'
> ok 269 - can run command 'closest'
> ok 270 - result files exists for command 'closest'
> ok 271 - can return output format for command 'closest'
> ok 272 - result claims to be in correct format for command 'closest'
> ok 273 - can return output file for command 'closest'
> ok 274 - file format of '/tmp/q2G4QtvBGE/27prIpT2yI.bedpe' consistent with
> claim for 'closest'
> ok 275 - can set want to IO object for command 'closest'
> ok 276 - can get the basic object result for command 'closest'
> ok 277 - 'returned object is correct for command 'closest'' isa
> 'Bio::Root::IO'
> ok 278 - can get the specific object result for command 'closest'
> ok 279 - 'returned object is correct for command 'closest'' isa
> 'Bio::SeqFeature::Collection'
> ok 280 - correct number of features for command 'closest' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 281 - make a factory using command 'links'
> ok 282 - factory command for 'links' is correct
> ok 283 - all available options for 'links'
> ok 284 - available parameters for 'links'
> ok 285 - available switches for 'links'
> ok 286 - get version for 'links'
> ok 287 - can run command 'links'
> ok 288 - result files exists for command 'links'
> ok 289 - can return output format for command 'links'
> ok 290 - result claims to be in correct format for command 'links'
> ok 291 - can return output file for command 'links'
> ok 292 - make readable output
> ok 293 - - html tag line
> ok 294 - - number of lines
> ok 295 - can set want to IO object for command 'links'
> ok 296 - can get the basic object result for command 'links'
> ok 297 - 'returned object is correct for command 'links'' isa 'Bio::Root::IO'
> ok 298 - make a factory using command 'sort'
> ok 299 - factory command for 'sort' is correct
> ok 300 - all available options for 'sort'
> ok 301 - available parameters for 'sort'
> ok 302 - available switches for 'sort'
> ok 303 - get version for 'sort'
> ok 304 - can run command 'sort'
> ok 305 - result files exists for command 'sort'
> ok 306 - can return output format for command 'sort'
> ok 307 - result claims to be in correct format for command 'sort'
> ok 308 - can return output file for command 'sort'
> ok 309 - file format of '/tmp/QiNllRhT_q/94IDJciMyO.bed' consistent with
> claim for 'sort'
> ok 310 - can set want to IO object for command 'sort'
> ok 311 - can get the basic object result for command 'sort'
> ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO'
> ok 313 - can get the specific object result for command 'sort'
> ok 314 - 'returned object is correct for command 'sort'' isa
> 'Bio::SeqFeature::Collection'
> ok 315 - correct number of features for command 'sort' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 316 - make a factory using command 'complement'
> ok 317 - factory command for 'complement' is correct
> ok 318 - all available options for 'complement'
> ok 319 - available parameters for 'complement'
> ok 320 - available switches for 'complement'
> ok 321 - get version for 'complement'
> ok 322 - can run command 'complement'
> ok 323 - result files exists for command 'complement'
> ok 324 - can return output format for command 'complement'
> ok 325 - result claims to be in correct format for command 'complement'
> ok 326 - can return output file for command 'complement'
> ok 327 - file format of '/tmp/nANjqsBrCZ/GTMXBHntt3.bed' consistent with
> claim for 'complement'
> ok 328 - can set want to IO object for command 'complement'
> ok 329 - can get the basic object result for command 'complement'
> ok 330 - 'returned object is correct for command 'complement'' isa
> 'Bio::Root::IO'
> ok 331 - can get the specific object result for command 'complement'
> ok 332 - 'returned object is correct for command 'complement'' isa
> 'Bio::SeqFeature::Collection'
> ok 333 - correct number of features for command 'complement' # TODO maybe
> adapt reference results to Debian specific dataset
> ok 334 - make a factory using command 'mask_fasta_from_bed'
> ok 335 - factory command for 'mask_fasta_from_bed' is correct
> ok 336 - all available options for 'mask_fasta_from_bed'
> ok 337 - available parameters for 'mask_fasta_from_bed'
> ok 338 - available switches for 'mask_fasta_from_bed'
> ok 339 - get version for 'mask_fasta_from_bed'
> ok 340 - can run command 'mask_fasta_from_bed'
> ok 341 - result files exists for command 'mask_fasta_from_bed'
> ok 342 - can return output format for command 'mask_fasta_from_bed'
> ok 343 - result claims to be in correct format for command
> 'mask_fasta_from_bed'
> ok 344 - can return output file for command 'mask_fasta_from_bed'
> ok 345 - file format consistent with claim for 'mask_fasta_from_bed'
> ok 346 - can set want to IO object for command 'mask_fasta_from_bed'
> ok 347 - can get the basic object result for command 'mask_fasta_from_bed'
> ok 348 - 'returned object is correct for command 'mask_fasta_from_bed'' isa
> 'Bio::Root::IO'
> ok 349 - can get the specific object result for command 'mask_fasta_from_bed'
> ok 350 - 'returned object is correct for command 'mask_fasta_from_bed'' isa
> 'Bio::SeqIO'
> ok 351 - correct number of sequences for command 'mask_fasta_from_bed'
> ok 352 - make a factory using command 'subtract'
> ok 353 - factory command for 'subtract' is correct
> ok 354 - all available options for 'subtract'
> ok 355 - available parameters for 'subtract'
> ok 356 - available switches for 'subtract'
> ok 357 - get version for 'subtract'
> ok 358 - can run command 'subtract'
> ok 359 - result files exists for command 'subtract'
> ok 360 - can return output format for command 'subtract'
> ok 361 - result claims to be in correct format for command 'subtract'
> ok 362 - can return output file for command 'subtract'
> ok 363 - file format of '/tmp/qaukvcBZH8/8Vz23hH1dR.bed' consistent with
> claim for 'subtract'
> ok 364 - can set want to IO object for command 'subtract'
> ok 365 - can get the basic object result for command 'subtract'
> ok 366 - 'returned object is correct for command 'subtract'' isa
> 'Bio::Root::IO'
> ok 367 - can get the specific object result for command 'subtract'
> ok 368 - 'returned object is correct for command 'subtract'' isa
> 'Bio::SeqFeature::Collection'
> not ok 369 - correct number of features for command 'subtract' # TODO maybe
> adapt reference results to Debian specific dataset
> # Failed (TODO) test 'correct number of features for command 'subtract''
> # at t/BEDTools.t line 364.
> # got: '1802'
> # expected: '57959'
> ok 370 - make a factory using command 'coverage'
> ok 371 - factory command for 'coverage' is correct
> ok 372 - all available options for 'coverage'
> ok 373 - available parameters for 'coverage'
> ok 374 - available switches for 'coverage'
> ok 375 - get version for 'coverage'
> ok 376 - can run command 'coverage'
> ok 377 - result files exists for command 'coverage'
> ok 378 - can return output format for command 'coverage'
> ok 379 - result claims to be in correct format for command 'coverage'
> ok 380 - can return output file for command 'coverage'
> ok 381 - file format of '/tmp/Zkfu6NxqYp/wbDMxWpLo0.bed' consistent with
> claim for 'coverage'
> ok 382 - can set want to IO object for command 'coverage'
> ok 383 - can get the basic object result for command 'coverage'
> ok 384 - 'returned object is correct for command 'coverage'' isa
> 'Bio::Root::IO'
> ok 385 - can get the specific object result for command 'coverage'
> ok 386 - 'returned object is correct for command 'coverage'' isa
> 'Bio::SeqFeature::Collection'
> not ok 387 - correct number of features for command 'coverage' # TODO maybe
> adapt reference results to Debian specific dataset
> # Failed (TODO) test 'correct number of features for command 'coverage''
> # at t/BEDTools.t line 364.
> # got: '828'
> # expected: '57261'
> ok 388 - make a factory using command 'merge'
> ok 389 - factory command for 'merge' is correct
> ok 390 - all available options for 'merge'
> ok 391 - available parameters for 'merge'
> ok 392 - available switches for 'merge'
> ok 393 - get version for 'merge'
> ok 394 - can run command 'merge'
> ok 395 - result files exists for command 'merge'
> ok 396 - can return output format for command 'merge'
> ok 397 - result claims to be in correct format for command 'merge'
> ok 398 - can return output file for command 'merge'
> ok 399 - file format of '/tmp/Uu7GCLEcES/xYT_TEr10M.bed' consistent with
> claim for 'merge'
> ok 400 - can set want to IO object for command 'merge'
> ok 401 - can get the basic object result for command 'merge'
> ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO'
> ok 403 - can get the specific object result for command 'merge'
> ok 404 - 'returned object is correct for command 'merge'' isa
> 'Bio::SeqFeature::Collection'
> ok 405 - correct number of features for command 'merge' # TODO maybe adapt
> reference results to Debian specific dataset
> ok 406 - make a factory using command 'window'
> ok 407 - factory command for 'window' is correct
> ok 408 - all available options for 'window'
> ok 409 - available parameters for 'window'
> ok 410 - available switches for 'window'
> ok 411 - get version for 'window'
> ok 412 - can run command 'window'
> ok 413 - result files exists for command 'window'
> ok 414 - can return output format for command 'window'
> ok 415 - result claims to be in correct format for command 'window'
> ok 416 - can return output file for command 'window'
> ok 417 - file format of '/tmp/caciJtXgnS/KtgAMNzBNw.bedpe' consistent with
> claim for 'window'
> ok 418 - can set want to IO object for command 'window'
> ok 419 - can get the basic object result for command 'window'
> ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO'
> ok 421 - can get the specific object result for command 'window'
> ok 422 - 'returned object is correct for command 'window'' isa
> 'Bio::SeqFeature::Collection'
> not ok 423 - correct number of features for command 'window' # TODO maybe
> adapt reference results to Debian specific dataset
> # Failed (TODO) test 'correct number of features for command 'window''
> # at t/BEDTools.t line 364.
> # got: '1331'
> # expected: '74998'
> ok
> # 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
> # Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not
> present
> t/Consense.t ..................
> 1..8
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense;
> ok 2 - use Bio::AlignIO;
> ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense
> is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense
> is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense
> is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense
> is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense
> is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense
> is not present
> 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
> # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not
> present
> t/DrawGram.t ..................
> 1..6
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram;
> ok 2 - use Bio::TreeIO;
> ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram
> is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram
> is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram
> is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram
> is not present
> ok
> # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not
> present
> t/DrawTree.t ..................
> 1..6
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree;
> ok 2 - use Bio::TreeIO;
> ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree
> is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree
> is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree
> is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree
> is not present
> 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
> 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 - Tree is defined
> ok 6 - Number of nodes is correct
> ok 7 - Tree is defined
> ok 8 - Tree is defined
> ok 9 - Tree is defined
> 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
> t/Kalign.t ....................
> 1..7
> ok 1 - use Bio::Tools::Run::Alignment::Kalign;
> ok 2 - use Bio::AlignIO;
> ok 3 - use Bio::SeqIO;
> ok 4 - Code tested only on kalign versions >= 2
>
> Kalign (3.4.0)
>
> Copyright (C) 2006,2019,2020,2021,2023 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
>
> [2024-07-28 17:54:29] : LOG : Detected protein sequences.
> [2024-07-28 17:54:29] : LOG : Read 7 sequences from standard input.
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed:
> 00:00:00.00
> [2024-07-28 17:54:29] : LOG : Calculating pairwise distances
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed:
> 00:00:00.00
> [2024-07-28 17:54:29] : LOG : Building guide tree.
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed:
> 00:00:00.00
> [2024-07-28 17:54:29] : LOG : Aligning
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed:
> 00:00:00.00
> ok 5
> ok 6
>
> Kalign (3.4.0)
>
> Copyright (C) 2006,2019,2020,2021,2023 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
>
> [2024-07-28 17:54:29] : LOG : Detected protein sequences.
> [2024-07-28 17:54:29] : LOG : Read 7 sequences from standard input.
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed:
> 00:00:00.00
> [2024-07-28 17:54:29] : LOG : Calculating pairwise distances
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed:
> 00:00:00.00
> [2024-07-28 17:54:29] : LOG : Building guide tree.
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed:
> 00:00:00.00
> [2024-07-28 17:54:29] : LOG : Aligning
> [2024-07-28 17:54:29] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed:
> 00:00:00.00
> ok 7
> ok
> # 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
> # Required executable for Bio::Tools::Run::Match is not present
> t/Match.t .....................
> 1..7
> ok 1 - use Bio::Tools::Run::Match;
> ok 2 - An object of class 'Bio::Tools::Run::Match' isa
> 'Bio::Tools::Run::Match'
> ok 3 - mxlib parameter was set
> ok 4 - program_dir returned correct default
> ok 5 - Correct exe default name
> ok 6 # skip Required executable for Bio::Tools::Run::Match is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Match is not present
> ok
> # 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..16
> 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 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 8 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 9 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 10 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 11 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 12 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 13 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 14 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 15 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok 16 # skip Only muscle version 3.6 or higher is supported by these tests.
> Skipping tests
> ok
> # Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not
> present
> 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 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor
> is not present
> 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
>
> --------------------- WARNING ---------------------
> MSG: In sequence pseudogene residue count gives end value 183.
> Overriding value [178] with value 183 for Bio::LocatableSeq::end().
> ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: In sequence pseudogene residue count gives end value 183.
> Overriding value [178] with value 183 for Bio::LocatableSeq::end().
> ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND
> ---------------------------------------------------
> 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
> ok 6 - use Bio::AlignIO;
> ok 7 - use Bio::SeqIO;
> ok 8
> ok 9
> ok
> # Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not
> present
> t/PhastCons.t .................
> 1..181
> ok 1 - use Bio::AlignIO;
> ok 2 - use Bio::TreeIO;
> ok 3 - use Bio::DB::Taxonomy;
> ok 4 - Found input alignment file
> ok 5 - Found input tree file
> ok 6 - use Bio::Tools::Run::Phylo::Phast::PhastCons;
> ok 7 - An object of class 'Bio::Tools::Run::Phylo::Phast::PhastCons' isa
> 'Bio::Tools::Run::Phylo::Phast::PhastCons'
> ok 8 - has a created method not in args
> ok 9 - dashed parameter with internal dash was set
> ok 10 - wrong-case method wasn't created
> ok 11 - dashless wrong-case parameter was set
> ok 12 - synonym installed and accessed primary value
> ok 13 - double-dashed parameter was set
> ok 14 - program_dir returned correct default
> ok 15 - Correct exe default name
> ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 34 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 35 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 36 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 37 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 38 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 39 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 40 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 41 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 42 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 43 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 44 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 45 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 46 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 47 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 48 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 49 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 50 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 51 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 52 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 53 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 54 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 55 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 56 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 57 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 58 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 59 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 60 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 61 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 62 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 63 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 64 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 65 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 66 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 67 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 68 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 69 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 70 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 71 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 72 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 73 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 74 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 75 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 76 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 77 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 78 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 79 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 80 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 81 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 82 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 83 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 84 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 85 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 86 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 87 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 88 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 89 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 90 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 91 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 92 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 93 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 94 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 95 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 96 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 97 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 98 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 99 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons
> is not present
> ok 100 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 101 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 102 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 103 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 104 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 105 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 106 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 107 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 108 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 109 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 110 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 111 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 112 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 113 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 114 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 115 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 116 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 117 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 118 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 119 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 120 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 121 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 122 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 123 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 124 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 125 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 126 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 127 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 128 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 129 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 130 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 131 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 132 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 133 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 134 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 135 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 136 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 137 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 138 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 139 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 140 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 141 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 142 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 143 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 144 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 145 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 146 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 147 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 148 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 149 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 150 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 151 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 152 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 153 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 154 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 155 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 156 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 157 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 158 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 159 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 160 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 161 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 162 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 163 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 164 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 165 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 166 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 167 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 168 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 169 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 170 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 171 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 172 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 173 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 174 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 175 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 176 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 177 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 178 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 179 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 180 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok 181 # skip Required executable for
> Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> ok
> # 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 ...................
> 1..9
> ok 1 - use Bio::Tools::Run::Primer3;
> ok 2 - use Bio::SeqIO;
> ok 3
> ok 4 # skip Primer3 wrapper only supports Primer3 v1
> ok 5 # skip Primer3 wrapper only supports Primer3 v1
> ok 6 # skip Primer3 wrapper only supports Primer3 v1
> ok 7 # skip Primer3 wrapper only supports Primer3 v1
> ok 8 # skip Primer3 wrapper only supports Primer3 v1
> ok 9 # skip Primer3 wrapper only supports Primer3 v1
> ok
> # 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/962rqFpX0l
> 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/bOUS86QI2c
> 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/GBRrsDwhRb
> 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
> # You named your test '15'. You shouldn't use numbers for your test
> names.
> # Very confusing.
> # You named your test '340'. You shouldn't use numbers for your test
> names.
> # Very confusing.
> 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 - An object of class 'Bio::SeqFeature::FeaturePair' isa
> 'Bio::SeqFeatureI'
> ok 6 - 15
> ok 7 - 340
> 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
> # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not
> present
> t/ProtDist.t ..................
> 1..14
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist;
> ok 2 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist
> is not present
> ok
> # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not
> present
> 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 Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars
> is not present
> 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
>
> # Failed test 'right type'
> # at t/SABlastPlus.t line 37.
> # got: undef
> # expected: 'nucl'
>
> # Failed test 'correct type'
> # at t/SABlastPlus.t line 53.
> # got: undef
> # expected: 'nucl'
>
> ------------- EXCEPTION -------------
> MSG: Masker 'windowmasker' can't use a blastdb as primary input
> STACK Bio::Tools::Run::StandAloneBlastPlus::make_mask
> /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm:818
> STACK toplevel t/SABlastPlus.t:55
> -------------------------------------
>
> # Looks like your test exited with 29 just after 14.
> 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
> not ok 8 - right type
> ok 9
> ok 10 - named db made
> ok 11 - check_db
> ok 12 - correct name
> ok 13 - dbinfo hash returned
> not ok 14 - correct type
> Dubious, test returned 29 (wstat 7424, 0x1d00)
> Failed 59/71 subtests
> # 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
> # Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not
> present
> t/SeqBoot.t ...................
> 1..9
> ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
> ok 2 - use Bio::AlignIO;
> ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot
> is not present
> ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot
> is not present
> ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot
> is not present
> ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot
> is not present
> ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot
> is not present
> ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot
> is not present
> ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot
> is not present
> 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 ..................
> 1..24
> ok 1 - use Bio::Tools::Run::TribeMCL;
> ok 2 - use Bio::SearchIO;
> ok 3 - An object of class 'Bio::Tools::Run::TribeMCL' isa
> 'Bio::Tools::Run::TribeMCL'
> ok 4 # skip Tribe Matrix program not found. Skipping tests...
> ok 5 # skip Tribe Matrix program not found. Skipping tests...
> ok 6 # skip Tribe Matrix program not found. Skipping tests...
> ok 7 # skip Tribe Matrix program not found. Skipping tests...
> ok 8 # skip Tribe Matrix program not found. Skipping tests...
> ok 9 # skip Tribe Matrix program not found. Skipping tests...
> ok 10 # skip Tribe Matrix program not found. Skipping tests...
> ok 11 # skip Tribe Matrix program not found. Skipping tests...
> ok 12 # skip Tribe Matrix program not found. Skipping tests...
> ok 13 # skip Tribe Matrix program not found. Skipping tests...
> ok 14 # skip Tribe Matrix program not found. Skipping tests...
> ok 15 # skip Tribe Matrix program not found. Skipping tests...
> ok 16 # skip Tribe Matrix program not found. Skipping tests...
> ok 17 # skip Tribe Matrix program not found. Skipping tests...
> ok 18 # skip Tribe Matrix program not found. Skipping tests...
> ok 19 # skip Tribe Matrix program not found. Skipping tests...
> ok 20 # skip Tribe Matrix program not found. Skipping tests...
> ok 21 # skip Tribe Matrix program not found. Skipping tests...
> ok 22 # skip Tribe Matrix program not found. Skipping tests...
> ok 23 # skip Tribe Matrix program not found. Skipping tests...
> ok 24 # skip Tribe Matrix program not found. Skipping tests...
> ok
> 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/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0)
> TODO passed: 20, 57, 75, 88, 110, 155, 190, 208, 226
> 262, 280, 315, 333, 405
> t/SABlastPlus.t (Wstat: 7424 (exited 29) Tests: 14 Failed: 2)
> Failed tests: 8, 14
> Non-zero exit status: 29
> Parse errors: Bad plan. You planned 71 tests but ran 14.
> Files=60, Tests=1595, 167 wallclock secs ( 0.31 usr 0.11 sys + 156.61 cusr
> 14.96 csys = 171.99 CPU)
> Result: FAIL
> Failed 1/60 test programs. 2/1595 subtests failed.
> dh_auto_test: error: /usr/bin/perl Build test --verbose 1 returned exit code
> 255
The full build log is available from:
http://qa-logs.debian.net/2024/07/28/bioperl-run_1.7.3-11_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240728;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240728&[email protected]&allbugs=1&cseverity=1&ctags=1&caffected=1#results
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!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: bioperl-run
Source-Version: 1.7.3-13
Done: Étienne Mollier <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 01 Dec 2024 10:57:53 +0100
Source: bioperl-run
Architecture: source
Version: 1.7.3-13
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1077454
Changes:
bioperl-run (1.7.3-13) unstable; urgency=medium
.
* Revert "skip_tests_for_ncbi-blast+.patch: remove."
* Revert "d/control: remove build dependency on ncbi-blast+-legacy."
* update-blastdbcmd-error-output.patch: fix test regression.
This patch updates the expected blastdbcmd error output parsed by the
StandAloneBlastPlus.pm runner, fixing the corresponding test item in
the maneuver.
Thanks to Aaron M. Ucko (Closes: #1077454)
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Files:
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