[Debian-med-packaging] Bug#1077454: bioperl-run: FTBFS: dh_auto_test: error: /usr/bin/perl Build test --verbose 1 returned exit code 255

[Lucas Nussbaum]

Source: bioperl-run
Version: 1.7.3-11
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
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;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240728&fusertaguser=lucas@debian.org&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.