{"action":"closed","issue":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/2125","repository_url":"https://api.github.com/repos/bioconda/bioconda-recipes","labels_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/2125/labels{/name}","comments_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/2125/comments","events_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/2125/events","html_url":"https://github.com/bioconda/bioconda-recipes/issues/2125","id":170621854,"number":2125,"title":"Docker tests: ASCIIGenome -h works, but tests still fail.","user":{"login":"endrebak","id":17778898,"avatar_url":"https://avatars.githubusercontent.com/u/17778898?v=3","gravatar_id":"","url":"https://api.github.com/users/endrebak","html_url":"https://github.com/endrebak","followers_url":"https://api.github.com/users/endrebak/followers","following_url":"https://api.github.com/users/endrebak/following{/other_user}","gists_url":"https://api.github.com/users/endrebak/gists{/gist_id}","starred_url":"https://api.github.com/users/endrebak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/endrebak/subscriptions","organizations_url":"https://api.github.com/users/endrebak/orgs","repos_url":"https://api.github.com/users/endrebak/repos","events_url":"https://api.github.com/users/endrebak/events{/privacy}","received_events_url":"https://api.github.com/users/endrebak/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-08-11T11:14:57Z","updated_at":"2016-08-12T10:48:55Z","closed_at":"2016-08-12T10:48:55Z","body":"I have the setup as described in #2124 \r\n\r\nNow it seems like the test `ASCIIGenome -h` runs, but still the tests fail. I have appended the error message below. Does anyone have an inkling about why my tests fail? The help command seems to work, since you can see the output several times.\r\n\r\n```\r\nbash-3.2$ docker run -v `pwd`:/bioconda-recipes bioconda/bioconda-builder --packages asciigenome --env-matrix /bioconda-recipes/scripts/env_matrix.yml\r\nCollecting git+https://github.com/conda/conda-build.git@1.20.3\r\n  Cloning https://github.com/conda/conda-build.git (to 1.20.3) to /tmp/pip-0v7ymt0x-build\r\n  Requirement already satisfied (use --upgrade to upgrade): conda-build==1.20.3 from git+https://github.com/conda/conda-build.git@1.20.3 in /anaconda/lib/python3.5/site-packages\r\nRequirement already satisfied (use --upgrade to upgrade): conda in /anaconda/lib/python3.5/site-packages (from conda-build==1.20.3)\r\nYou are using pip version 8.1.1, however version 8.1.2 is available.\r\nYou should consider upgrading via the 'pip install --upgrade pip' command.\r\ngcc (GCC) 4.8.2 20140120 (Red Hat 4.8.2-15)\r\nCopyright (C) 2013 Free Software Foundation, Inc.\r\nThis is free software; see the source for copying conditions.  There is NO\r\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\r\n\r\nldd (GNU libc) 2.5\r\nCopyright (C) 2006 Free Software Foundation, Inc.\r\nThis is free software; see the source for copying conditions.  There is NO\r\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\r\nWritten by Roland McGrath and Ulrich Drepper.\r\nPackages to build\r\nasciigenome\r\nBuilding/testing subdag 0 of recipes in order:\r\n/bioconda-recipes/recipes/asciigenome\r\nF\r\n======================================================================\r\nFAIL: __main__.test_recipes('/bioconda-recipes/recipes/asciigenome', <__main__.EnvMatrix object at 0x7fe92bd29588>)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/anaconda/lib/python3.5/site-packages/nose/case.py\", line 198, in runTest\r\n    self.test(*self.arg)\r\n  File \"/bioconda-recipes/scripts/build-packages.py\", line 103, in build_recipe\r\n    assert False, \"At least one build of recipe {} failed.\".format(recipe)\r\nAssertionError: At least one build of recipe /bioconda-recipes/recipes/asciigenome failed.\r\n-------------------- >> begin captured stdout << ---------------------\r\nFetching package metadata: ............\r\nASCIIGenome\r\nASCIIGenome.jar\r\n#!/bin/sh\r\nexec java -Xmx8000m -jar /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome.jar \"$@\"\r\nRemoving old build environment\r\nBUILD START: asciigenome-0.2.0-0\r\nSource cache directory is: /anaconda/conda-bld/src_cache\r\nDownloading source to cache: ASCIIGenome-0.2.0.zip\r\nDownloading https://github.com/dariober/ASCIIGenome/releases/download/v0.1.0/ASCIIGenome-0.2.0.zip\r\nSuccess\r\nExtracting download\r\nPackage: asciigenome-0.2.0-0\r\nsource tree in: /anaconda/conda-bld/work/ASCIIGenome-0.2.0\r\nnumber of files: 3\r\nFixing permissions\r\nMaking absolute symlink bin/ASCIIGenome -> /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome relative\r\nDetected hard-coded path in text file share/asciigenome-0.2.0-0/ASCIIGenome\r\nFixing permissions\r\nBUILD END: asciigenome-0.2.0-0\r\nTEST START: asciigenome-0.2.0-0\r\nFetching package metadata: ............\r\nSolving package specifications: .........\r\nusage: ASCIIGenome [-h] [--region REGION] [--genome GENOME] [--fasta FASTA]\r\n                   [--exec EXEC] [--maxReadsStack MAXREADSSTACK]\r\n                   [--noFormat] [--nonInteractive] [--version]\r\n                   [input [input ...]]\r\n\r\nDESCRIPTION\r\nText viewer for genome alignment and annotation files.\r\nFor details see https://github.com/dariober/ASCIIGenome\r\n\r\n\r\npositional arguments:\r\n  input                  Input  files  to  be  displayed:  bam,  bed,  gtf,\r\n                         bigwig, bedgraph, etc\r\n\r\noptional arguments:\r\n  -h, --help             show this help message and exit\r\n  --region REGION, -r REGION\r\n                         Go to region. Format  1-based as 'chrom:start-end'\r\n                         or  'chrom:start'  or  'chrom'.  E.g.  chr1:1-1000\r\n                         (default: )\r\n  --genome GENOME, -g GENOME\r\n                         A genome file or a  tag identifying a genome build\r\n                         (e.g. hg19),  or  bam  file  with  suitable header\r\n                         (default: )\r\n  --fasta FASTA, -fa FASTA\r\n                         Optional reference fasta file.\r\n                         If given, must  be  indexed,  e.g.  with `samtools\r\n                         faidx ref.fa`\r\n  --exec EXEC, -x EXEC   Commands to be executed at  the  prompt. Must be a\r\n                         single  string.  E.g.  'goto   chr1   &&  next  &&\r\n                         seqRegex ACTG' (default: )\r\n  --maxReadsStack MAXREADSSTACK, -M MAXREADSSTACK\r\n                         Maximum  number  of  reads  to  accumulate  before\r\n                         printing. If more than this  many reads map to the\r\n                         window\r\n                         randomy select them (default: 2000)\r\n  --noFormat, -nf        Do  not  format  output   with   non  ascii  chars\r\n                         (colour, bold, etc.) (default: false)\r\n  --nonInteractive, -ni  Non interactive mode: Exit  after having processed\r\n                         cmd line args. (default: false)\r\n  --version, -v\r\n\r\nThe following packages will be downloaded:\r\n\r\n    package                    |            build\r\n    ---------------------------|-----------------\r\n    java-jdk-8.0.92            |                1       122.3 MB\r\n    asciigenome-0.2.0          |                0        27.8 MB\r\n    ------------------------------------------------------------\r\n                                           Total:       150.1 MB\r\n\r\nThe following NEW packages will be INSTALLED:\r\n\r\n    asciigenome: 0.2.0-0\r\n    java-jdk:    8.0.92-1\r\n\r\n\r\n+ outdir=/anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ mkdir -p /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ mkdir -p /anaconda/envs/_build/bin\r\n+ cp ASCIIGenome.jar /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ echo '#!/bin/sh'\r\n+ echo exec java -Xmx8000m -jar /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome.jar '\"$@\"'\r\n+ chmod +x /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome\r\n+ ln -s /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome /anaconda/envs/_build/bin\r\n+ ls /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ cat /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome\r\n+ ASCIIGenome -h\r\nUsing Anaconda Cloud api site https://api.anaconda.org\r\n\r\nWARNING: conda-build appears to be out of date. You have version 1.20.3 but the\r\nlatest version is 1.21.11. Run\r\n\r\nconda update -n root conda-build\r\n\r\nto get the latest version.\r\n\r\nTESTS FAILED: asciigenome-0.2.0-0\r\n\r\nFetching package metadata: ............\r\nASCIIGenome\r\nASCIIGenome.jar\r\n#!/bin/sh\r\nexec java -Xmx8000m -jar /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome.jar \"$@\"\r\nRemoving old build environment\r\nBUILD START: asciigenome-0.2.0-0\r\nSource cache directory is: /anaconda/conda-bld/src_cache\r\nFound source in cache: ASCIIGenome-0.2.0.zip\r\nExtracting download\r\nPackage: asciigenome-0.2.0-0\r\nsource tree in: /anaconda/conda-bld/work/ASCIIGenome-0.2.0\r\nnumber of files: 3\r\nFixing permissions\r\nMaking absolute symlink bin/ASCIIGenome -> /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome relative\r\nDetected hard-coded path in text file share/asciigenome-0.2.0-0/ASCIIGenome\r\nFixing permissions\r\nBUILD END: asciigenome-0.2.0-0\r\nTEST START: asciigenome-0.2.0-0\r\nFetching package metadata: ............\r\nSolving package specifications: .........\r\nusage: ASCIIGenome [-h] [--region REGION] [--genome GENOME] [--fasta FASTA]\r\n                   [--exec EXEC] [--maxReadsStack MAXREADSSTACK]\r\n                   [--noFormat] [--nonInteractive] [--version]\r\n                   [input [input ...]]\r\n\r\nDESCRIPTION\r\nText viewer for genome alignment and annotation files.\r\nFor details see https://github.com/dariober/ASCIIGenome\r\n\r\n\r\npositional arguments:\r\n  input                  Input  files  to  be  displayed:  bam,  bed,  gtf,\r\n                         bigwig, bedgraph, etc\r\n\r\noptional arguments:\r\n  -h, --help             show this help message and exit\r\n  --region REGION, -r REGION\r\n                         Go to region. Format  1-based as 'chrom:start-end'\r\n                         or  'chrom:start'  or  'chrom'.  E.g.  chr1:1-1000\r\n                         (default: )\r\n  --genome GENOME, -g GENOME\r\n                         A genome file or a  tag identifying a genome build\r\n                         (e.g. hg19),  or  bam  file  with  suitable header\r\n                         (default: )\r\n  --fasta FASTA, -fa FASTA\r\n                         Optional reference fasta file.\r\n                         If given, must  be  indexed,  e.g.  with `samtools\r\n                         faidx ref.fa`\r\n  --exec EXEC, -x EXEC   Commands to be executed at  the  prompt. Must be a\r\n                         single  string.  E.g.  'goto   chr1   &&  next  &&\r\n                         seqRegex ACTG' (default: )\r\n  --maxReadsStack MAXREADSSTACK, -M MAXREADSSTACK\r\n                         Maximum  number  of  reads  to  accumulate  before\r\n                         printing. If more than this  many reads map to the\r\n                         window\r\n                         randomy select them (default: 2000)\r\n  --noFormat, -nf        Do  not  format  output   with   non  ascii  chars\r\n                         (colour, bold, etc.) (default: false)\r\n  --nonInteractive, -ni  Non interactive mode: Exit  after having processed\r\n                         cmd line args. (default: false)\r\n  --version, -v\r\n\r\nThe following packages will be downloaded:\r\n\r\n    package                    |            build\r\n    ---------------------------|-----------------\r\n    asciigenome-0.2.0          |                0        27.8 MB\r\n\r\nThe following NEW packages will be INSTALLED:\r\n\r\n    asciigenome: 0.2.0-0\r\n    java-jdk:    8.0.92-1\r\n\r\n\r\n+ outdir=/anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ mkdir -p /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ mkdir -p /anaconda/envs/_build/bin\r\n+ cp ASCIIGenome.jar /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ echo '#!/bin/sh'\r\n+ echo exec java -Xmx8000m -jar /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome.jar '\"$@\"'\r\n+ chmod +x /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome\r\n+ ln -s /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome /anaconda/envs/_build/bin\r\n+ ls /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ cat /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome\r\n+ ASCIIGenome -h\r\nUsing Anaconda Cloud api site https://api.anaconda.org\r\n\r\nWARNING: conda-build appears to be out of date. You have version 1.20.3 but the\r\nlatest version is 1.21.11. Run\r\n\r\nconda update -n root conda-build\r\n\r\nto get the latest version.\r\n\r\nTESTS FAILED: asciigenome-0.2.0-0\r\n\r\nFetching package metadata: ............\r\nASCIIGenome\r\nASCIIGenome.jar\r\n#!/bin/sh\r\nexec java -Xmx8000m -jar /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome.jar \"$@\"\r\nRemoving old build environment\r\nBUILD START: asciigenome-0.2.0-0\r\nSource cache directory is: /anaconda/conda-bld/src_cache\r\nFound source in cache: ASCIIGenome-0.2.0.zip\r\nExtracting download\r\nPackage: asciigenome-0.2.0-0\r\nsource tree in: /anaconda/conda-bld/work/ASCIIGenome-0.2.0\r\nnumber of files: 3\r\nFixing permissions\r\nMaking absolute symlink bin/ASCIIGenome -> /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome relative\r\nDetected hard-coded path in text file share/asciigenome-0.2.0-0/ASCIIGenome\r\nFixing permissions\r\nBUILD END: asciigenome-0.2.0-0\r\nTEST START: asciigenome-0.2.0-0\r\nFetching package metadata: ............\r\nSolving package specifications: .........\r\nusage: ASCIIGenome [-h] [--region REGION] [--genome GENOME] [--fasta FASTA]\r\n                   [--exec EXEC] [--maxReadsStack MAXREADSSTACK]\r\n                   [--noFormat] [--nonInteractive] [--version]\r\n                   [input [input ...]]\r\n\r\nDESCRIPTION\r\nText viewer for genome alignment and annotation files.\r\nFor details see https://github.com/dariober/ASCIIGenome\r\n\r\n\r\npositional arguments:\r\n  input                  Input  files  to  be  displayed:  bam,  bed,  gtf,\r\n                         bigwig, bedgraph, etc\r\n\r\noptional arguments:\r\n  -h, --help             show this help message and exit\r\n  --region REGION, -r REGION\r\n                         Go to region. Format  1-based as 'chrom:start-end'\r\n                         or  'chrom:start'  or  'chrom'.  E.g.  chr1:1-1000\r\n                         (default: )\r\n  --genome GENOME, -g GENOME\r\n                         A genome file or a  tag identifying a genome build\r\n                         (e.g. hg19),  or  bam  file  with  suitable header\r\n                         (default: )\r\n  --fasta FASTA, -fa FASTA\r\n                         Optional reference fasta file.\r\n                         If given, must  be  indexed,  e.g.  with `samtools\r\n                         faidx ref.fa`\r\n  --exec EXEC, -x EXEC   Commands to be executed at  the  prompt. Must be a\r\n                         single  string.  E.g.  'goto   chr1   &&  next  &&\r\n                         seqRegex ACTG' (default: )\r\n  --maxReadsStack MAXREADSSTACK, -M MAXREADSSTACK\r\n                         Maximum  number  of  reads  to  accumulate  before\r\n                         printing. If more than this  many reads map to the\r\n                         window\r\n                         randomy select them (default: 2000)\r\n  --noFormat, -nf        Do  not  format  output   with   non  ascii  chars\r\n                         (colour, bold, etc.) (default: false)\r\n  --nonInteractive, -ni  Non interactive mode: Exit  after having processed\r\n                         cmd line args. (default: false)\r\n  --version, -v\r\n\r\nThe following packages will be downloaded:\r\n\r\n    package                    |            build\r\n    ---------------------------|-----------------\r\n    asciigenome-0.2.0          |                0        27.8 MB\r\n\r\nThe following NEW packages will be INSTALLED:\r\n\r\n    asciigenome: 0.2.0-0\r\n    java-jdk:    8.0.92-1\r\n\r\n\r\n+ outdir=/anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ mkdir -p /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ mkdir -p /anaconda/envs/_build/bin\r\n+ cp ASCIIGenome.jar /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ echo '#!/bin/sh'\r\n+ echo exec java -Xmx8000m -jar /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome.jar '\"$@\"'\r\n+ chmod +x /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome\r\n+ ln -s /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome /anaconda/envs/_build/bin\r\n+ ls /anaconda/envs/_build/share/asciigenome-0.2.0-0\r\n+ cat /anaconda/envs/_build/share/asciigenome-0.2.0-0/ASCIIGenome\r\n+ ASCIIGenome -h\r\nUsing Anaconda Cloud api site https://api.anaconda.org\r\n\r\nWARNING: conda-build appears to be out of date. You have version 1.20.3 but the\r\nlatest version is 1.21.11. Run\r\n\r\nconda update -n root conda-build\r\n\r\nto get the latest version.\r\n\r\nTESTS FAILED: asciigenome-0.2.0-0\r\n\r\n\r\n--------------------- >> end captured stdout << ----------------------\r\n\r\n----------------------------------------------------------------------\r\nRan 1 test in 110.935s\r\n\r\nFAILED (failures=1)\r\n```"}}
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