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  1. pvh@grids1:/cip0/research/scratch/pvh/bioconda-recipes$ ./simulate-travis.py --packages repeatmasker
  2. + bioconda-utils lint recipes config.yml --git-range HEAD
  3. 21:00:47 BIOCONDA WARNING git version (1.9.1) is < 2.0. Running git diff using shell=True. Please consider upgrading git
  4. 21:00:50 BIOCONDA INFO Recipes newly unblacklisted:
  5.  
  6. 21:00:50 BIOCONDA INFO Recipes with modified meta.yaml files according to git: recipes/repeatmasker
  7. + set +x
  8. + bioconda-utils build recipes config.yml --docker --loglevel=info --mulled-test --packages repeatmasker --git-range HEAD
  9. 21:00:57 BIOCONDA INFO DOCKER: Pulling docker image condaforge/linux-anvil
  10. 21:01:01 BIOCONDA INFO DOCKER: Done pulling image
  11. 21:01:01 BIOCONDA INFO DOCKER: Built docker image tag=tmp-bioconda-builder
  12. 21:01:01 BIOCONDA WARNING git version (1.9.1) is < 2.0. Running git diff using shell=True. Please consider upgrading git
  13. 21:01:03 BIOCONDA INFO Recipes newly unblacklisted:
  14.  
  15. 21:01:03 BIOCONDA INFO Recipes modified according to git: repeatmasker
  16. 21:01:03 BIOCONDA INFO blacklist: bioconductor-bubbletree, bioconductor-cexor, bioconductor-deseq2/1.10.1, bioconductor-diffbind, bioconductor-genelendatabase/1.6.0, bioconductor-iranges/2.4.6, bioconductor-iranges/2.4.7, bioconductor-limma/3.26.7, bioconductor-limma/3.28.2, bioconductor-limma/3.28.6, bioconductor-mmdiff, bioconductor-s4vectors/0.8.7, bioconductor-summarizedexperiment/1.0.2, bioconductor-systempiper, blast/2.2.21, cap-mirseq, delly, denovogear, detonate, ensembl-vep, gdsctools, mothur/1.36.1, mysqlclient, perl-font-afm, r-hdrcde, r-knitr, r-ks, r-mutoss, r-phonr, r-rainbow, r-readr, r-sartools/1.2.0, r-spp, triform2
  17. 21:01:03 BIOCONDA INFO Filtering recipes
  18.  
  19. Filtering 1 of 1 (100.0%) recipes/repeatmasker
  20. 21:01:07 BIOCONDA INFO Building and testing 1 recipes in total
  21. 21:01:07 BIOCONDA INFO Recipes to build:
  22. repeatmasker
  23. 21:01:07 BIOCONDA INFO Building and testing subdag 0 of 1 (1 recipes)
  24. 21:01:07 BIOCONDA INFO BUILD START recipes/repeatmasker, env: CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.4;CONDA_NCURSES=5.9;CONDA_NPY=110;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.3.1
  25. 21:01:34 BIOCONDA ERROR COMMAND FAILED: docker run --net host --rm -v /tmp/tmpdxon1nbq/build_script.bash:/opt/build_script.bash -v /cip0/research/pvh/mc3/conda-bld:/opt/host-conda-bld -v /net/ceph-mon1.sanbi.ac.za/sanbi/scratch/pvh/bioconda-recipes/recipes/repeatmasker:/opt/recipe -e CONDA_NPY=110 -e CONDA_GMP=5.1 -e CONDA_R=3.3.1 -e TRAVIS_REPO_SLUG=false -e TRAVIS_BRANCH=false -e CONDA_PERL=5.22.0 -e CONDA_HTSLIB=1.4 -e CONDA_GSL=1.16 -e CONDA_BOOST=1.61 -e CONDA_HDF5=1.8.17 -e CONDA_PY=27 -e CONDA_NCURSES=5.9 -e TRAVIS_PULL_REQUEST=false -e TRAVIS_OS_NAME=linux tmp-bioconda-builder /bin/bash /opt/build_script.bash
  26. 21:01:34 BIOCONDA ERROR STDOUT+STDERR:
  27. bash: cannot set terminal process group (-1): Inappropriate ioctl for device
  28. bash: no job control in this shell
  29. Fetching package metadata .............
  30. Solving package specifications: ..........
  31.  
  32. Package plan for installation in environment /opt/conda:
  33.  
  34. The following packages will be downloaded:
  35.  
  36. package | build
  37. ---------------------------|-----------------
  38. libffi-3.2.1 | 1 38 KB defaults
  39. idna-2.2 | py35_0 123 KB defaults
  40. pyasn1-0.2.3 | py35_0 79 KB defaults
  41. pycparser-2.17 | py35_0 156 KB defaults
  42. requests-2.13.0 | py35_0 811 KB defaults
  43. cffi-1.9.1 | py35_0 338 KB defaults
  44. cryptography-1.7.1 | py35_0 842 KB defaults
  45. pyopenssl-16.2.0 | py35_0 70 KB defaults
  46. conda-4.2.15 | py35_0 407 KB defaults
  47. ------------------------------------------------------------
  48. Total: 2.8 MB
  49.  
  50. The following NEW packages will be INSTALLED:
  51.  
  52. cffi: 1.9.1-py35_0 defaults
  53. cryptography: 1.7.1-py35_0 defaults
  54. idna: 2.2-py35_0 defaults
  55. libffi: 3.2.1-1 defaults
  56. pyasn1: 0.2.3-py35_0 defaults
  57. pycparser: 2.17-py35_0 defaults
  58. pyopenssl: 16.2.0-py35_0 defaults
  59.  
  60. The following packages will be UPDATED:
  61.  
  62. conda: 4.2.9-py35_0 defaults --> 4.2.15-py35_0 defaults
  63. requests: 2.10.0-py35_0 defaults --> 2.13.0-py35_0 defaults
  64.  
  65. Proceed ([y]/n)?
  66. Pruning fetched packages from the cache ...
  67. Fetching packages ...
  68. libffi-3.2.1-1 100% |###############################| Time: 0:00:00 1.01 MB/s
  69. idna-2.2-py35_ 100% |###############################| Time: 0:00:00 1.44 MB/s
  70. pyasn1-0.2.3-p 100% |###############################| Time: 0:00:00 1.23 MB/s
  71. pycparser-2.17 100% |###############################| Time: 0:00:00 1.62 MB/s
  72. requests-2.13. 100% |###############################| Time: 0:00:00 2.99 MB/s
  73. cffi-1.9.1-py3 100% |###############################| Time: 0:00:00 2.32 MB/s
  74. cryptography-1 100% |###############################| Time: 0:00:00 1.40 MB/s
  75. pyopenssl-16.2 100% |###############################| Time: 0:00:00 1.15 MB/s
  76. conda-4.2.15-p 100% |###############################| Time: 0:00:00 2.53 MB/s
  77. Extracting packages ...
  78. [ COMPLETE ]|##################################################| 100%
  79. Unlinking packages ...
  80. [ COMPLETE ]|##################################################| 100%
  81. Linking packages ...
  82. [ COMPLETE ]|##################################################| 100%
  83. BUILD START: repeatmasker-4.0.6-pl5.22.0_6
  84. updating index in: /opt/conda/conda-bld/linux-64
  85. updating index in: /opt/conda/conda-bld/noarch
  86. Traceback (most recent call last):
  87. File "/opt/conda/lib/python3.5/site-packages/conda/fetch.py", line 120, in fetch_repodata
  88. resp.raise_for_status()
  89. File "/opt/conda/lib/python3.5/site-packages/requests/models.py", line 909, in raise_for_status
  90. raise HTTPError(http_error_msg, response=self)
  91. requests.exceptions.HTTPError: 404 Client Error: None for url: file:///opt/host-conda-bld/linux-64/repodata.json.bz2
  92.  
  93. During handling of the above exception, another exception occurred:
  94.  
  95. Traceback (most recent call last):
  96. File "/opt/conda/bin/conda-build", line 6, in <module>
  97. sys.exit(conda_build.cli.main_build.main())
  98. File "/opt/conda/lib/python3.5/site-packages/conda_build/cli/main_build.py", line 242, in main
  99. execute(sys.argv[1:])
  100. File "/opt/conda/lib/python3.5/site-packages/conda_build/cli/main_build.py", line 234, in execute
  101. already_built=None, config=config)
  102. File "/opt/conda/lib/python3.5/site-packages/conda_build/api.py", line 77, in build
  103. need_source_download=need_source_download, config=config)
  104. File "/opt/conda/lib/python3.5/site-packages/conda_build/build.py", line 1099, in build_tree
  105. config=recipe_config)
  106. File "/opt/conda/lib/python3.5/site-packages/conda_build/build.py", line 634, in build
  107. create_env(config.build_prefix, specs, config=config)
  108. File "/opt/conda/lib/python3.5/site-packages/conda_build/build.py", line 494, in create_env
  109. index = get_build_index(config=config, clear_cache=True)
  110. File "/opt/conda/lib/python3.5/site-packages/conda_build/build.py", line 449, in get_build_index
  111. use_cache=not clear_cache)
  112. File "/opt/conda/lib/python3.5/site-packages/conda/api.py", line 24, in get_index
  113. index = fetch_index(channel_urls, use_cache=use_cache, unknown=unknown)
  114. File "/opt/conda/lib/python3.5/site-packages/conda/fetch.py", line 300, in fetch_index
  115. repodatas = [(u, f.result()) for u, f in zip(urls, futures)]
  116. File "/opt/conda/lib/python3.5/site-packages/conda/fetch.py", line 300, in <listcomp>
  117. repodatas = [(u, f.result()) for u, f in zip(urls, futures)]
  118. File "/opt/conda/lib/python3.5/concurrent/futures/_base.py", line 398, in result
  119. return self.__get_result()
  120. File "/opt/conda/lib/python3.5/concurrent/futures/_base.py", line 357, in __get_result
  121. raise self._exception
  122. File "/opt/conda/lib/python3.5/concurrent/futures/thread.py", line 55, in run
  123. result = self.fn(*self.args, **self.kwargs)
  124. File "/opt/conda/lib/python3.5/site-packages/conda/fetch.py", line 75, in func
  125. res = f(*args, **kwargs)
  126. File "/opt/conda/lib/python3.5/site-packages/conda/fetch.py", line 223, in fetch_repodata
  127. e.response.reason if e.response else None)
  128. conda.exceptions.CondaHTTPError: HTTP 404 None
  129. for url <None>
  130.  
  131. The remote server could not find the channel you requested.
  132.  
  133. You will need to adjust your conda configuration to proceed.
  134. Use `conda config --show` to view your configuration's current state.
  135. Further configuration help can be found at <http://conda.pydata.org/docs/config.html>.
  136.  
  137.  
  138. 21:01:34 BIOCONDA ERROR BUILD FAILED recipes/repeatmasker, CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.4;CONDA_NCURSES=5.9;CONDA_NPY=110;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.3.1
  139. 21:01:34 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
  140. 21:01:34 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe repeatmasker-4.0.6-pl5.22.0_6.tar.bz2, environment CONDA_NPY=110;CONDA_GMP=5.1;CONDA_R=3.3.1;CONDA_PERL=5.22.0;CONDA_HTSLIB=1.4;CONDA_GSL=1.16;CONDA_BOOST=1.61;CONDA_HDF5=1.8.17;CONDA_PY=27;CONDA_NCURSES=5.9
  141. Traceback (most recent call last):
  142. File "./simulate-travis.py", line 162, in <module>
  143. sp.run(['scripts/travis-run.sh'], env=env, universal_newlines=True, check=True)
  144. File "/cip0/research/pvh/mc3/lib/python3.5/subprocess.py", line 708, in run
  145. output=stdout, stderr=stderr)
  146. subprocess.CalledProcessError: Command '['scripts/travis-run.sh']' returned non-zero exit status 1
  147. pvh@grids1:/cip0/research/scratch/pvh/bioconda-recipes$ conda config --show
  148. add_anaconda_token: True
  149. add_pip_as_python_dependency: True
  150. allow_softlinks: True
  151. always_copy: False
  152. always_yes: False
  153. auto_update_conda: True
  154. binstar_upload: None
  155. changeps1: True
  156. channel_alias: https://conda.anaconda.org/
  157. channel_priority: True
  158. channels:
  159. - bioconda
  160. - r
  161. - defaults
  162. - conda-forge
  163. client_cert:
  164. client_cert_key:
  165. create_default_packages: []
  166. debug: False
  167. default_channels:
  168. - https://repo.continuum.io/pkgs/free
  169. - https://repo.continuum.io/pkgs/pro
  170. disallow: []
  171. json: False
  172. offline: False
  173. proxy_servers: {}
  174. quiet: False
  175. shortcuts: True
  176. show_channel_urls: None
  177. ssl_verify: True
  178. track_features: []
  179. update_dependencies: True
  180. use_pip: True
  181. verbosity: 0
  182. pvh@grids1:/cip0/research/scratch/pvh/bioconda-recipes$
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