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BUILD report for destiny on malbec2

This page was generated on 2020-10-17 11:54:39 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE destiny PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 462/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
destiny 3.2.0
Philipp Angerer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/destiny
Branch: RELEASE_3_11
Last Commit: 90e85a4
Last Changed Date: 2020-04-27 14:50:22 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: destiny
Version: 3.2.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data destiny
StartedAt: 2020-10-16 18:46:36 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:47:34 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 57.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data destiny
###
##############################################################################
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* checking for file ‘destiny/DESCRIPTION’ ... OK
* preparing ‘destiny’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DPT.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--template' 'destiny-bib.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'DPT.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: processing vignette 'DPT.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--template' 'destiny-bib.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'DPT.ipynb'” failed with exit status 1
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--to' 'script' 'DPT.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: tangling vignette 'DPT.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--to' 'script' 'DPT.ipynb'” failed with exit status 1
--- failed re-building ‘DPT.ipynbmeta’

--- re-building ‘Diffusion-Map-recap.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--template' 'destiny-base.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Diffusion-Map-recap.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: processing vignette 'Diffusion-Map-recap.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--template' 'destiny-base.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Diffusion-Map-recap.ipynb'” failed with exit status 1
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--to' 'script' 'Diffusion-Map-recap.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: tangling vignette 'Diffusion-Map-recap.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--to' 'script' 'Diffusion-Map-recap.ipynb'” failed with exit status 1
--- failed re-building ‘Diffusion-Map-recap.ipynbmeta’

--- re-building ‘Diffusion-Maps.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--template' 'destiny.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Diffusion-Maps.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: processing vignette 'Diffusion-Maps.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--template' 'destiny.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Diffusion-Maps.ipynb'” failed with exit status 1
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--to' 'script' 'Diffusion-Maps.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: tangling vignette 'Diffusion-Maps.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--to' 'script' 'Diffusion-Maps.ipynb'” failed with exit status 1
--- failed re-building ‘Diffusion-Maps.ipynbmeta’

--- re-building ‘Gene-Relevance.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--template' 'destiny-base.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Gene-Relevance.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: processing vignette 'Gene-Relevance.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--template' 'destiny-base.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Gene-Relevance.ipynb'” failed with exit status 1
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--to' 'script' 'Gene-Relevance.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: tangling vignette 'Gene-Relevance.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--to' 'script' 'Gene-Relevance.ipynb'” failed with exit status 1
--- failed re-building ‘Gene-Relevance.ipynbmeta’

--- re-building ‘Global-Sigma.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--template' 'destiny-bib.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Global-Sigma.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: processing vignette 'Global-Sigma.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--template' 'destiny-bib.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'Global-Sigma.ipynb'” failed with exit status 1
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--to' 'script' 'Global-Sigma.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: tangling vignette 'Global-Sigma.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--to' 'script' 'Global-Sigma.ipynb'” failed with exit status 1
--- failed re-building ‘Global-Sigma.ipynbmeta’

--- re-building ‘tidyverse.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--template' 'destiny-base.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'tidyverse.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: processing vignette 'tidyverse.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--template' 'destiny-base.tplx' '--LatexExporter.preprocessors=["destiny_processors.LatexTracPreprocessor"]' '--to' 'latex' 'tidyverse.ipynb'” failed with exit status 1
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = env,  :
  running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' '--to' 'script' 'tidyverse.ipynb' 2>&1' had status 1
Call failed. Output:
Traceback (most recent call last):
  File "/usr/local/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/__init__.py", line 4, in <module>
    from .exporters import *
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .base import (export, get_exporter, 
  File "/usr/local/lib/python3.6/dist-packages/nbconvert/exporters/base.py", line 8, in <module>
    import entrypoints
ModuleNotFoundError: No module named 'entrypoints'
Error: tangling vignette 'tidyverse.ipynbmeta' failed with diagnostics:
The call “PYTHONPATH=.:.: jupyter 'nbconvert' '--to' 'script' 'tidyverse.ipynb'” failed with exit status 1
--- failed re-building ‘tidyverse.ipynbmeta’

SUMMARY: processing the following files failed:
  ‘DPT.ipynbmeta’ ‘DPT.ipynbmeta’ ‘Diffusion-Map-recap.ipynbmeta’
  ‘Diffusion-Map-recap.ipynbmeta’ ‘Diffusion-Maps.ipynbmeta’
  ‘Diffusion-Maps.ipynbmeta’ ‘Gene-Relevance.ipynbmeta’
  ‘Gene-Relevance.ipynbmeta’ ‘Global-Sigma.ipynbmeta’
  ‘Global-Sigma.ipynbmeta’ ‘tidyverse.ipynbmeta’ ‘tidyverse.ipynbmeta’

Error: Vignette re-building failed.
Execution halted