Workflow highthroughputassays can't install properly
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@kristofferhaurum-12352
Last seen 4.7 years ago

When I try to install the hightrokghput assays workflow The following happens:

> source("https://bioconductor.org/workflows.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> workflowInstall("highthroughputassays")
Installing package into ‘/Users/johansenkh/Library/R/3.3/library’
(as ‘lib’ is unspecified)

Warning in install.packages :
  URL 'https://bioconductor.org/packages/3.4/workflows/bin/macosx/mavericks/contrib/3.3/PACKAGES.gz': status was '404 Not Found'

Warning in install.packages :
  URL 'https://bioconductor.org/packages/3.4/workflows/bin/macosx/mavericks/contrib/3.3/PACKAGES': status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository https://bioconductor.org/packages/3.4/workflows/bin/macosx/mavericks/contrib/3.3:
  cannot download all files
installing the source package ‘highthroughputassays’

trying URL 'https://bioconductor.org/packages/3.4/workflows/src/contrib/highthroughputassays_0.99.120889.tar.gz'
Content type 'application/x-gzip' length 441585 bytes (431 KB)
==================================================
downloaded 431 KB

* installing *source* package ‘highthroughputassays’ ...
** inst
** help
No man pages found in package  ‘highthroughputassays’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'rgl', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so':
  dlopen(/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib
  Referenced from: /Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so
  Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/johansenkh/Library/R/3.3/library/highthroughputassays’
Warning in install.packages :
  installation of package ‘highthroughputassays’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/hb/sc3x6vtj0ys009qnyplbp2_h1g5hgm/T/RtmptgIUo5/downloaded_packages’

What should I do about it? I have tried on 3 computers (Mac).

workflows flowcore flowstats flowworkspace • 1.2k views
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@kristofferhaurum-12352
Last seen 4.7 years ago

So now I got rgl to work by installing XCODE 11 here: https://www.xquartz.org

And this resulted in the package working.

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Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 12 months ago
Heidelberg, Germany

The error message indicates some problems with the rgl package, so please double check that you meet the required system dependencies.

Also, please note that the fact that the workflow package is not provided as a mac binary in first place indicates that its author for some reason decided not to support it on that platform, most probably because of some missing tools/functionality on mac.

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@kristofferhaurum-12352
Last seen 4.7 years ago

So I tried out the rgl package, and it fails to load. how can one fix that?

​library(rgl)
Error : .onLoad failed in loadNamespace() for 'rgl', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so':
  dlopen(/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib
  Referenced from: /Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so
  Reason: image not found
Error: package or namespace load failed for ‘rgl’​
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Entering edit mode

I assume you previously had a working installation of rgl, but probably because of some system changes (?) it stopped loading. The easiest thing to try is to re-install the package.

install.packages(rgl)

 

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It gives the exact same error after doing that. Further, I have tried on 2 other macs, and it wouldn't work there either.

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