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Installation fails #44

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erikfel97 opened this issue Mar 9, 2020 · 12 comments
Closed

Installation fails #44

erikfel97 opened this issue Mar 9, 2020 · 12 comments

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@erikfel97
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Hi,
Trying to install the package on R-3.6.3
Always the same error:
Error: Failed to install 'cmapR' from GitHub: (converted from warning) installation of package ..... had non-zero exit status
How should I solve this problem?
@tnat1031
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tnat1031 commented Mar 9, 2020 via email

@erikfel97
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First - devtools::install_github("cmap/cmapR")
Then using the script: install_cmapR.R
Same error message in both cases

@tnat1031
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tnat1031 commented Mar 9, 2020 via email

@erikfel97
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This is the only error message to be produced
Actually, in order to run ssGSEA2.0 I should have this package installed...

@tnat1031
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tnat1031 commented Mar 9, 2020 via email

@ebrgstrm
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ebrgstrm commented Mar 27, 2020 •
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Hi, I got a similar install error after having no problems until today:

Error: Failed to install 'cmapR' from GitHub:
(converted from warning) installation of package ‘C:/.../cmapR_0.99.18.tar.gz’ had non-zero exit status

Earlier in the console I got a more specific message at this point in the installation:

** byte-compile and prepare package for lazy loading
Error in findpack(package, lib.loc) : there is no package called 'cmapR'
Calls: -> findpack
Execution halted
ERROR: lazy loading failed for package 'cmapR'
* removing '.../R/win-library/3.6/cmapR'

I tried the install_cmapR.R script as it is and then devtools::install_github('cmap/cmapR') in the same session and got the same error both times. Is this a problem on my end? Hope the extra info helps, thank you!

@tnat1031
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tnat1031 commented Mar 27, 2020 via email

@ebrgstrm
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Yes, I used that yesterday and it seems to be what kicked off the problems with my libraries (specifically, the ssGSEA2.0/PTM-SEA implementation). Since then, I updated R 3.5 -> 3.6, and clean installed other libraries with no issues.

@tnat1031
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tnat1031 commented Mar 27, 2020 via email

@karstenkrug
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karstenkrug commented Mar 28, 2020 •
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Hi, I just want to chime in here and share some of my experience with the cmapR package. First of all kudos for developing this package! We heavily rely on the GCT 1.3 format and the functions in the cmapR package provide and easy and intuitve I/O interface.

I am pretty sure that the ssGSEA2.0 package does not cause the problems when trying to install the cmapR package. In fact, I was using the cmapR package in ssGSEA2.0 for quite some time without problems. Only recently, users reported problems with the cmapR package (e.g. no deprecated versions when functions were renamed for BioC submission, see below).

broadinstitute/ssGSEA2.0#14 (comment)
broadinstitute/ssGSEA2.0#15 (comment)

As a temporary solution I decided to include and use the io.R file. Once the cmapR package will be available via Bioconductor (which hopefully will be backwards compatible with R<4.0) I will switch back to the "official" version.

The most common problem that I encountered during installation of cmapR on different OS were caused by the rhdf5 package. I partly solved some of the problems by installing the rhdf5 package before cmapR but especially on some versions of Debian I was not able to install the package at all (well, I just gave up at some point..).

Another point to keep in mind is the switch to the BiocManager package introduced in R 3.6 which changed the way how to install packages from Bioconductor. In ssGSEA2.0 I used the code below to make it work on R<3.5 and R >= 3.6. I am just bringing this up because @ebrgstrm updated from 3.5 to 3.6 which might or might not be related to his problems.

RVERSION <- as.numeric(paste(R.version$major, sub('\\..*','',R.version$minor), sep='.')) 
  if(RVERSION >= 3.6) {
    p_load(BiocManager)
    BiocManager::install("rhdf5")
 } else {
    source("https://bioconductor.org/biocLite.R")
    biocLite("rhdf5")
}

The code above uses p_load from the pacman R package management tool, which does an awesome job in resolving dependencies between packages.

Anyways, I just wanted to share my thoughts on that.

Best,
Karsten

@ebrgstrm
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Thanks for the response, @karstenkrug ! Based on that I think my issues were just coincidentally timed somehow.
Update: turns out my problem was most likely on my end, as my default library path was on a mapped network drive, and either BioConductor or GitHub or something was running into a permission error at some point. After a clean install of R and this change, cmapR installed perfectly and works fine after running ssGSEA.

Thanks all for the help! I will update if I encounter any more issues like this. I would like to echo Karsten's kudos as well, cmapR is very helpful to our group.

@tnat1031
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tnat1031 commented Mar 30, 2020 via email

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4 participants
@tnat1031 @karstenkrug @erikfel97 @ebrgstrm