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Aufiero / circRNAprofiler

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Cannot install circRNAprofiler on R version 4.2.2 #12

Closed simeix00 closed 1 year ago

simeix00 commented 1 year ago

I'm unable to install circRNAprofiler on the latest version of RStudio (last updated 31/10/22). This is the message I get when trying to install circRNAprofiler:

> install.packages("circRNAprofiler")
Warning in install.packages :
  unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning in install.packages :
  unable to access index for repository https://R-Forge.R-project.org/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://R-Forge.R-project.org/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning in install.packages :
  unable to access index for repository https://www.rforge.net/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://www.rforge.net/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES

This is what happens once I try to load the package:

> library(circRNAprofiler)
Error: package or namespace load failed for ‘circRNAprofiler’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so, 0x0006): Library not loaded: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib'
  Referenced from: '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so'
  Reason: tried: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file)
simoauf commented 1 year ago

Hi simeix00, I will check and let you know.

simoauf commented 1 year ago

Hi simeix, I just noticed that you used install.packages("circRNAprofiler"), you should not use install.packages but BiocManager::install("circRNAprofiler"). Have a look also here: https://bioconductor.org/packages/release/bioc/html/circRNAprofiler.html

simeix00 commented 1 year ago

Hello simoauf, I tried both methods and I believe both did not work. Sorry for the confusion there.

Aufiero commented 1 year ago

For me, everything works fine. I also checked the Bioconductor and both the release (R version 4.2, Bioconductor version 3.16) and the development versions (R version 4.3, Bioconductor version 3.17) of circRNAprofiler were built correctly.

Maybe something got corrupted during the installation, so you can try to delete the R folder (e.g. R-4.2.0) where the packages are installed, usually in C:\Program Files\R, and then reinstall everything with BiocManager::install.