Hi fellow coders,
I need to install a package called "RAPInetMHCpan" from github. I did so by executing the code:
remotes::install_github("elmerfer/RAPInetMHCpan")
which yielded the following error:
Downloading GitHub repo elmerfer/RAPInetMHCpan@HEAD
Skipping 1 packages not available: BiocParallel
Running R CMD build
...
- checking for file 'C:\Users\il7327\AppData\Local\Temp\RtmpaQ40aR\remotesb0c32c772f\elmerfer-RAPInetMHCpan-30f3d1e/DESCRIPTION' ... OK
- preparing 'RAPInetMHCpan':
- checking DESCRIPTION meta-information ... OK
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
Omitted 'LazyData' from DESCRIPTION - building 'RAPInetMHCpan_0.1.0.tar.gz'
- installing source package 'RAPInetMHCpan' ...
** using staged installation
** R
Error in parse(outFile) :
C:/Users/il7327/AppData/Local/Temp/Rtmp2Bkokb/R.INSTALL1b783b8d75bd/RAPInetMHCpan/R/GeneralRAPIFunctions.R:265:3: '}' inattendu(e)
264:
265: }
^
ERROR: unable to collate and parse R files for package 'RAPInetMHCpan' - removing 'C:/DATA/R.Apps/R-4.1.1-win/library/RAPInetMHCpan'
Warning message:
In i.p(...) :
installation of package ‘C:/Users/il7327/AppData/Local/Temp/RtmpaQ40aR/fileb0c6a16af9/RAPInetMHCpan_0.1.0.tar.gz’ had non-zero exit status
I interpreted this as a problem with the installation of the package "BiocParallel". I proceeded to install this package seperately (with help of another package called "BiocManager"), and it seems to have worked because when I execute the line:
library(BiocParallel)
there was no error.
Then I tried to install "RAPInetMHCpan" again with:
remotes::install_github("elmerfer/RAPInetMHCpan", dependencies = FALSE)
which again resulted in an error:
Downloading GitHub repo elmerfer/RAPInetMHCpan@HEAD
Running R CMD build
...
- checking for file 'C:\Users\il7327\AppData\Local\Temp\RtmpaQ40aR\remotesb0c4b1e6e13\elmerfer-RAPInetMHCpan-30f3d1e/DESCRIPTION' ... OK
- preparing 'RAPInetMHCpan':
- checking DESCRIPTION meta-information ... OK
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
Omitted 'LazyData' from DESCRIPTION - building 'RAPInetMHCpan_0.1.0.tar.gz'
- installing source package 'RAPInetMHCpan' ...
** using staged installation
** R
Error in parse(outFile) :
C:/Users/il7327/AppData/Local/Temp/RtmpGEhLxV/R.INSTALL1e28348e244f/RAPInetMHCpan/R/GeneralRAPIFunctions.R:265:3: '}' inattendu(e)
264:
265: }
^
ERROR: unable to collate and parse R files for package 'RAPInetMHCpan' - removing 'C:/DATA/R.Apps/R-4.1.1-win/library/RAPInetMHCpan'
Warning message:
In i.p(...) :
installation of package ‘C:/Users/il7327/AppData/Local/Temp/RtmpaQ40aR/fileb0c48a23b46/RAPInetMHCpan_0.1.0.tar.gz’ had non-zero exit status
which is trying to tell me, I believe, that the "BiocParallel" package installation is not the problem anymore.
My questions are:
- Am I correct in assuming that "BiocParallel" was successfully installed?
- Is this:
remotes::install_github("elmerfer/RAPInetMHCpan", dependencies = FALSE)
the right choice to install "RAPInetMHCpan" without having it trying to download "BiocParallel" again? Without dependencies = FALSE I get the same error as before my independant installation of "BiocParallel".
3. What can I do to install "RAPInetMHCpan"? I don't understand what the second error means, it looks like it has problem reading something in, or generating some kind of output.
Now: there are instructions on the authors' github page, but they didn't help. I know it says that it will run on Linux, but I'd really like to get it to work on windows. If this isnt possible: is there an easy way to install a Linux tool / shell and then somehow run it from there?
Any help would be greatly appreciated!