jackbibby1 / SCPA

R package for pathway analysis in scRNA-seq data
https://jackbibby1.github.io/SCPA/
GNU General Public License v3.0
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Multicross no longer valid for New R Versions #66

Closed JyoRoy21 closed 9 months ago

JyoRoy21 commented 10 months ago

The multicross package seems to be no longer available in CRAN and as a result I am not able to download SCPA. I am not sure how to go about it. Following is the error I get when I run: devtools::install_version("multicross", version = "2.1.0", repos = "http://cran.us.r-project.org") I have tried manually uploading the package by downloading from CRAN archive but it doesn't work as well.

ERROR: dependencies ‘nbpMatching’, ‘crossmatch’ are not available for package ‘multicross’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/multicross’
Warning in install.packages :
  installation of package ‘/Users/jyotirmoyroy/Documents/multicross_2.1.0.tar.gz’ had non-zero exit status
> devtools::install_version("multicross", version = "2.1.0", repos = "http://cran.us.r-project.org")
Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/multicross/multicross_2.1.0.tar.gz
Skipping 1 packages not available: crossmatch
Installing 2 packages: crossmatch, nbpMatching
trying URL 'http://cran.us.r-project.org/src/contrib/nbpMatching_1.5.4.tar.gz'
Content type 'application/x-gzip' length 37546 bytes (36 KB)
==================================================
downloaded 36 KB

* installing *source* package ‘nbpMatching’ ...
** package ‘nbpMatching’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
sh: /opt/gfortran/bin/gfortran: No such file or directory
using SDK: ‘MacOSX13.3.sdk’
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c fcorematch.f -o fcorematch.o
make: /opt/gfortran/bin/gfortran: No such file or directory
make: *** [fcorematch.o] Error 1
ERROR: compilation failed for package ‘nbpMatching’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/nbpMatching’

The downloaded source packages are in
    ‘/private/var/folders/wr/0xn73dps2_j22h_swv8b1j140000gn/T/RtmpMImBKj/downloaded_packages’
ERROR: dependencies ‘nbpMatching’, ‘crossmatch’ are not available for package ‘multicross’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/multicross’
Warning messages:
1: package ‘crossmatch’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
2: In i.p(...) :
  installation of package ‘nbpMatching’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘/var/folders/wr/0xn73dps2_j22h_swv8b1j140000gn/T//RtmpMImBKj/remotes4a9b133564e4/multicross’ had non-zero exit stat
jackbibby1 commented 10 months ago

Hi,

It looks like this is an issue with Fortran. Your error says:

sh: /opt/gfortran/bin/gfortran: No such file or directory

You need to install the GNU Fortran compiler. You can get this from the R installation instructions here https://archive.linux.duke.edu/cran/. Click on Download R for MacOS > then follow the link to the Fortran compiler.

Jack

JyoRoy21 commented 10 months ago

I was initially using SCPA in my old R and it was working fine. But early 2024 I updated it and since then SCPA is no longer downloadable due to the mismatch of multicross package with the new version. It seems like multicross package has been removed and not available for the current versions of R. Can something be done about it

jackbibby1 commented 10 months ago

Hi,

The issue isn't with multicross. The issue comes from your newer version of R that relies on having the GNU Fortran compiler installed for packages that use Fortan code. nbpMatching uses Fortran, so you need to install the GNU Fortran compiler

Jack