Error install SCPA on R 4.3.1

[camilla0801]

Hi!

I am having issue installing the package. R version 4.3.1 (2023-06-16) -- "Beagle Scouts". When I do:

# install.packages("devtools")
devtools::install_version("crossmatch", version = "1.3.1", repos = "http://cran.us.r-project.org")
devtools::install_version("multicross", version = "2.1.0", repos = "http://cran.us.r-project.org")
devtools::install_github("jackbibby1/SCPA")

I got massive error saying:

Warning in install.packages :
  dependency ‘singscore’ is not available
installing the source package ‘clustermole’

trying URL 'http://cran.rstudio.com/src/contrib/clustermole_1.1.0.tar.gz'
Content type 'application/x-gzip' length 1298322 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

ERROR: dependency ‘singscore’ is not available for package ‘clustermole’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/clustermole’
Warning in install.packages :
  installation of package ‘clustermole’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/w2/826prqh14cq_pjljhh87q2lh0000gq/T/RtmpKBwyM4/downloaded_packages’
> # install.packages("devtools")
> devtools::install_version("crossmatch", version = "1.3.1", repos = "http://cran.us.r-project.org")
Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/crossmatch/crossmatch_1.3-1.tar.gz
Installing 1 packages: nbpMatching
trying URL 'http://cran.us.r-project.org/src/contrib/nbpMatching_1.5.1.tar.gz'
Content type 'application/x-gzip' length 28872 bytes (28 KB)
==================================================
downloaded 28 KB

* installing *source* package ‘nbpMatching’ ...
** package ‘nbpMatching’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
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/w2/826prqh14cq_pjljhh87q2lh0000gq/T/RtmpKBwyM4/downloaded_packages’
ERROR: dependency ‘nbpMatching’ is not available for package ‘crossmatch’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/crossmatch’
Warning messages:
1: In i.p(...) :
  installation of package ‘nbpMatching’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘/var/folders/w2/826prqh14cq_pjljhh87q2lh0000gq/T//RtmpKBwyM4/remotesb6e2c7eb61f/crossmatch’ 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_1.5.1.tar.gz'
Content type 'application/x-gzip' length 28872 bytes (28 KB)
==================================================
downloaded 28 KB

* installing *source* package ‘nbpMatching’ ...
** package ‘nbpMatching’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
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/w2/826prqh14cq_pjljhh87q2lh0000gq/T/RtmpKBwyM4/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/w2/826prqh14cq_pjljhh87q2lh0000gq/T//RtmpKBwyM4/remotesb6e24cf96bf9/multicross’ had non-zero exit status
> devtools::install_github("jackbibby1/SCPA")
Downloading GitHub repo jackbibby1/SCPA@HEAD
Skipping 6 packages not available: singscore, GSVA, GSEABase, SummarizedExperiment, multicross, ComplexHeatmap
Installing 3 packages: singscore, multicross, clustermole
Warning: dependency ‘singscore’ is not available
installing the source package ‘clustermole’

trying URL 'http://cran.rstudio.com/src/contrib/clustermole_1.1.0.tar.gz'
Content type 'application/x-gzip' length 1298322 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

ERROR: dependency ‘singscore’ is not available for package ‘clustermole’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/clustermole’

The downloaded source packages are in
	‘/private/var/folders/w2/826prqh14cq_pjljhh87q2lh0000gq/T/RtmpKBwyM4/downloaded_packages’
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/w2/826prqh14cq_pjljhh87q2lh0000gq/T/RtmpKBwyM4/remotesb6e2365647ca/jackbibby1-SCPA-e4357fb/DESCRIPTION’ ...
─  preparing ‘SCPA’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in
     serialize/load version 3 cannot be read in older versions of R.
     File(s) containing such objects:
       ‘SCPA/inst/rds_files/th1_tcm.rds’
─  building ‘SCPA_1.5.3.tar.gz’
   
ERROR: dependencies ‘clustermole’, ‘multicross’ are not available for package ‘SCPA’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SCPA’
Warning messages:
1: packages ‘singscore’, ‘multicross’ are not available for this version of R

Versions of these packages 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 ‘clustermole’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘/var/folders/w2/826prqh14cq_pjljhh87q2lh0000gq/T//RtmpKBwyM4/fileb6e25d7f1368/SCPA_1.5.3.tar.gz’ had non-zero exit status
> 

Any idea why is that?

Thank you very much for the help!

Camilla

[jackbibby1]

Hi Camilla,

It looks to be an issue with installing some dependencies. Can you try installing singscore and nbpMatching first, restart R, and then install SCPA? i.e.

packages <- c("nbpMatching", "singscore")
BiocManager::install(packages)
**** restart R ****
devtools::install_version("crossmatch", version = "1.3.1", repos = "http://cran.us.r-project.org")
devtools::install_version("multicross", version = "2.1.0", repos = "http://cran.us.r-project.org")
devtools::install_github("jackbibby1/SCPA")

Jack

[camilla0801]

it worked! thank you very much!