Installation of package ‘scran’ had non-zero exit status

[awurmser]

Hello,

I have tried to install the package "scran", but will receive the following error code. I have tried to google the error, but have not been able to come up with a workable solution. I am currently using R version 4.0.4 (2021-02-15). I also tried to install the other missing packages, but they returned the same error codes.

BiocManager::install('scran')
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.4 (2021-02-15)
Installing package(s) 'scran'
also installing the dependencies ‘sparseMatrixStats’, ‘scuttle’, ‘DelayedMatrixS
tats’

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/sparseMatrix
Stats_1.2.1.tar.gz'
Content type 'application/x-gzip' length 698554 bytes (682 KB)

downloaded 682 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/scuttle_1.0.
4.tar.gz'
Content type 'application/x-gzip' length 387528 bytes (378 KB)

downloaded 378 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/DelayedMatri
xStats_1.12.3.tar.gz'
Content type 'application/x-gzip' length 271827 bytes (265 KB)

downloaded 265 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/scran_1.18.5
.tar.gz'
Content type 'application/x-gzip' length 1818765 bytes (1.7 MB)

downloaded 1.7 MB

• installing source package ‘sparseMatrixStats’ ...
  ** using staged installation
  ** libs
  Error: C++14 standard requested but CXX14 is not defined
• removing ‘/home/aamw4/R-4.0.4/library/sparseMatrixStats’
  ERROR: dependency ‘sparseMatrixStats’ is not available for package ‘DelayedMatri
  xStats’
• removing ‘/home/aamw4/R-4.0.4/library/DelayedMatrixStats’
  ERROR: dependency ‘DelayedMatrixStats’ is not available for package ‘scuttle’
• removing ‘/home/aamw4/R-4.0.4/library/scuttle’
  ERROR: dependencies ‘scuttle’, ‘DelayedMatrixStats’ are not available for packag
  e ‘scran’
• removing ‘/home/aamw4/R-4.0.4/library/scran’

The downloaded source packages are in
‘/tmp/Rtmps6q95U/downloaded_packages’
Old packages: 'boot', 'cluster', 'MASS', 'mgcv'
Update all/some/none? [a/s/n]: a
trying URL 'https://cran.rstudio.com/src/contrib/boot_1.3-27.tar.gz'
Content type 'application/x-gzip' length 236799 bytes (231 KB)

downloaded 231 KB

trying URL 'https://cran.rstudio.com/src/contrib/cluster_2.1.1.tar.gz'
Content type 'application/x-gzip' length 397306 bytes (387 KB)

downloaded 387 KB

trying URL 'https://cran.rstudio.com/src/contrib/MASS_7.3-53.1.tar.gz'
Content type 'application/x-gzip' length 505007 bytes (493 KB)

downloaded 493 KB

trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.8-34.tar.gz'
Content type 'application/x-gzip' length 1149538 bytes (1.1 MB)

downloaded 1.1 MB

• installing source package ‘boot’ ...
  ** package ‘boot’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (boot)
• installing source package ‘cluster’ ...
  ** package ‘cluster’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c clara.c -o clara.o
  gfortran -fpic -g -O2 -c daisy.f -o daisy.o
  gfortran -fpic -g -O2 -c dysta.f -o dysta.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c fanny.c -o fanny.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c init.c -o init.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c mona.c -o mona.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c pam.c -o pam.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c sildist.c -o sildist.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c spannel.c -o spannel.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c twins.c -o twins.o
  gcc -std=gnu99 -shared -L/home/aamw4/R-4.0.4/lib64/R/lib -L/usr/local/lib64 -o c
  luster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.
  o twins.o -lgfortran -lm -lquadmath -L/home/aamw4/R-4.0.4/lib64/R/lib -lR
  installing to /home/aamw4/R-4.0.4/lib64/R/library/00LOCK-cluster/00new/cluster/l
  ibs
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  ** checking absolute paths in shared objects and dynamic libraries
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (cluster)
• installing source package ‘MASS’ ...
  ** package ‘MASS’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c MASS.c -o MASS.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fpic -g -O2 -c lqs.c -o lqs.o
  gcc -std=gnu99 -shared -L/home/aamw4/R-4.0.4/lib64/R/lib -L/usr/local/lib64 -o M
  ASS.so MASS.o lqs.o -L/home/aamw4/R-4.0.4/lib64/R/lib -lR
  installing to /home/aamw4/R-4.0.4/lib64/R/library/00LOCK-MASS/00new/MASS/libs
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  ** checking absolute paths in shared objects and dynamic libraries
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (MASS)
• installing source package ‘mgcv’ ...
  ** package ‘mgcv’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fopenmp -fpic -g -O2 -c coxph.c -o coxph.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fopenmp -fpic -g -O2 -c davies.c -o davies.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  nclude -fopenmp -fpic -g -O2 -c discrete.c -o discrete.o
  gcc -std=gnu99 -I"/home/aamw4/R-4.0.4/lib64/R/include" -DNDEBUG -I/usr/local/i
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  ** checking absolute paths in shared objects and dynamic libraries
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (mgcv)

The downloaded source packages are in
‘/tmp/Rtmps6q95U/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(...) :
installation of package ‘sparseMatrixStats’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘DelayedMatrixStats’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘scuttle’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘scran’ had non-zero exit status

I would very much appreciate your help,

Best, Annabelle

[LTLA]

This is really a sparseMatrixStats problem, see my comments in the linked issue.

[awurmser]

Thank you LTLA, it was indeed a problem with the compiler version. I updated to gcc 7.2 and was fine.
Best,