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,