Question

Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'

0

Entering edit mode

Najla Abassi • 0

@c38f6201

Last seen 8 hours ago

Germany

I was trying to run the function runPCA() but I got the error

function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'

I looked online and found that installing Matrix and irlba from source is a solution. However, I wasn't able to do so due to this error

process_begin: CreateProcess(NULL, basename irlba.dll .dll, ...) failed.
C:/PROGRA~1/R/R-43~1.2/share/make/winshlib.mk:16: pipe: No error
process_begin: CreateProcess(NULL, basename irlba.dll .dll, ...) failed.
C:/PROGRA~1/R/R-43~1.2/share/make/winshlib.mk:16: pipe: No error
process_begin: CreateProcess(NULL, basename irlba.dll .dll, ...) failed.
C:/PROGRA~1/R/R-43~1.2/share/make/winshlib.mk:16: pipe: No error
"zirlb.o utility.o" was unexpected.
make: *** [C:/PROGRA~1/R/R-43~1.2/share/make/winshlib.mk:16: irlba.dll] Error 255
ERROR: compilation failed for package 'irlba'
* removing 'C:/Users/Lenovo/AppData/Local/R/win-library/4.3/irlba'
Warning in install.packages:
   installation of package 'irlba' had non-zero exit status

which makes me think that I have another underlying error. Some links point to installing gfortran but I already did and still have my original problem.

Anyone has an idea on how to proceed? Thanks!

sessionInfo( )

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=French_France.utf8  LC_CTYPE=French_France.utf8    LC_MONETARY=French_France.utf8
[4] LC_NUMERIC=C                   LC_TIME=French_France.utf8    

time zone: Europe/Paris
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 Biobase_2.62.0             
 [4] GenomicRanges_1.54.1        GenomeInfoDb_1.38.5         IRanges_2.36.0             
 [7] S4Vectors_0.40.2            BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
[10] matrixStats_1.2.0          

loaded via a namespace (and not attached):
 [1] Matrix_1.6-1.1          crayon_1.5.2            dplyr_1.1.4            
 [4] compiler_4.3.2          tidyselect_1.2.0        bitops_1.0-7           
 [7] fastmap_1.1.1           lattice_0.21-9          R6_2.5.1               
[10] XVector_0.42.0          S4Arrays_1.2.1          generics_0.1.3         
[13] knitr_1.45              DelayedArray_0.28.0     tibble_3.2.1           
[16] GenomeInfoDbData_1.2.11 DBI_1.2.1               pillar_1.9.0           
[19] rlang_1.1.2             utf8_1.2.4              xfun_0.41              
[22] SparseArray_1.2.4       cli_3.6.2               magrittr_2.0.3         
[25] zlibbioc_1.48.0         grid_4.3.2              digest_0.6.33          
[28] rstudioapi_0.15.0       dbplyr_2.4.0            lifecycle_1.0.4        
[31] vctrs_0.6.5             glue_1.6.2              abind_1.4-5            
[34] RCurl_1.98-1.13         fansi_1.0.6             tools_4.3.2            
[37] pkgconfig_2.0.3         htmltools_0.5.7

scater runPCA • 1.4k views

ADD COMMENT • link updated 8 months ago by alan.ocallaghan ▴ 160 • written 8 months ago by Najla Abassi • 0

1

Entering edit mode

I'm not really familiar with installing from source on Windows. My only suggestion is to ensure you've got all of the relevant bits installed, ie RTools and such. Or perhaps see if you can find any info posted by the irlba devs. As I've posted elsewhere there's not anything I can do to scater to fix this issue, and I've already asked if a solution can be pushed for the general Matrix issue.

ADD REPLY • link 8 months ago alan.ocallaghan ▴ 160

2

Entering edit mode

That's exactly right. I have RTools installed, and this is what happens.

> library(BiocManager)
> install("irlba", type = "source", force = TRUE)
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
Bioconductor version 3.18
  (BiocManager 1.30.22), R 4.3.1
  (2023-06-16 ucrt)
Installing package(s) 'irlba'
trying URL 'https://cran.rstudio.org/src/contrib/irlba_2.3.5.1.tar.gz'
Content type 'application/x-gzip' length 233555 bytes (228 KB)
downloaded 228 KB

* installing *source* package 'irlba' ...
** package 'irlba' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"c:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.3/Matrix/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c irlb.c -o irlb.o
gcc  -I"c:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.3/Matrix/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility.c -o utility.o
gcc -shared -s -static-libgcc -o irlba.dll tmp.def irlb.o utility.o -Lc:/PROGRA~1/R/R-43~1.1/bin/x64 -lRlapack -Lc:/PROGRA~1/R/R-43~1.1/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -Lc:/PROGRA~1/R/R-43~1.1/bin/x64 -lR
installing to C:/Users/jmacdon/AppData/Local/R/win-library/4.3/00LOCK-irlba/00new/irlba/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
package 'Matrix' was built under R version 4.3.2 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package 'Matrix' was built under R version 4.3.2
** testing if installed package can be loaded from final location
Warning: package 'Matrix' was built under R version 4.3.2
** testing if installed package keeps a record of temporary installation path
* DONE (irlba)

ADD REPLY • link 8 months ago James W. MacDonald 67k