Unable to download CATALYST
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Entering edit mode
David • 0
@4aed4ce5
Last seen 6 weeks ago
United States

Hi, I'm currently trying to use R to analyze mass cytometry data. I attempted to download CATALYST several times, however, it keeps giving me error messages. I use the following code as specified on Bioconductor:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("edgeR")


sessionInfo( )
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

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

other attached packages:
[1] edgeR_3.38.1        limma_3.52.2        BiocManager_1.30.18

loaded via a namespace (and not attached):
[1] compiler_4.2.1  tools_4.2.1     Rcpp_1.0.9     
[4] grid_4.2.1      locfit_1.5-9.6  lattice_0.20-45

And I keep receiving this error message:

'getOption("repos")' replaces Bioconductor standard
repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1
  (2022-06-23 ucrt)
Installing package(s) 'CATALYST'
also installing the dependency ‘FlowSOM’

Package which is only available in source form, and may
  need compilation of C/C++/Fortran: ‘FlowSOM’
installing the source packages ‘FlowSOM’, ‘CATALYST’

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/FlowSOM_2.4.0.tar.gz'
Content type 'application/x-gzip' length 6078511 bytes (5.8 MB)
downloaded 5.8 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/CATALYST_1.20.1.tar.gz'
Content type 'application/x-gzip' length 10723172 bytes (10.2 MB)
downloaded 10.2 MB

* installing *source* package 'FlowSOM' ...
** using staged installation
** libs
gcc  -I"C:/PROGRA~1/R/R-42~1.1/include" -DNDEBUG     -I"C:/RBuildTools/4.2/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c som.c -o som.o
gcc -shared -s -static-libgcc -o FlowSOM.dll tmp.def som.o -LC:/RBuildTools/4.2/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/RBuildTools/4.2/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-42~1.1/bin/x64 -lR
installing to C:/Users/DWQWork/AppData/Local/R/win-library/4.2/00LOCK-FlowSOM/00new/FlowSOM/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'interp'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package 'FlowSOM'
* removing 'C:/Users/DWQWork/AppData/Local/R/win-library/4.2/FlowSOM'
ERROR: dependency 'FlowSOM' is not available for package 'CATALYST'
* removing 'C:/Users/DWQWork/AppData/Local/R/win-library/4.2/CATALYST'

The downloaded source packages are in
    ‘C:\Users\DWQWork\AppData\Local\Temp\RtmpQ7tbG7\downloaded_packages’
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.1/library
  packages:
    MASS, nlme
Warning messages:
1: In install.packages(...) :
  installation of package ‘FlowSOM’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘CATALYST’ had non-zero exit status

What exactly does a non-zero exit status mean, and how can I prevent it from happening again? I have not received any errors when attempting to use BiocManager to download other packages like edgeR. I would greatly appreciate any advice on this matter.

CATALYST • 326 views
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shepherl 3.4k
@lshep
Last seen 2 hours ago
United States
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'interp'

Could you try installing interp and then try again?
BiocManager::install('interp')

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Thank you, it worked like a charm!

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