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:  LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8  LC_MONETARY=English_United States.utf8  LC_NUMERIC=C  LC_TIME=English_United States.utf8 attached base packages:  stats graphics grDevices utils datasets methods  base other attached packages:  edgeR_3.38.1 limma_3.52.2 BiocManager_1.30.18 loaded via a namespace (and not attached):  compiler_4.2.1 tools_4.2.1 Rcpp_1.0.9  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.