Install error

[Sunyp-IM]

Hello everyone,

I tried to install irGSEA in Windows 10 system, but got the following error:

ERROR: dependencies 'AUCell', 'ComplexHeatmap', 'decoupleR', 'ggtree', 'Nebulosa', 'singscore' are not available for package 'irGSEA'
* removing 'C:/R/R-4.2.2/library/irGSEA'
Warning messages:
1: packages ‘singscore’, ‘Nebulosa’, ‘ggtree’, ‘decoupleR’, ‘ComplexHeatmap’, ‘AUCell’ are not available for this version of R

Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\R\R-4.2.2\library\00LOCK\cli\libs\x64\cli.dll to C:\R\R-4.2.2\library\cli\libs\x64\cli.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\R\R-4.2.2\library\00LOCK\fastmap\libs\x64\fastmap.dll to C:\R\R-4.2.2\library\fastmap\libs\x64\fastmap.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\R\R-4.2.2\library\00LOCK\htmltools\libs\x64\htmltools.dll to C:\R\R-4.2.2\library\htmltools\libs\x64\htmltools.dll: Permission denied
5: In i.p(...) :
  installation of package ‘C:/Users/ys738/AppData/Local/Temp/RtmpSuQ8C1/file28ac5c0453f/irGSEA_2.1.3.tar.gz’ had non-zero exit status

Do you have any idea of how to fix this?

Best regards and many thanks!

[chuiqin]

First, packages 'AUCell', 'ComplexHeatmap', 'decoupleR', 'ggtree', 'Nebulosa', 'singscore' are not available in CRAN. Please consider to install them from Bioconductor as follow:

# install packages from Bioconductor
bioconductor.packages <- c("AUCell", "BiocParallel", "ComplexHeatmap", "decoupleR", "fgsea",
                           "ggtree", "GSEABase", "GSVA", "Nebulosa", "scde", "singscore",
                           "SummarizedExperiment", "UCell", "viper")
if (!requireNamespace(bioconductor.packages, quietly = TRUE)) { 
    BiocManager::install(bioconductor.packages, ask = F, update = F)
}

Second, R installed on the C drive does not seem to have sufficient permissions to read and write. Please consider reinstalling R and installing R on another disk, such as D drive.

[surinderchd]

Please help me to solve this error, Warning in install.packages : packages ‘UCell’, ‘irGSEA’ are not available for this version of R

Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages,

Thanks and Regards Surinder Pal

[chuiqin]

Please help me to solve this error, Warning in install.packages : packages ‘UCell’, ‘irGSEA’ are not available for this version of R

Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages,

Thanks and Regards Surinder Pal

You can install UCell and irGSEA packages by the following methods.

BiocManager::install("UCell", ask = F, update = F)
devtools::install_github("chuiqin/irGSEA", force =T)