Issue installing package CiteFuse

[Delphine44]

>library(CiteFuse)
Error: package or namespace load failed for ‘CiteFuse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘propr’

However, I cannot install propr as it's been removed from CRAN repository.

Here is the R code:

> if (!requireNamespace("BiocManager", quietly = TRUE)) {
+     install.packages("BiocManager")
+ }
> BiocManager::install("CiteFuse")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Old packages: 'matrixStats', 'nlme'
Update all/some/none? [a/s/n]: 
a
Warning: package ‘matrixStats’ is in use and will not be installed

  There is a binary version available but the source version is later:
      binary  source needs_compilation
nlme 3.1-160 3.1-161              TRUE

installing the source package ‘nlme’

trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-161.tar.gz'
Content type 'application/x-gzip' length 847304 bytes (827 KB)
downloaded 827 KB

* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
ERROR: cannot remove earlier installation, is it in use?
* removing 'C:/Users/d.guillotin/AppData/Local/Programs/R/R-4.2.2/library/nlme'
* restoring previous 'C:/Users/d.guillotin/AppData/Local/Programs/R/R-4.2.2/library/nlme'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:\Users\d.guillotin\AppData\Local\Programs\R\R-4.2.2\library\00LOCK-nlme\nlme\libs\x64\nlme.dll to C:\Users\d.guillotin\AppData\Local\Programs\R\R-4.2.2\library\nlme\libs\x64\nlme.dll: Permission denied

The downloaded source packages are in
    ‘C:\Users\d.guillotin\AppData\Local\Temp\RtmpGqOZKG\downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'CiteFuse' 
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘nlme’ had non-zero exit status

> library(CiteFuse)
Error: package or namespace load failed for ‘CiteFuse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘propr’

> install.packages("~/propr_4.2.6.tar.gz", repos = NULL)
* installing *source* package 'propr' ...
** package 'propr' successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11  -I"C:/Users/DF0E3~1.GUI/AppData/Local/Programs/R/R-42~1.2/include" -DNDEBUG  -I'C:/Users/d.guillotin/AppData/Local/Programs/R/R-4.2.2/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
sh: line 1: g++: command not found
make: *** [C:/Users/DF0E3~1.GUI/AppData/Local/Programs/R/R-42~1.2/etc/x64/Makeconf:260: RcppExports.o] Error 127
ERROR: compilation failed for package 'propr'
* removing 'C:/Users/d.guillotin/AppData/Local/Programs/R/R-4.2.2/library/propr'
Warning in install.packages :
  installation of package ‘C:/Users/d.guillotin/OneDrive - Achilles Therapeutics Limited/Documents/propr_4.2.6.tar.gz’ had non-zero exit status

[Delphine44]

I solved the problem by installing propr from Github directly:

devtools::install_github("tpq/propr")

[nick-robo]

We are working on replacing propr, but this is a good interim solution.