I am trying to load the flowUtils package from Bioconductor 3.16 (BiocManager 1.30.19) using RStudio on my Windows 11 laptop but for some reason I am unable to. I know the package has been released for this version of Bioconductor (https://bioconductor.org/packages/release/bioc/), so I am very confused as to why I cannot download flowUtils. Any help is greatly welcome. Thanks in advance!
Please see my code below.
#problematic code
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("flowUtils", type = "binary")
#output of the code below
> if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
>
> BiocManager::install("flowUtils")
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'flowUtils'
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.2/library
packages:
boot, Matrix
Old packages: 'xfun'
Update all/some/none? [a/s/n]: a
trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.2/xfun_0.35.zip'
Content type 'application/zip' length 406240 bytes (396 KB)
downloaded 396 KB
package ‘xfun’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘xfun’
Warning: restored ‘xfun’
The downloaded binary packages are in
C:\Users\zaqai\AppData\Local\Temp\Rtmp6NbbuT\downloaded_packages
Warning messages:
1: package ‘flowUtils’ is not available for Bioconductor version '3.16'
A version of this package 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:\Users\zaqai\AppData\Local\R\win-library\4.2\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\zaqai\AppData\Local\R\win-library\4.2\xfun\libs\x64\xfun.dll: Permission denied
#session information
sessionInfo( )
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_India.utf8 LC_CTYPE=English_India.utf8 LC_MONETARY=English_India.utf8 LC_NUMERIC=C LC_TIME=English_India.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.19
loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2
Unfortunately the flowUtils package is deprecated in Bioconductor 3.16. You can see this at the top of the landing page at https://www.bioconductor.org/packages/release/bioc/html/flowUtils.html There's a paragraph that says:
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is because the package is consistently failing one or more of the checks Bioconductor requires packages to pass. This means the package can't be built and really is "not available for 3.16".
It actually looks like the author of flowUtils requested the deprecation (List of Deprecated Packages for Bioc3.16) so, if the package is very important to you, I'd recommend reaching out to them to ask if there is an alternative package they suggest or if they might reconsider the deprecation.