Installation error on Windows (R 4.3.3): unable to load pagoda2.dll – LoadLibrary failure

[Dacy34]

Hello,

I am trying to install pagoda2 from GitHub on a Windows machine, but the installation fails when testing the package loading step. I would like to ask whether this issue might be related to compatibility with newer R versions.

System information

• OS: Windows 10 (64-bit)
• R version: 4.3.3
• Rtools: 4.3
• Installation method: devtools::install_github("kharchenkolab/pagoda2")

Installation command

devtools::install_github("kharchenkolab/pagoda2")

Error message

Error: package or namespace load failed for 'pagoda2' in inDL(x, as.logical(local), as.logical(now), ...):
 unable to load shared object '.../pagoda2/libs/x64/pagoda2.dll':
  LoadLibrary failure: The specified module could not be found.

Full message during installation:

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'pagoda2' in inDL(x, as.logical(local), as.logical(now), ...):
 unable to load shared object '.../pagoda2/libs/x64/pagoda2.dll':
  LoadLibrary failure: The specified module could not be found.

What I have already tried

• Installed required dependencies (Rcpp, RcppArmadillo, Matrix, igraph, Rtsne, RANN, irlba)
• Confirmed that Rtools is correctly installed (pkgbuild::check_build_tools(debug = TRUE))
• Restarted R session and reinstalled
• Removed the 00LOCK-pagoda2 folder and tried installing again

However, the same DLL loading error persists.

Question

Could this be related to compatibility with R 4.3 on Windows?
If so, is there a recommended R version or installation method for pagoda2?

Any suggestions would be greatly appreciated.

Thank you for developing and maintaining this package.

[evanbiederstedt]

Hi @Dacy34

Pagoda2 should still install on Windows.

Please try:

git clone https://github.com/kharchenkolab/pagoda2.git
cd pagoda2
R CMD build . 
R CMD INSTALL

The issue here is rather the packages N2R, conos, and pagoda2 were archived on CRAN in the past 48 hours given they started using gcc-UBSan on packages. There was a misaligned pointer flag tripped in N2R, which led to all packages being archived as I try to update the code.

Hopefully these will be back up CRAN soon as I fix this.

I hope the above helps

Best, Evan

[Dacy34]

Hi Evan (@evanbiederstedt),

Thank you very much for your quick and detailed response — I really appreciate it.

That explains the issue clearly, especially regarding the recent CRAN archiving related to N2R and the gcc-UBSan checks. I understand now that the installation problem is not specific to my setup.

I will try installing pagoda2 from source using the steps you suggested.

Thanks again for your help and for maintaining the package — looking forward to the updated version on CRAN.

Best regards,
Dacy

[evanbiederstedt]

@Dacy34

Thanks for the patience with this. The package was updated on CRAN on 31 March 2026: https://cran.r-project.org/web/packages/pagoda2/index.html