Installation errors for windows

[saezlab]

Installation errors for windows

[deeenes]

Hi Pau,

The current version of OmnipathR is 3.6.* (BioC 3.16) or 3.7.* (BioC 3.17). Here it installs a version from 2021:

OmnipathR (NA -> 3.2.8) [CRAN]
Installing 1 packages: OmnipathR
Installing package into 'D:/a/_temp/Library'
(as 'lib' is unspecified)

  There is a binary version available but the source version is later:
          binary source needs_compilation
OmnipathR  3.2.0  3.2.8             FALSE

installing the source package 'OmnipathR'

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/OmnipathR_3.2.8.tar.gz'
Content type 'application/octet-stream' length 2248[36](https://github.com/saezlab/decoupleR/actions/runs/3882127815/jobs/6625972480#step:15:37)7 bytes (2.1 MB)

You can update the BioC version here, though it's hardcoded at many other points in the action file.

Then the reason of the error is missing purrr. OmnipathR 2021 autumn already had purrr as a dependency, probably the package is installed on the Windows build server, but fails to load its main shared object (dll):

** testing if installed package can be loaded from temporary location
*** arch - i386
Error: Error: package or namespace load failed for 'OmnipathR' in library.dynam(lib, package, package.lib):
*** arch - x64
 DLL 'purrr' not found: maybe not installed for this architecture?
Error: Error: loading failed
Execution halted
ERROR: loading failed for 'i386'
* removing 'D:/a/_temp/Library/OmnipathR'

Also note that the issue is reported for i386 arch only. It suggests you should just disable that architecture, I can't imagine anyone runs Decoupler on such an ancient machine. According to this answer, you could pass the --no-multiarch switch to R CMD INSTALL (here). To achieve the same effect with install.packages or any remotes function, you can pass INSTALL_opts = '--no-multiarch'.

Best,

Denes

[PauBadiaM]

Thanks for the suggestions @deeenes! It seems to work, but now the problem is that the Omnipath server is down (I tried it both in R and Python)

[deeenes]

Yes, sorry, now the server is up again :)

[deeenes]

Hi Pau, I'm closing this as the actions seem to be working now :)