installation error

[TahneeMa]

Hi, when trying to install lemur I got the following error:
Error: object ‘vars’ is not exported by 'namespace:glmGamPoi'
Execution halted
ERROR: lazy loading failed for package ‘lemur’

I think it might have to do with packages previously installed that are not compatible?

[const-ae]

Hey, thanks for reporting the issue. I assume that you are using glmGamPoi version 1.9 or 1.10? lemur is using the pseudobulk function from glmGamPoi which I only added recently in the development version. Can you see if installing glmGamPoi from Github fixes the issue?

devtools::install_github("const-ae/glmGamPoi")

[TahneeMa]

Hi, thank you! I tried as I saw something similar in previous issues but then got a completely different error:

ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [glmGamPoi.so] Error 1
ERROR: compilation failed for package ‘glmGamPoi’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/glmGamPoi’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/glmGamPoi’ ```

[const-ae]

Sorry for the tedious experience and thank you so much for giving my packages a try. This is really valuable feedback that will hopefully make things easier for everyone in the future.

I have already adapted the DESCRIPTION to state the minimum required version of glmGamPoi and amended the README with a note that one needs to install glmGamPoi from source.

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I am surprised by the error message, because glmGamPoi does not contain Fortran code. But anyways, could you maybe try to follow the advice on https://mac.r-project.org/tools/ to install the GNU Fortran compiler? (Based on the error message I assume that you are using a mac, right?)