Installation failed due to missing dependency (WGCNA)

umerijaz / microbiomeSeq

An R package for microbial community analysis in an environmental context

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Installation failed due to missing dependency (WGCNA) #10

Closed DSLUCB closed 6 years ago

DSLUCB commented 6 years ago

I am running R v.3.4.3. The error is about the "WGCNA" package not being available for microbiomeSeq.

"ERROR: dependency ‘WGCNA’ is not available for package ‘microbiomeSeq’

removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/microbiomeSeq’ Installation failed: Command failed (1)"

Any advice on how to solve this?

Thanks.

AlfredUg commented 6 years ago

Hey @DSLUCB, please install "WGCNA" package from Cran https://cran.r-project.org/web/packages/WGCNA/index.html, alternatively, if you are using Rstudio you can directly install it using the install button on the packages tab.

I hope that helps.

DSLUCB commented 6 years ago

Hi @AlfredUg , I tried to do that too but it may need compilation from source. "Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘WGCNA’ Do you want to attempt to install these from sources? "

I will try this if it is not too hard but microbiomeSeq's functions look great and worst case is to run independently those that do not rely on WGCNA.

Thank you and very good work!

AlfredUg commented 6 years ago

Hi @DSLUCB, you could follow the procedure here see if it gets you to install WGCNA successfully. It is not hard, following those instructions may solve this issue really fast. Please kindly let us know how it goes.

Thanks.

motroy commented 6 years ago

Hi all,

If it helps, I am using R version 3.4.3 (on ubuntu 14.04), also had a problem with WGCNA...then installed it through bioconductor, and it works.

source("http://bioconductor.org/biocLite.R") biocLite('WGCNA')

then retry the microbiomeSeq installation

regards

rolo1323 commented 5 years ago

I am having the same issue trying to install WGCNA. I tried installing directly from Cran and bioconductor to no avail.

"Warning: package ‘fastcluster’ was built under R version 3.4.4 Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘mvtnorm’ ERROR: lazy loading failed for package ‘WGCNA’

removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/WGCNA’ installation of package ‘WGCNA’ had non-zero exit status"

Any help would be greatly appreciated.

Thanks.

AlfredUg commented 5 years ago

Heya @rolo1323, from the error message above, there is no package called ‘mvtnorm’, install mvtnorm normally from cran and you will be good to go.

I hope that helps.

rolo1323 commented 5 years ago

It did! Thanks.