WGCNA not working with R 3.6.2

Question

[nicholas.macknight]

Hi,

I have previously and recently used WGCNA. I updated R to 3.6.2 and the installation of WGCNA is required and not working.

install.packages("WGCNA")

which gives me this response:

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? (Yes/no/cancel) Yes

installing the source package ‘WGCNA’

trying URL 'https://cran.rstudio.com/src/contrib/WGCNA_1.68.tar.gz'

Content type 'application/x-gzip' length 1166156 bytes (1.1 MB)

downloaded 1.1 MB

• installing source package ‘WGCNA’ ... * package ‘WGCNA’ successfully unpacked and MD5 sums checked * using staged installation ** libs xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ERROR: compilation failed for package ‘WGCNA’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/WGCNA’ Warning in install.packages : installation of package ‘WGCNA’ had non-zero exit status

The downloaded source packages are in ‘/private/var/folders/nx/_07512cx3cdfz3464ts6glqw0000gn/T/Rtmp9dbXqM/downloaded_packages’

Any help or suggestions is appreciated.

Answer 1

[nicholas.macknight]

This worked:

xcode-select --install

Thank you, everyone, for your time and help.

Answer 2

[tothepoint]

Try this:

install.packages("WGCNA", dependencies=TRUE)

[nicholas.macknight]

Thank you for your time, devarora, here is my attempt at your suggestion:

install.packages("WGCNA", dependencies=TRUE)

Warning in install.packages : dependencies ‘org.Hs.eg.db’, ‘org.Mm.eg.db’, ‘minet’ are not available also installing the dependencies ‘infotheo’, ‘entropy’

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? (Yes/no/cancel) Yes trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/infotheo_1.2.0.tgz'

Content type 'application/x-gzip' length 130670 bytes (127 KB)

downloaded 127 KB

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/entropy_1.2.1.tgz'

Content type 'application/x-gzip' length 79449 bytes (77 KB)

downloaded 77 KB

The downloaded binary packages are in /var/folders/nx/_07512cx3cdfz3464ts6glqw0000gn/T//RtmpEfzNmA/downloaded_packages installing the source package ‘WGCNA’

trying URL 'https://cran.rstudio.com/src/contrib/WGCNA_1.68.tar.gz'

Content type 'application/x-gzip' length 1166156 bytes (1.1 MB)

downloaded 1.1 MB

• installing source package ‘WGCNA’ ... * package ‘WGCNA’ successfully unpacked and MD5 sums checked * using staged installation ** libs xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ERROR: compilation failed for package ‘WGCNA’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/WGCNA’ Warning in install.packages : installation of package ‘WGCNA’ had non-zero exit status

The downloaded source packages are in ‘/private/var/folders/nx/_07512cx3cdfz3464ts6glqw0000gn/T/RtmpEfzNmA/downloaded_packages’

[tothepoint]

When such error occurs to me I just manually install the libraries first which are not available. For instance here "dependencies ‘org.Hs.eg.db’, ‘org.Mm.eg.db’, ‘minet’ are not available also installing the dependencies ‘infotheo’, ‘entropy’". Most of the time it works. You could also give a try. Try installing these first and then WGCNA hope this work well.

I have not experienced this but recently I saw somewhere posted in these situation where: 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? Proceed with "no" and installation was successful.

Answer 3

[h.mon]

You are probably on a Mac (you should have stated your operating system so we don't have to guess), and you should install Apple's XCode.

[nicholas.macknight]

so sassy!,

mac