Question: Error installing WGCNA for R 3.6 in RStudio Version 1.2.1335
0
gravatar for rm1238
4 weeks ago by
rm12380
rm12380 wrote:

Hello there,

I was just wondering why I am getting the following error when I am trying to install WGCNA in R Studio Version 1.2.1335 R version 3.6. When trying to install I get the error highlighted in bold.

Any help would be greatly appreciated.

Ricardo

if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") BiocManager::install("WGCNA", version = "3.9") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'WGCNA' 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) y installing the source package ‘WGCNA’

trying URL 'https://cran.rstudio.com/src/contrib/WGCNA_1.67.tar.gz'

Content type 'application/x-gzip' length 1163525 bytes (1.1 MB)

downloaded 1.1 MB

  • installing source package ‘WGCNA’ ... * package ‘WGCNA’ successfully unpacked and MD5 sums checked * using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DWITH_THREADS -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c corFunctions-utils.c -o corFunctions-utils.o clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot] corFunctions-utils.c:16:10: fatal error: 'stdio.h' file not found

    include <stdio.h>

     ^~~~~~~~~
    

    **1 error generated. make: * [corFunctions-utils.o] Error 1 ERROR: compilation failed for package ‘WGCNA’

  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/WGCNA’**
ADD COMMENTlink modified 4 weeks ago by Peter Langfelder2.1k • written 4 weeks ago by rm12380
Answer: Error installing WGCNA for R 3.6 in RStudio Version 1.2.1335
0
gravatar for Peter Langfelder
4 weeks ago by
United States
Peter Langfelder2.1k wrote:

You seem to be missing the very basic header files that any standard C compiler should have available. I not a Mac user but the previous warning

clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]

may have something to do with it. I would guess that you are pointing clang to a non-existent directory tree. Check your clang installation (and potentially that of all development tools).

ADD COMMENTlink written 4 weeks ago by Peter Langfelder2.1k
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