Question: Error in WGCNA packages installation in R?
0
gravatar for harshraje19
4 months ago by
harshraje1930
harshraje1930 wrote:

Dear all. I am trying to install the WGCNA, but whenever i install it, it gives me following error,

Warning in install.packages : installation of package ‘WGCNA’ had non-zero exit status

can anyone help me to solve this error?

Thanks and regards Harshraj

snp R software error • 515 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by harshraje1930

Hi Thank you for your suggestions. I tried but not working

ADD REPLYlink written 4 months ago by harshraje1930

Check the pages below!

WGCNA installation

FAQ

ADD REPLYlink modified 4 months ago • written 4 months ago by mbk0asis550
0
gravatar for devarora
4 months ago by
devarora160
SouthKorea
devarora160 wrote:

Try this:

install.packages(c("matrixStats", "Hmisc", "splines", "foreach", "doParallel", "fastcluster", "dynamicTreeCut", "survival"))

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

biocLite(c("GO.db", "preprocessCore", "impute"))

or install locally : For Linux For Windows For Unix.

ADD COMMENTlink written 4 months ago by devarora160

Hi Thank you for your suggestions. I tried but not working

ADD REPLYlink written 4 months ago by harshraje1930

Try this:

install.packages("BiocManager")

BiocManager::install("WGCNA")

and what is the error? Is there any library missing or what you are getting there.

ADD REPLYlink modified 4 months ago • written 4 months ago by devarora160

install.packages("BiocManager") BiocManager::install("WGCNA") Error: unexpected symbol in "install.packages("BiocManager") BiocManager"

ADD REPLYlink written 4 months ago by harshraje1930

There was formatting issue. Try now

ADD REPLYlink written 4 months ago by devarora160

Following error has found

he downloaded source packages are in ‘/tmp/Rtmp7SFM5k/downloaded_packages’ Installation path not writeable, unable to update packages: boot, class, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, survival Warning messages: 1: In install.packages(...) : installation of package ‘png’ had non-zero exit status 2: In install.packages(...) : installation of package ‘jpeg’ had non-zero exit status 3: In install.packages(...) : installation of package ‘acepack’ had non-zero exit status 4: In install.packages(...) : installation of package ‘impute’ had non-zero exit status 5: In install.packages(...) : installation of package ‘preprocessCore’ had non-zero exit status 6: In install.packages(...) : installation of package ‘latticeExtra’ had non-zero exit status 7: In install.packages(...) : installation of package ‘Hmisc’ had non-zero exit status 8: In install.packages(...) : installation of package ‘WGCNA’ had non-zero exit status

ADD REPLYlink written 4 months ago by harshraje1930
1

There is a trick that worked for me when I got such error. I installed all the packages manually which exit with non-zero exit status such:

install.packages(c('libraries list ', 'with', 'non-zero', 'error'))

enter all the packages name in it like acepack, impute etc and finally installed the package again with

BiocManager::install('WGCNA')
ADD REPLYlink modified 4 months ago • written 4 months ago by devarora160

Yes. It is working for me. Thank you very much

ADD REPLYlink written 4 months ago by harshraje1930

Type 'sessionInfo()', and post the output here. That could be helpful for experts (not me) to solve your problem.

ADD REPLYlink written 4 months ago by mbk0asis550
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