please find the attached doc which contains error while installing limma..
*Ayushi Dwivedi* *Ph.D. Scholar* *Dept. of Biotechnology & Bioinformatics,* School of Life Sciences, University of Hyderabad, Hyderabad - 500046 ( India ). Phone No. :- +91 - 8858037252 Email Id :- ayushi.crea...@gmail.com* <swapnilkr...@gmail.com>** <swapnil...@yahoo.com>* On Wed, Dec 23, 2020 at 4:25 PM Martin Morgan <mtmorgan.b...@gmail.com> wrote: > Show the entire command and output. I have > > > BiocManager::install("limma") > Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) > Installing package(s) 'limma' > trying URL ' > https://bioconductor.org/packages/3.12/bioc/src/contrib/limma_3.46.0.tar.gz > ' > Content type 'application/x-gzip' length 1527170 bytes (1.5 MB) > ================================================== > downloaded 1.5 MB > > * installing *source* package ‘limma’ ... > ** using staged installation > ** libs > gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic > -g -O2 -fstack-protector-strong -Wformat -Werror=format-security > -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o > gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic > -g -O2 -fstack-protector-strong -Wformat -Werror=format-security > -Wdate-time -D_FORTIFY_SOURCE=2 -g -c normexp.c -o normexp.o > gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic > -g -O2 -fstack-protector-strong -Wformat -Werror=format-security > -Wdate-time -D_FORTIFY_SOURCE=2 -g -c weighted_lowess.c -o > weighted_lowess.o > gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o limma.so init.o > normexp.o weighted_lowess.o -L/usr/local/lib/R/lib -lR > installing to /usr/local/lib/R/site-library/00LOCK-limma/00new/limma/libs > ** R > ** inst > ** byte-compile and prepare package for lazy loading > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded from temporary location > ** checking absolute paths in shared objects and dynamic libraries > ** testing if installed package can be loaded from final location > ** testing if installed package keeps a record of temporary installation > path > * DONE (limma) > > > From: Ayushi Dwivedi <ayushi.crea...@gmail.com> > Date: Wednesday, December 23, 2020 at 12:52 AM > To: Martin Morgan <mtmorgan.b...@gmail.com> > Cc: "r-help@r-project.org" <r-help@r-project.org>, " > r-help-requ...@r-project.org" <r-help-requ...@r-project.org> > Subject: Re: [R] error in installing limma > > > hey.. I used this command to install limma but after running sometime it > terminated with error "installation of package ‘limma’ had non-zero exit > status". > > if (!requireNamespace("BiocManager", quietly = TRUE)) > + install.packages("BiocManager") > > BiocManager::install("limma") > > > Ayushi Dwivedi > Ph.D. Scholar > Dept. of Biotechnology & Bioinformatics, > School of Life Sciences, University of Hyderabad, > Hyderabad - 500046 ( India ). > Phone No. :- +91 - 8858037252 > Email Id :- mailto:ayushi.crea...@gmail.com > > > On Wed, Dec 23, 2020 at 12:21 AM Martin Morgan <mailto: > mtmorgan.b...@gmail.com> wrote: > limma is a Bioconductor package so you should use > https://support.bioconductor.org > > I'd guess that you've trimmed your screen shot just after the informative > information. Just copy and paste as plain text the entire output of your > installation attempt. Presumably you are using standard practices > documented on, e.g., https://bioconductor.org/packages/limma to install > packages > > > BiocManager::install("limma") > > Martin Morgan > > On 12/22/20, 1:11 PM, "R-help on behalf of Ayushi Dwivedi" <mailto: > r-help-boun...@r-project.org on behalf of mailto:ayushi.crea...@gmail.com> > wrote: > > Good afternoon Sir, > With due respect I want to convey that while installing limma package > in > R, I am getting the error message, not just limma If I am installing > any > package in R like biomaRt the same error message is coming it is > terminating with "installation of package ‘limma’ had non-zero exit > status". > Hereby, I am attaching the screenshot of the error. Kindly, go through > it. > I shall be highly obliged. > > > > > > > > *Ayushi Dwivedi* > *Ph.D. Scholar* > *Dept. of Biotechnology & Bioinformatics,* > School of Life Sciences, University of Hyderabad, > Hyderabad - 500046 ( India ). > Phone No. :- +91 - 8858037252 > Email Id :- mailto:ayushi.crea...@gmail.com* <mailto: > swapnilkr...@gmail.com>** > <mailto:swapnil...@yahoo.com>* > ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.