[R] error in installing limma

[Martin Morgan]

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.creator using gmail.com>
Date: Wednesday, December 23, 2020 at 12:52 AM
To: Martin Morgan <mtmorgan.bioc using gmail.com>
Cc: "r-help using r-project.org" <r-help using r-project.org>, "r-help-request using r-project.org" <r-help-request using 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.creator using gmail.com


On Wed, Dec 23, 2020 at 12:21 AM Martin Morgan <mailto:mtmorgan.bioc using 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-bounces using r-project.org on behalf of mailto:ayushi.creator using 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.creator using gmail.com* <mailto:swapnilkr.bi using gmail.com>**
    <mailto:swapnil.kr using yahoo.com>*