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>*
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