[R] error in installing limma

[Ayushi Dwivedi]

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.creator using gmail.com* <swapnilkr.bi using gmail.com>**
<swapnil.kr using yahoo.com>*


On Wed, Dec 23, 2020 at 4:25 PM Martin Morgan <mtmorgan.bioc using 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.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>*
>