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error in installing limma

5 messages · Martin Morgan, Ayushi Dwivedi

Original
Ayushi Dwivedi
# 
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 :- ayushi.creator at gmail.com* <swapnilkr.bi at gmail.com>**
<swapnil.kr at yahoo.com>*

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Martin Morgan
# 
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" <r-help-bounces at r-project.org on behalf of ayushi.creator at 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 :- ayushi.creator at gmail.com* <swapnilkr.bi at gmail.com>**
    <swapnil.kr at yahoo.com>*
Ayushi Dwivedi
# 
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")
*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 at gmail.com* <swapnilkr.bi at gmail.com>**
<swapnil.kr at yahoo.com>*


On Wed, Dec 23, 2020 at 12:21 AM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
      #
    

  


  

      
Show the entire command and output. I have

            

      
      
      
    

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

            

      
      
      
    

        
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 at gmail.com

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

  
  


  


      

    

    

      
      

        


  

        

      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 at gmail.com* <swapnilkr.bi at gmail.com>**
<swapnil.kr at yahoo.com>*


On Wed, Dec 23, 2020 at 4:25 PM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote: