Search
Question: Installation of package DESeq2
0
gravatar for Rémi Willamme
10 months ago by
University of Liege, Belgium
Rémi Willamme0 wrote:

Hello everybody,

 

I'm quite new to both Linux and R but would like to use both for analysis of RNA-Seq data.

I desperately would like to install R package DESeq2 but always get a error message whatever the way i try to install it :

 

> source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘DESeq2’
also installing the dependencies ‘RCurl’, ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz'
Content type 'application/x-gzip' length 916934 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/annotate_1.52.1.tar.gz'
Content type 'application/x-gzip' length 1860820 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz'
Content type 'application/x-gzip' length 1407436 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/geneplotter_1.52.0.tar.gz'
Content type 'application/x-gzip' length 1426298 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/DESeq2_1.14.1.tar.gz'
Content type 'application/x-gzip' length 1406022 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘annotate’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmpRxerxe/downloaded_packages’
installation path not writeable, unable to update packages: survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

 

I also tried to install the package via the package menu but I got this :

>  install.packages("DESeq2")

Installing package into ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3’ (as ‘lib’ is unspecified)

Warning in install.packages :  package ‘DESeq2’ is not available (for R version 3.3.2)

 

Finally i downloaded the package archive file (.tar.gz) and tried once again but without success :

> install.packages("~/Downloads/DESeq2_1.14.1.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3’ (as ‘lib’ is unspecified)
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/DESeq2’
Warning in install.packages :
  installation of package ‘/home/rwillamme/Downloads/DESeq2_1.14.1.tar.gz’ had non-zero exit status 

 

I tried to solve it myself by checking the already existing posts, and made 

$ sudo apt-get install libxml2-dev

And got this for an answer :

sudo: unable to resolve host gene-remi
[sudo] password for rwillamme: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
libxml2-dev is already the newest version (2.9.3+dfsg1-1ubuntu0.1).
The following packages were automatically installed and are no longer required:
  linux-headers-4.4.0-47 linux-headers-4.4.0-47-generic linux-headers-4.4.0-51
  linux-headers-4.4.0-51-generic linux-image-4.4.0-47-generic
  linux-image-4.4.0-51-generic linux-image-extra-4.4.0-47-generic
  linux-image-extra-4.4.0-51-generic
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

 

But it didn't help...

> sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2

 

Any help would be sooo welcome!

Thanks already!

ADD COMMENTlink modified 10 months ago by Martin Morgan ♦♦ 20k • written 10 months ago by Rémi Willamme0
1
gravatar for Martin Morgan
10 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

Solve the first problem -- RCurl -- first. You're on the right track with the system dependency; you'll also need, e.g.,

$ sudo apt-get install libcurl4-openssl-dev

and then

> biocLite("RCurl")
ADD COMMENTlink written 10 months ago by Martin Morgan ♦♦ 20k
1

This comes up a lot :)

I've added it to the DESeq2 FAQ

https://github.com/Bioconductor-mirror/DESeq2/commit/1a2b72504aea8d351930e8de868351fdcaf4722e#diff-0a5eedd893e500963c6c91d921d160cd

ADD REPLYlink written 10 months ago by Michael Love14k

Done, thanks!


It looks OK both for the terminal and R commands.

I however have that "not writeable" at the end :

(...)

installing to /home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/RCurl/libs

** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RCurl)

The downloaded source packages are in    ‘/tmp/RtmpRxerxe/downloaded_packages’
installation path not writeable, unable to update packages: survival

Should I go on with the next step ("annotate")? And if so, how?

ADD REPLYlink written 10 months ago by Rémi Willamme0
1

Not writeable means that the library (directory) where survival was installed is not owned by the account running biocLite(). Probably this means that 'recommended' packages were installed using an administrator account. You could (a) ignore it; (b) run R and update survival under an administrator account (but then exit R and return to your normal user account); or (c) re-install R without recommended packages as administrator, then install recommended packages as a regular user. (a) would be a reasonable short term solution, (c) the best long-term solution. (b) would mostly perpetuate a confusing situation, leading eventually to (a) or (c).

Yes, you could try annotation, biocLite("annotate"), but likely you can now jump to biocLite("DESeq2").

ADD REPLYlink written 10 months ago by Martin Morgan ♦♦ 20k

Thanks a lot! I directly jumped to biocLite("DESeq2") and it worked.

 

Looking forward to analyzing my data and keeping on discovering bioinformatics world!

 

NB : I will go for option (a) for the moment since i'm not an expert. As long as it works, that's fine for me..

ADD REPLYlink modified 10 months ago • written 10 months ago by Rémi Willamme0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 170 users visited in the last hour