Question: codelink package is not installing
2
gravatar for Agaz Hussain Wani
4.6 years ago by
India
Agaz Hussain Wani260 wrote:

I am trying to install codelink package from bioconductor using 

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

It throws me some warnings

 

Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘codelink’ had non-zero exit status


when i try library(codelink), it gives an error: 


Error in library(codelink) : there is no package called ‘codelink’
codelink R • 836 views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Agaz Hussain Wani260

Hi Hussain, thats weird... what is the output of sessionInfo()? Incidentally, Bioc 3.1 has just been released. There might have been some reason why the package was not available before. But it certainly is part of the release. I would try to install again then if you still have problems come back here with the output of sessionInfo() to give us some more information.

ADD REPLYlink written 4.6 years ago by Diego Diez750
1

The problem is that codelink has dependencies, one of which is the XML package. The XML package itself has system dependencies, in particular on linux the existence of the libxml2-dev (and I think libcurl-openssl-dev) libraries. So swim upstream to the original problem, fix it, and work down stream again. Likely this is apparent from a more careful scrutiny of the output from the attempted installation.

ADD REPLYlink written 4.6 years ago by Martin Morgan ♦♦ 24k
R version 3.1.3 RC (2015-03-06 r67947)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 14.04.2 LTS
sessionInfo();

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

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

other attached packages:
[1] BiocInstaller_1.16.4

loaded via a namespace (and not attached):
[1] tools_3.1.3
ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Agaz Hussain Wani260
2

Don't be afraid to provide complete output. You've trimmed the part that tells us what operating system you're using!

ADD REPLYlink written 4.6 years ago by Martin Morgan ♦♦ 24k

Sorry to miss some part. check updated.
 

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Agaz Hussain Wani260
2

Yes, you need to install the system dependency libxml2-dev, from the command line (not inside R) sudo apt-get install libxml2-dev

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Martin Morgan ♦♦ 24k

@ Dear Martin. Thanks a lot for your valuable comments. Its was waiting for dependency libxml2-dev as per you.

ADD REPLYlink written 4.6 years ago by Agaz Hussain Wani260

Oh, my bad. I wrongly understood in your question that biocLite() was suggesting codelink could not be found. But indeed was the lack of xml devel libraries the reason behind the error. Glad to hear your problem is solved.

ADD REPLYlink written 4.6 years ago by Diego Diez750

:) . I am also happy to see it working. let me ask you , why all the dependencies are not installing automatically with codelink. I wish it should go like this.

And i played with your codelink package last night. The thing about targets.txt was not clear to me. I got  expression and SNR but not probe id.

ADD REPLYlink written 4.6 years ago by Agaz Hussain Wani260
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