Question

codelink package is not installing

2

Entering edit mode

Agaz Hussain Wani ▴ 260

@agaz-hussain-wani-7620

Last seen 6.0 years ago

India

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 • 1.7k views

ADD COMMENT • link 9.0 years ago Agaz Hussain Wani ▴ 260

0

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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 REPLY • link 9.0 years ago Diego Diez ▴ 760

1

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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 REPLY • link 9.0 years ago Martin Morgan 25k

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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 REPLY • link 9.0 years ago Agaz Hussain Wani ▴ 260

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

ADD REPLY • link 9.0 years ago Martin Morgan 25k

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Sorry to miss some part. check updated.

ADD REPLY • link 9.0 years ago Agaz Hussain Wani ▴ 260

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

ADD REPLY • link 9.0 years ago Martin Morgan 25k

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

ADD REPLY • link 9.0 years ago Agaz Hussain Wani ▴ 260

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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 REPLY • link 9.0 years ago Diego Diez ▴ 760

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:) . 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 REPLY • link 9.0 years ago Agaz Hussain Wani ▴ 260