Hi,

when I do library(XML) inside R, it loads properly, but if I do:

R> biocLite(c("RCurl", "rtracklayer")), it results:

Warning message:

In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :

installation of package ‘rtracklayer’ had non-zero exit status

or:

R> biocLite(“Genomic Features”)

Warning messages:

1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :

installation of package ‘rtracklayer’ had non-zero exit status

2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :

installation of package ‘GenomicFeatures’ had non-zero exit status


 > sessionInfo()

R version 3.0.1 (2013-05-16)

Platform: x86_64-pc-linux-gnu (64-bit)

 locale:

[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C

[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8

[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8

[7] LC_PAPER=C LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C

 attached base packages:

[1] stats graphics grDevices utils datasets methods base

 other attached packages:

[1] RCurl_1.95-4.1 bitops_1.0-6 XML_3.98-1.1

[4] BiocInstaller_1.10.3

 loaded via a namespace (and not attached):

[1] tools_3.0.


2013/9/24 Steve Lianoglou <lianoglou.steve@gene.com>

> Hi Fran,
>
> Please keep all emails on list (hit "reply-all") so that your emails go
> back to the main bioconductor list as well.
>
> In this way you'll have more people able to help you, and others can
> benefit from our conversations in the future by searching the email
> archives.
>
> Now:
>
> > I performed this command and I solved the problem only for installation
> of XML packages, because if I try to perform biocLite for the other
> packages it results:
> > Warning messages:
> > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> >   installation of package ‘rtracklayer’ had non-zero exit status
> > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> >   installation of package ‘GenomicFeatures’ had non-zero exit status
> > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> >   installation of package ‘VariantAnnotation’ had non-zero exit status
> > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> >   installation of package ‘gmapR’ had non-zero exit status
> >
> > This is the same warning message that I had with XML packages. How I can
> solve it?
>
> You will need to provide more output than that to get help.
>
> You say that after installing libcurl-dev and libxml2-dev on your system,
> the  XML library install worked in R?
>
> So when you do `library(XML)` inside R, does it load properly?
>
> Can you please provide the entire output when you do:
>
> R> library(BiocInstaller)
> R> biocLite(c("RCurl", "rtracklayer"))
>
> Please also include the entire output of sessionInfo() after the above
> commands fail.
>
> Thanks,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>
>
>
>

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