[BioC] installation packages

[Steve Lianoglou]

Hi Fran,

On Wed, Sep 25, 2013 at 2:25 AM, fran vino <biocesca at gmail.com> wrote:
> 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

Surely there must have been more errors than these ... please paste in
the entire output you get that includes the errors.

The information you are providing is not sufficient to offer any help.
We need to see the actual errors that are reported during the
installation of rtracklayer, not the notice afterwards that says it
wasn't able to be installed.

At least from the sessionInfo you provided below, we can tell that
RCurl now installs successfully, though.

> R> biocLite(“Genomic Features”)

This command did not produce the errors below, as there is no package
with that name (notice the space)!

Please, load BiocInstaller, then type `biocLite("rtracklayer")` and
then copy and paste *everything* that happens after that.

-steve

> 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 at 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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>
>
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-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech