[BioC] installation of Rsamtools

[Steve Lianoglou]

Hi Cornellia,

Brief aside: don't forget to hit reply-all when responding to
bioconductor emails so other people can benefit from the help ((and
more people can help you).

The errors you are getting suggest that you do not have some (or
all(?)) of the library installed in your system itself (this isn't an
R thing, but a system setup/install thing). In fact, it seemslike your
problems with your RCurl install can be explained from information
here:

http://www.omegahat.org/RCurl/FAQ.html

Use your package manager to search for and install the libraries
related to libcurl .. is there a libcurl-devel also? The FAQ suggests
grabbing a package called "libcurl4-openssl-dev" ... I guess you
should use apt-get to find something named similar ...

HTH,
-steve

On Mon, Jan 2, 2012 at 6:11 AM, Cornelia Vesely
<cornelia.vesely at univie.ac.at> wrote:
> Thanks for you answer.
> I was now removing and then installing again the latest R version to make
> sure that there are no problems with the installation or upgrade.
> Then I tried to install just the "limma" package and it worked, however for
> R> biocLite(c("GenomicFeatures", "AnnotationDbi"))
>
> I got several warnings:
>
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ‘XML’ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ‘RCurl’ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ‘biomaRt’ had non-zero exit status
> 4: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ‘rtracklayer’ had non-zero exit status
> 5: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ‘GenomicFeatures’ had non-zero exit status
>
> And also for:
>
> R> biocLite("RCurl")
> * 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 ‘/root/R/x86_64-pc-linux-gnu-library/2.14/RCurl’
>
> The downloaded packages are in
>        ‘/tmp/RtmpPta7xE/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package ‘RCurl’ had non-zero exit status
>
> R> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] 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
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] limma_3.10.0        BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.1
>
>
> I am sorry to bother you again, but I am a quite new Bioconductor user and
> unfortunately also the only one in our lab.
>
> Thank you!
>
> Best
> Conny
>
>
> On Fr, 30.12.2011, 16:16, Steve Lianoglou wrote:
>> Hi again,
>>
>> On Fri, Dec 30, 2011 at 5:39 AM, Conny [guest] <guest at bioconductor.org>
>> wrote:
>>>
>>> I still have problems installing Rsamtools. The first idea was that my R
>>> version was too old - so I updated it to the latest version.
>>
>> Ok, getting close ...
>>
>>> still the installation does not work - any ideas?
>>> this is just the end of the list after:
>>>
>>>> biocLite("Rsamtools")
>>> Warning: S3 methods ‘[<-.CURLOptions’, ‘[[<-.CURLOptions’ were
>>> declared in NAMESPACE but not found
>>> Error in library.dynam(lib, package, package.lib) :
>>>  shared object ‘RCurl.so’ not found
>>> ERROR: lazy loading failed for package ‘Rsamtools’
>>> * removing ‘/home/lab/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
>>> * restoring previous
>>> ‘/home/lab/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
>>
>> [snip]
>>
>> It seems that your RCurl installation is somehow hosed. Did you notice
>> any errors when you tried to install it into your new R-2.14.1
>> install?
>>
>> Or maybe ... did you copy your old packages from your previous R
>> install's library folder to your new version of R? That can open a
>> whole can of worms. I think there are a few ways to go from here.
>>
>> If that's what happened, maybe you can try this maneuver to update
>> your installed packages first. This will try to update all of your
>> installed packages w/o any further intervention from you:
>>
>> R> library(BiocInstaller)
>> R> biocLite(character(), ask=FALSE)
>>
>> If you didn't copy your old R packages to your new install, I'm not
>> sure what happened. You can try to install RCurl again, seeing as how
>> this is the first problem you are running into:
>>
>> R> library(BiocInstaller)
>> R> biocLite('RCurl')
>>
>> Then try Rsamtools again ... keep your eyes open for other packages
>> that are broken and reinstall until the dust settles.
>>
>> If you're still having problems, feel free to reply back with any new
>> surprises you're running into.
>>
>> HTH,
>>
>> -steve
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>  | Memorial Sloan-Kettering Cancer Center
>>  | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
>
>
> --
> DI Cornelia Vesely
> Max F. Perutz Laboratories
> University of Vienna
> Lab of Dr. Michael Jantsch
> Dr. Bohr Gasse 1
> A-1030 Vienna
> AUSTRIA
> Europe
> +43 1 4277 56231
> cornelia.vesely at univie.ac.at
>
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact