[BioC] 'namespace:Biostrings' error when installing VariantAnnotation

[Thomas Damm Als]

Hi Steve & Martin,

Thanks for your input - it is greatly appreciated!


I wanted to use VariantAnnotation/Bioconductor on our cluster facility,
and I'm a little reluctant for updating to R 3.01 on the cluster.

I tried various things, and ended up with recompiling installed
Bioconductor packages like this:

	source("http://bioconductor.org/biocLite.R")
	pkgs <- rownames(installed.packages())
	biocLite(pkgs)

After that I was able to install VariantAnnotation successfully, but when
I check package versions as suggested by Steve versions differed from when
I initially checked (see below):

	> packageVersion("IRanges")
	[1] ‘1.14.4’
	> packageVersion("Biostrings")
	[1] ‘2.24.1’
	> packageVersion("GenomicRanges")
	[1] ‘1.8.13’


I came across the following error when I tried "various things", and think
that this may very well have been the main problem:


	ERROR: failed to lock directory
‘/home/als/R/x86_64-unknown-linux-gnu-library/2.15’ for modify	
	Try removing 
‘/home/als/R/x86_64-unknown-linux-gnu-library/2.15/00LOCK-IRanges’

	The downloaded source packages are in
	‘/tmp/RtmpVmN90j/downloaded_packages’
	Warning messages:
	1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
	installation of package ‘IRanges’ had non-zero exit status
	2: installed directory not writable, cannot update packages 'akima',
	'AnnotationDbi', 'BiasedUrn', 'BiocInstaller', 'bitops', 'caTools',
	'cluster', 'DBI', 'doMC', 'doParallel', 'doSNOW', 'foreach', 'foreign',
	'gdata', 'gtools', 'igraph', 'KernSmooth', 'labeling', 'lattice',
'locfit',
	'Matrix', 'mgcv', 'nnet', 'RCurl', 'rpart', 'RSQLite', 'snow', 'survival',
	'XML', 'xtable' 

Cheers,
Thomas

------------------------------------------------------
Thomas Damm Als, PhD

Associate Professor
Department of Biomedicine
Aarhus University
Building 1243

Wilhelm Meyers Allé 4
8000 Aarhus C, Denmark
Direct: +45 8716 8498

email: tda at hum-gen.au.dk
------------------------------------------------------











Den 25/06/13 18.50 skrev "Martin Morgan" <mtmorgan at fhcrc.org>:

>On 06/25/2013 04:47 PM, Steve Lianoglou wrote:
>> Hi Thomas,
>>
>> Please use "reply all" when replying to emails on the bioconductor
>>lists so that more people can help you and also so that the back and
>>forths can remain useful to others in general.
>>
>> That having been said:
>>
>> On Jun 25, 2013, at 6:45 AM, Thomas Damm Als <tda at hum-gen.au.dk> wrote:
>>
>>> Hi Steve,
>>>
>>> I have tried installing the package in two ways:
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("VariantAnnotation")
>>>
>>> library(BiocInstaller)
>>> biocLite("VariantAnnotation")
>>>
>>>
>>> Here's the output from the commands you asked me to run:
>>>> packageVersion("IRanges")
>>> [1] Œ1.16.6¹
>>>> packageVersion("Biostrings")
>>> [1] Œ2.26.3¹
>>>> packageVersion("GenomicRanges")
>>> [1] Œ1.10.7¹
>>
>> It looks like your version numbers are matching up with the version of
>>R/Bioconductor that you are using, so I'm not sure what's going on.
>>
>
>I think Steve is on the right track; it could be GenomicFeatures, or you
>might 
>discover the problem with
>
>   trace(loadNamespace, quote(print(package)))
>   library(GenomicFeatures)
>
>you'll a package name printed each time a dependency is asked to be
>loaded. 
>Probably the last package displayed is the one that is out of sync with
>your 
>installation; compare it with the version available at
>
>   http://bioconductor.org/packages/2.11/bioc/html/GenomicRanges.html
>
>with 'GenomicRanges' replaced by whatever package appears to be the
>problem.
>
>For what it's worth (not relevant in this immediate case), in 3.0.1 it
>might 
>have been possible to ask
>
>   BiocInstaller::biocValid()
>
>for some hints.
>
>Martin
>
>> I'd recommend that you update to the latest version of R (3.0.1) and
>>reinstall your packages via biocLite (I just installed VariantAnnotation
>>without a problem on R-3.0.1), but that advice isn't too helpful if for
>>some reason you need R 2.15.x
>>
>> HTH,
>> -steve
>>
>> --
>> Steve Lianoglou
>> Computational Biologist
>> Bioinformatics and Computational Biology
>> Genentech
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>-- 
>Computational Biology / Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N.
>PO Box 19024 Seattle, WA 98109
>
>Location: Arnold Building M1 B861
>Phone: (206) 667-2793