[BioC] GenomicFeatures install error on developement version

Wed Mar 9 02:26:19 CET 2011

Hi Paul,

GenomicFeatures is now fixed (in devel) and the new version should
become available thru biocLite() in 7 to 8 hours.

Cheers,
H.

On 03/07/2011 04:21 PM, Paul Leo wrote:
> HI Martin
> Many Thanks, especially for the instructions and the web sites so I can
> check for myself in the future.
> Cheers
> Paul
>
>
>
>
>
>
> -----Original Message-----
> From: Martin Morgan<mtmorgan at fhcrc.org>
> To: Paul Leo<p.leo at uq.edu.au>
> Cc: bioconductor<bioconductor at r-project.org>
> Subject: Re: [BioC] GenomicFeatures install error on developement
> version
> Date: Tue, 8 Mar 2011 09:55:30 +1000
>
>
> On 03/07/2011 03:16 PM, Paul Leo wrote:
>> Failure to install on a fresh development/R version everything appears
>> up to date:
>>
>> ###Check
>>
>>> source("http://bioconductor.org/biocLite.R")
>> BioC_mirror = http://www.bioconductor.org
>> Change using chooseBioCmirror().
>>>
>> update.packages(lib.loc="/home/pleo/R_latest/library",repos=biocinstallRepos(), ask=FALSE)
>>>
>>
>> #### The Error: "Error : object Ã¢â‚¬ËœextractTranscriptsÃ¢â‚¬â„¢ is not exported by
>> 'namespace:Biostrings'" in below
>>
>>>   biocLite(c("GenomicFeatures"))
>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2.
>> Installing Bioconductor version 2.8 packages:
>> [1] "GenomicFeatures"
>> Please wait...
>>
>> trying URL
>> 'http://www.bioconductor.org/packages/2.8/bioc/src/contrib/GenomicFeatures_1.3.13.tar.gz'
>> Content type 'application/x-gzip' length 412765 bytes (403 Kb)
>> opened URL
>> ==================================================
>> downloaded 403 Kb
>>
>> * installing *source* package Ã¢â‚¬ËœGenomicFeaturesÃ¢â‚¬â„¢ ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>>
>> Attaching package: 'IRanges'
>>
>> The following object(s) are masked from 'package:base':
>>
>>      Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
>>      pmin, pmin.int, rbind, rep.int, setdiff, table, union
>>
>> Error : object Ã¢â‚¬ËœextractTranscriptsÃ¢â‚¬â„¢ is not exported by
>> 'namespace:Biostrings'
>> ERROR: lazy loading failed for package Ã¢â‚¬ËœGenomicFeaturesÃ¢â‚¬â„¢
>
> There was a change in Biostrings. GenomicFeatures was updated, but from
>
>    http://bioconductor.org/checkResults/devel/bioc-LATEST/
>
> GenomicFeatures failed to pass check and so the updated version is not
> available via biocLite. You could wait for GenomicFeatures to be fixed
> (my guess: network issue with biomaRt, but not sure) or download and
> INSTALL (no check) GenomicFeatures from svn
>
>    http://bioconductor.org/developers/source-control/
>
> Martin
>
>> * removing Ã¢â‚¬Ëœ/home/pleo/R_latest/library/GenomicFeaturesÃ¢â‚¬â„¢
>>
>> The downloaded packages are in
>> 	Ã¢â‚¬Ëœ/tmp/RtmpulmTn5/downloaded_packagesÃ¢â‚¬â„¢
>> Updating HTML index of packages in '.Library'
>> Making packages.html  ... done
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>>    installation of package 'GenomicFeatures' had non-zero exit status
>>> sessionInfo()
>> R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>>   [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>>   [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods
>> base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.13.0
>>>
>>
>>
>>
>>
>>
>>
>> ########## try loading the namespace
>>
>>> library(Biostrings)
>> Loading required package: IRanges
>>
>> Attaching package: 'IRanges'
>>
>> The following object(s) are masked from 'package:base':
>>
>>      cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
>>      pmin, pmin.int, rbind, rep.int, setdiff, table, union
>>
>>>   biocLite(c("GenomicFeatures"))
>> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2.
>> Installing Bioconductor version 2.8 packages:
>> [1] "GenomicFeatures"
>> Please wait...
>>
>> trying URL
>> 'http://www.bioconductor.org/packages/2.8/bioc/src/contrib/GenomicFeatures_1.3.13.tar.gz'
>> Content type 'application/x-gzip' length 412765 bytes (403 Kb)
>> opened URL
>> ==================================================
>> downloaded 403 Kb
>>
>> * installing *source* package Ã¢â‚¬ËœGenomicFeaturesÃ¢â‚¬â„¢ ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>>
>> Attaching package: 'IRanges'
>>
>> The following object(s) are masked from 'package:base':
>>
>>      Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
>>      pmin, pmin.int, rbind, rep.int, setdiff, table, union
>>
>> Error : object Ã¢â‚¬ËœextractTranscriptsÃ¢â‚¬â„¢ is not exported by
>> 'namespace:Biostrings'
>> ERROR: lazy loading failed for package Ã¢â‚¬ËœGenomicFeaturesÃ¢â‚¬â„¢
>> * removing Ã¢â‚¬Ëœ/home/pleo/R_latest/library/GenomicFeaturesÃ¢â‚¬â„¢
>>
>> The downloaded packages are in
>> 	Ã¢â‚¬Ëœ/tmp/RtmpulmTn5/downloaded_packagesÃ¢â‚¬â„¢
>> Updating HTML index of packages in '.Library'
>> Making packages.html  ... done
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>>    installation of package 'GenomicFeatures' had non-zero exit status
>>
>>> sessionInfo()
>> R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>>   [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>>   [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods
>> base
>>
>> other attached packages:
>> [1] Biostrings_2.19.15 IRanges_1.9.25
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.11.9 tools_2.13.0
>>>
>>
>>
>> ######### Note sure if I have missed something obvious?
>>
>> Thanks
>> Paul
>>
>> 	[[alternative HTML version deleted]]
>>
>>
>>
>>
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>
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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-- 
Hervé Pagès

Program in Computational Biology
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