[BioC] GenomicFeatures install error on developement version

[Martin Morgan]

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 ‘extractTranscripts’ 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 ‘GenomicFeatures’ ...
> ** 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 ‘extractTranscripts’ is not exported by
> 'namespace:Biostrings'
> ERROR: lazy loading failed for package ‘GenomicFeatures’

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 ‘/home/pleo/R_latest/library/GenomicFeatures’
> 
> The downloaded packages are in
> 	‘/tmp/RtmpulmTn5/downloaded_packages’
> 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 ‘GenomicFeatures’ ...
> ** 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 ‘extractTranscripts’ is not exported by
> 'namespace:Biostrings'
> ERROR: lazy loading failed for package ‘GenomicFeatures’
> * removing ‘/home/pleo/R_latest/library/GenomicFeatures’
> 
> The downloaded packages are in
> 	‘/tmp/RtmpulmTn5/downloaded_packages’
> 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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