[BioC] GenomicFeatures installation error -- object ‘readDNAStringSet’ is not exported by 'namespace:Biostrings'

[Dan Tenenbaum]

Looks like you are mixing and matching release and devel packages
(AnnotationDbi_1.19.15 is a devel package).
This can lead to unpredictable results.
You can either maintain two separate R installations for release and
devel, or maintain one but use the technique described here:

http://bioconductor.org/developers/useDevel/

Dan


On Fri, Jun 29, 2012 at 1:24 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> Installing package(s) 'GenomicFeatures'
> trying URL '
> http://www.bioconductor.org/packages/2.10/bioc/src/contrib/GenomicFeatures_1.8.2.tar.gz
> '
> Content type 'application/x-gzip' length 1745766 bytes (1.7 Mb)
> opened URL
> ==================================================
> downloaded 1.7 Mb
>
> * installing *source* package ‘GenomicFeatures’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : object ‘readDNAStringSet’ is not exported by 'namespace:Biostrings'
> ERROR: lazy loading failed for package ‘GenomicFeatures’
> * removing ‘/usr/lib64/R/library/GenomicFeatures’
> * restoring previous ‘/usr/lib64/R/library/GenomicFeatures’
>
> The downloaded source packages are in
>        ‘/tmp/Rtmp3aHGQx/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Making packages.html  ... done
>
> sessionInfo():
>
> R> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
>          LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
>  [1] AnnotationDbi_1.19.15 GenomicRanges_1.9.28  IRanges_1.15.15
> matrixStats_0.5.0     MASS_7.3-19           methylumi_2.3.4
> ggplot2_0.9.1
>  [8] reshape2_1.2.1        scales_0.2.1          Biobase_2.17.6
>  BiocGenerics_0.3.0    BiocInstaller_1.4.7   dataframe_2.5
> devtools_0.7
> [15] gtools_2.7.0
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.35.2    biomaRt_2.13.1     Biostrings_2.24.1
>  colorspace_1.1-1   DBI_0.2-5          dichromat_1.2-4    digest_0.5.2
>  grid_2.15.0        httr_0.1.1
> [10] labeling_0.1       lattice_0.20-6     memoise_0.1        munsell_0.3
>     plyr_1.7.1         proto_0.3-9.2      R.methodsS3_1.4.2
>  RColorBrewer_1.0-5 RCurl_1.91-1
> [19] RSQLite_0.11.1     stats4_2.15.0      stringr_0.6        tools_2.15.0
>      XML_3.9-4          xtable_1.7-0       zlibbioc_1.3.0
>
>
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
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>
>
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