[Bioc-devel] Error: package 'BSgenome' 1.7.6 was found, but >= 1.7.7 is required

[Herve Pages]

Hi Laurent,

Can you try again? BSgenome 1.7.7 is now on line (since noon, Seattle time).
I needed to push the new BSgenome.* data packages (1.3.3) to the data repo first
so the build system could actually find them and latest Biostrings+BSgenome would
build and check properly. So for a few hours, the new BSgenome.* data package were
available but not usable, sorry!

H.


Laurent Gautier wrote:
> I get the error
> Error: package 'BSgenome' 1.7.6 was found, but >= 1.7.7 is required
> with a fresh download of the package with
> biocLite.
> 
> biocLite('BSgenome') seem to download and install v. 1.7.6.
> 
> 
> I enclose a copy a session done a minute ago below:
> 
>> biocLite("BSgenome")
> Running biocinstall version 2.2.6 with R version 2.7.0 (under development)
> Your version of R requires version 2.2 of Bioconductor.
> trying URL 'http://bioconductor.org/packages/2.2/bioc/src/contrib/BSgenome_1.7.6.tar.gz'
> Content type 'application/x-gzip' length 8770 bytes
> opened URL
> ==================================================
> downloaded 8770 bytes
> 
> * Installing *source* package 'BSgenome' ...
> ** R
> ** preparing package for lazy loading
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Loading required package: Biostrings
> ** help
>  >>> Building/Updating help pages for package 'BSgenome'
>      Formats: text html ex example
>   BSgenome-class                    text    html    latex   example
>   available.genomes                 text    html    latex   example
> Note: removing empty section \value
> Note: removing empty section \details
> Note: removing empty section \seealso
> Note: removing empty section \examples
>   buildDataFiles                    text    html    latex
> Note: removing empty section \details
>   getSeq                            text    html    latex   example
> ** building package indices ...
> * DONE (BSgenome)
> 
> The downloaded packages are in
> 	/tmp/RtmpUnMbIX/downloaded_packages
> Updating HTML index of packages in '.Library'
> 
>> biocLite("BSgenome.Dmelanogaster.FlyBase.r51")
> Running biocinstall version 2.2.6 with R version 2.7.0 (under development)
> Your version of R requires version 2.2 of Bioconductor.
> trying URL 'http://bioconductor.org/packages/2.2/data/annotation/src/contrib/BSgenome.Dmelanogaster.FlyBase.r51_1.3.3.tar.gz'
> Content type 'application/x-gzip' length 38738570 bytes (36.9 Mb)
> opened URL
> ==================================================
> downloaded 36.9 Mb
> 
> * Installing *source* package 'BSgenome.Dmelanogaster.FlyBase.r51' ...
> ** R
> ** inst
> ** help
>  >>> Building/Updating help pages for package
> 'BSgenome.Dmelanogaster.FlyBase.r51'
>      Formats: text html latex example
>   BSgenome.Dmelanogaster.FlyBase.r5 text    html    latex
> ** building package indices ...
> * DONE (BSgenome.Dmelanogaster.FlyBase.r51)
> 
> The downloaded packages are in
> 	/tmp/RtmpUnMbIX/downloaded_packages
> Updating HTML index of packages in '.Library'
>> library(BSgenome.Dmelanogaster.FlyBase.r51)
> Error: package 'BSgenome' 1.7.6 was found, but >= 1.7.7 is required by
> 'BSgenome.Dmelanogaster.FlyBase.r51'
>>  sessionInfo()
> R version 2.7.0 alpha (2008-04-01 r45026)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;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 utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
> 
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