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

[Laurent Gautier]

Sorry for the late answer. I answered to an other email without
realizing that it was off-list.

It looks that I was unlucky. I did think that it was a transient
issue, but reported it after about 24 hours.

Thanks,


L.


2008/4/2, Herve Pages <hpages at fhcrc.org>:
> 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
> >
> > _______________________________________________
> > Bioc-devel at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>