[BioC] BiocGenerics 0.5.6 not loading properly

[Dan Tenenbaum]

On Wed, Mar 20, 2013 at 11:54 AM, Seb <seba.bat at gmail.com> wrote:
> this is what i get
>
>> biocinstallRepos()
> Error: could not find function "biocinstallRepos"
>
>

OK, do this:

source("http://bioconductor.org/biocLite.R")
biocinstallRepos()

Dan


>
>
>
> On Wed, Mar 20, 2013 at 1:37 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> On Wed, Mar 20, 2013 at 10:35 AM, Seb <seba.bat at gmail.com> wrote:
>> > i just did that and this is the error before R crashes...
>> >
>> > BioC_mirror: http://bioconductor.org
>> > Using R version 2.15, BiocInstaller version 1.4.9.
>> > Error in readRDS(file) : embedded nul in string: '\0'
>> >
>> > ..?!??
>> >
>> >
>>
>> What's the output of the command:
>>
>> biocinstallRepos()
>>
>> ?
>>
>> Dan
>>
>>
>> > On Wed, Mar 20, 2013 at 12:57 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>> > wrote:
>> >>
>> >> Hi Seb,
>> >>
>> >> On Wed, Mar 20, 2013 at 9:53 AM, Seb <seba.bat at gmail.com> wrote:
>> >> > i tried to open Rsamtools but got an error message of
>> >> >
>> >> > Error in eval(expr, envir, enclos) :
>> >> >   could not find function ".getNamespace"
>> >> >
>> >> > i found out if depends on the BiocGenerics tool, so that when i try
>> >> > to
>> >> > open
>> >> > it i get the following error.
>> >> >
>> >> >> library(BiocGenerics)
>> >> > Error in eval(expr, envir, enclos) :
>> >> >   could not find function ".getNamespace"
>> >> > In addition: Warning message:
>> >> > package ‘BiocGenerics’ was built under R version 3.0.0
>> >> > Error : unable to load R code in package ‘BiocGenerics’
>> >> > Error: package/namespace load failed for ‘BiocGenerics’
>> >> >
>> >> > i googled it but i couldn't find any real help to solve this...any
>> >> > idea?
>> >> >
>> >>
>> >>
>> >> It looks like you installed the devel version of some packages. The
>> >> quickest way to fix this is:
>> >>
>> >> source("http://bioconductor.org/biocLite.R")
>> >> biocLite(character())
>> >>
>> >> Then answer "a" at the prompt to reinstall all packages.
>> >> If you always use biocLite() to install packages you won't run into
>> >> this situation.
>> >>
>> >> Dan
>> >>
>> >>
>> >> > thanks
>> >> >
>> >> > Seb
>> >> >
>> >> > ==============================
>> >> >> sessionInfo()
>> >> > R version 2.15.1 (2012-06-22)
>> >> > Platform: x86_64-pc-mingw32/x64 (64-bit)
>> >> >
>> >> > locale:
>> >> > [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> >> > States.1252    LC_MONETARY=English_United States.1252
>> >> > [4] LC_NUMERIC=C                           LC_TIME=English_United
>> >> > States.1252
>> >> >
>> >> > attached base packages:
>> >> > [1] parallel  stats     graphics  grDevices utils     datasets
>> >> > methods
>> >> > base
>> >> >
>> >> > loaded via a namespace (and not attached):
>> >> > [1] tools_2.15.1
>> >> >
>> >> >         [[alternative HTML version deleted]]
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > Bioconductor mailing list
>> >> > Bioconductor at r-project.org
>> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> > Search the archives:
>> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>
>