[BioC] BiocGenerics 0.5.6 not loading properly

[Dan Tenenbaum]

On Wed, Mar 20, 2013 at 11:58 AM, Seb <seba.bat at gmail.com> wrote:
> this is what i get
>
>> source("http://bioconductor.org/biocLite.R")
> BiocInstaller version 1.4.9, ?biocLite for help
> A newer version of Bioconductor is available for this version of R,
> ?BiocUpgrade for help
>> biocinstallRepos()
>                                                BioCsoft
> BioCann
>            "http://bioconductor.org/packages/2.10/bioc"
> "http://bioconductor.org/packages/2.10/data/annotation"
>                                                 BioCexp
> BioCextra
> "http://bioconductor.org/packages/2.10/data/experiment"
> "http://bioconductor.org/packages/2.10/extra"
>                                                    CRAN
> CRANextra
>                                 "http://cran.case.edu/"
> "http://www.stats.ox.ac.uk/pub/RWin"
>> 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 still cannot load BiocGenerics :(


Sorry, I gave you the wrong advice.

biocLite(character())
will update all your outdated packages but your packages are too new.


So here is how to replace all your packages that are too new:

pkgs <- installed.packages()
blt <- pkgs [, "Built"]
v <- package_version(blt)
names(v) <- names(blt)
res <- v >= 3
installme <- names(res)
source("http://bioconductor.org/biocLite.R")
biocLite(installme)

Dan

>
> On Wed, Mar 20, 2013 at 2:55 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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
>> >> >
>> >> >
>> >
>> >
>
>