[BioC] BiocGenerics 0.5.6 not loading properly

[Dan Tenenbaum]

On Wed, Mar 20, 2013 at 2:22 PM, Seb <seba.bat at gmail.com> wrote:
> Dan, no problems and thanks for following up with tips.
>
> the problem with that script is that as soon as i run
>
> installed.packages()
>
> i get:
>> installed.packages()
> Error in readRDS(file) : embedded nul in string: '\0'
>
> and R crashes...
>
> do you think it might be time to uninstall R with all the packages and then
> re-install everything?
>
>

Yes, definitely.
Dan


>
> On Wed, Mar 20, 2013 at 5:03 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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 will update all your outdated packages but your packages are too new.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
>> >> >> >
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>