thanks for the follow up comments.
what i know, is that i had R 2.15.1 (the one that crashed). i installed the
2.15.3 and that seemed to fix the problem, i had no more crashes or weird
error messages.
i didn't have to use the code that Dan wrote, however, when i tried to use
it in the 2.15.1 it crashed and the crash was caused by the
installed.packages() call.


On Wed, Mar 20, 2013 at 8:19 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> Nice, I seem to recall a similar discussion before.
>
> Kasper
>
> On Wed, Mar 20, 2013 at 8:12 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:
> > On 3/20/2013 5:03 PM, Kasper Daniel Hansen wrote:
> >>
> >> Do we have some kind of reporting tool in BiocInstaller like, check
> >> all packages on my system - do they match what I would get with
> >> BiocLite (perhaps up to minor version differences).  That way we can
> >> get users to do something like
> >>    biocLite(report = TRUE)
> >> If we don't have it, it would be handy.
> >
> >
> > We've tried to implement things in the BiocInstaller package, rather than
> > biocLite.R, so perhaps
> >
> >   library(BiocInstaller)
> >   validPackages()
> >
> > (or is that validLibraries()?) with validPackages having argument pkgs =
> > installed.packages() ? It seems like Seb's installation was sufficiently
> > messed up that this wouldn't have been too helpful in the current
> situation.
> > validPackages() (or similar) could also report sessionInfo() as a matter
> of
> > course.
> >
> > Martin
> >
> >
> >>
> >> Kasoer
> >>
> >> On Wed, Mar 20, 2013 at 5:24 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
> wrote:
> >>>
> >>> On Wed, Mar 20, 2013 at 2:22 PM, Seb <seba.bat@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@fhcrc.org>
> >>>> wrote:
> >>>>>
> >>>>>
> >>>>> On Wed, Mar 20, 2013 at 11:58 AM, Seb <seba.bat@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@fhcrc.org>
> >>>>>> wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, Mar 20, 2013 at 11:54 AM, Seb <seba.bat@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@fhcrc.org>
> >>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Wed, Mar 20, 2013 at 10:35 AM, Seb <seba.bat@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@fhcrc.org>
> >>>>>>>>>> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> Hi Seb,
> >>>>>>>>>>>
> >>>>>>>>>>> On Wed, Mar 20, 2013 at 9:53 AM, Seb <seba.bat@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@r-project.org
> >>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>>>>>>>>> Search the archives:
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
> > --
> > Dr. Martin Morgan, PhD
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
> > PO Box 19024 Seattle, WA 98109
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
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>

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