[BioC] BiocGenerics 0.5.6 not loading properly
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Thu Mar 21 20:24:59 CET 2013
I suggests removing all your bioc packages and installing them again
from scratch. This sounds like something which will cause you plenty
of grief in the future.
Perhaps you have already implicitly done this, by upgrading.
Kasper
On Thu, Mar 21, 2013 at 3:22 PM, Seb <seba.bat at gmail.com> wrote:
> 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 at 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 at 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 at fhcrc.org>
>> >> wrote:
>> >>>
>> >>> 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
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>
>> >>>>
>> >>>
>> >>> _______________________________________________
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>> >>
>> >>
>> >> _______________________________________________
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>> >>
>> >
>> >
>> > --
>> > Dr. Martin Morgan, PhD
>> > Fred Hutchinson Cancer Research Center
>> > 1100 Fairview Ave. N.
>> > PO Box 19024 Seattle, WA 98109
>>
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>
>
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