[BioC] BiocGenerics 0.5.6 not loading properly
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Thu Mar 21 01:03:42 CET 2013
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.
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 will update all your outdated packages but your packages are too new.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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