[BioC] BiocGenerics 0.5.6 not loading properly
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Thu Mar 21 01:19:06 CET 2013
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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