[BioC] BiocGenerics 0.5.6 not loading properly

Martin Morgan mtmorgan at fhcrc.org
Thu Mar 21 01:12:39 CET 2013 

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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