[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
Laurent Gatto
lg390 at cam.ac.uk
Tue Nov 4 23:16:37 CET 2014
On 4 November 2014 20:39, Martin Morgan wrote:
> On 11/04/2014 11:03 AM, Laurent Gatto wrote:
>>
>> On 4 November 2014 13:41, Martin Morgan wrote:
>>
>>> Hi Laurent --
>>>
>>> On 11/04/2014 01:33 AM, Laurent Gatto wrote:
>>>>
>>>> Something's fishy with my R devel/Bioc 3.1 installation and I fail to
>>>> see what is wrong.
>>>>
>>
>> [...]
>>
>>>>> bioclite("homo.sapiens")
>>>> ## bioc_mirror: http://bioconductor.org
>>>> ## using bioconductor version 3.1 (biocinstaller 1.17.1), r version 3.2.0.
>>>> ## installing package(s) 'homo.sapiens'
>>>> ## trying url 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/homo.sapiens_1.1.2.tar.gz'
>>>> ## content type 'application/x-gzip' length 1511 bytes
>>>> ## opened url
>>>> ## ==================================================
>>>> ## downloaded 1511 bytes
>>>> ##
>>>> ## * installing *source* package ‘homo.sapiens’ ...
>>>> ## ** r
>>>> ## ** data
>>>> ## ** preparing package for lazy loading
>>>> ## error : .onload failed in loadnamespace() for 'go.db', details:
>>>> ## call: ls(envir, all.names = true)
>>>> ## error: 2 arguments passed to .internal(ls) which requires 3
>>>> ## error : package ‘go.db’ could not be loaded
>>>> ## error: lazy loading failed for package ‘homo.sapiens’
>>>> ## * removing ‘/home/lg390/r/x86_64-unknown-linux-gnu-library/3.2/homo.sapiens’
>>>> ## * restoring previous ‘/home/lg390/r/x86_64-unknown-linux-gnu-library/3.2/homo.sapiens’
>>>> ##
>>>> ## the downloaded source packages are in
>>>> ## ‘/tmp/rtmprr15y4/downloaded_packages’
>>>> ## warning message:
>>>> ## in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>> ## installation of package ‘homo.sapiens’ had non-zero exit status
>>>>
>>>> I have the exact same error with ReportingTools/PFAM.db,
>>>> Mus.musculus/GO.db and probably others.
>>>>
>>>> Session info with other relevant package versions below. I experienced
>>>> the same error with a slightly older R-devel (2014-10-29 r66897).
>>>>
>>>> Any hints?
>>>
>>> Somewhere I think there's a stale serialized R-3.1 reference to ls(), derived
>>> from a package build with R-3.1 rather than R-devel.
>>>
>>> A little detective work shows that packages are loaded in the following order
>>>
>>> ...
>>> [43] "graph" "RBGL"
>>> [45] "GO.db" "org.Hs.eg.db"
>>> [47] "TxDb.Hsapiens.UCSC.hg19.knownGene" "Homo.sapiens"
>>>
>>> so I wonder if org.Hs.eg.db or TxDb.... is actually the problem, and
>>> biocLite(org.Hs.eg.db) or TxDb... (maybe with type="source") would help?
>
> I saw that you said biocLite('homo.sapiens') and that there was a reference to
> 'go.db' (lower case!). It seems really weird that these work ??
>
> > biocLite('homo.sapiens')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
> Installing package(s) 'homo.sapiens'
> Warning messages:
> 1: package 'homo.sapiens' is not available (for R version 3.1.2 Patched)
> 2: Perhaps you meant 'Homo.sapiens' ?
>
> but now I guess this is some of that emacs magic you've got going?
Yes, probably an unexpected key combination.
>>
>> I tried to re-install all TxDb*, org* packages (using type="source"),
>> but without success.
>>
>> Is type = "source" not the default (and only option) on linux? Does is
>> matter if I specify it or not?
>
> yep, you're right, type="source" wouldn't be relevant on a Linux environment.
>
>>
>>> It might help to (maybe before biocLite(), to find the source of the problem)
>>>
>>> biocLite("Homo.sapiens", INSTALL_opts="--no-test-load")
>>
>> Unfortunately that fails too.
>
> Not sure what 'that fails too' means...? I think the package would fail to load
> (next step, library(Homo.sapiens) but not install, and that when it failed to
> load you could do traceback() or options(error=recover); library(Homo.sapiens)
> and gain some insight into what package was actually failing to load.
> library("BiocInstaller")
Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help
> biocLite("Homo.sapiens", INSTALL_opts="--no-test-load")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version 3.2.0.
Installing package(s) 'Homo.sapiens'
trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/Homo.sapiens_1.1.2.tar.gz'
Content type 'application/x-gzip' length 1511 bytes
opened URL
==================================================
downloaded 1511 bytes
* installing *source* package ‘Homo.sapiens’ ...
** R
** data
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
call: ls(envir, all.names = TRUE)
error: 2 arguments passed to .Internal(ls) which requires 3
Error : package ‘GO.db’ could not be loaded
ERROR: lazy loading failed for package ‘Homo.sapiens’
* removing ‘/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/Homo.sapiens’
I will investigate the R version used to built packages, as suggested by
Dan and Kasper and report back.
Thanks,
Laurent
> Martin
>
>>
>> Laurent
>>
>>> and then
>>>
>>> library(Homo.sapiens)
>>>
>>> followed by traceback() -- this way you'll at least be able to explore the call
>>> stack.
>>>
>>> Martin
>>>
>>>
>>>>
>>>> Best wishes,
>>>>
>>>> Laurent
>>>>
>>>>> library("RSQLite")
>>>>> library("AnnotationDbi")
>>>>> sessionInfo()
>>>> ## R Under development (unstable) (2014-11-01 r66923)
>>>> ## Platform: x86_64-unknown-linux-gnu (64-bit)
>>>> ##
>>>> ## locale:
>>>> ## [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>>>> ## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>>>> ## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
>>>> ## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
>>>> ## [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>> ## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>> ##
>>>> ## attached base packages:
>>>> ## [1] parallel stats4 stats graphics grDevices utils datasets
>>>> ## [8] methods base
>>>> ##
>>>> ## other attached packages:
>>>> ## [1] GO.db_3.0.0 RSQLite_1.0.0 DBI_0.3.1
>>>> ## [4] AnnotationDbi_1.29.1 GenomeInfoDb_1.3.6 IRanges_2.1.4
>>>> ## [7] S4Vectors_0.5.2 Biobase_2.27.0 BiocGenerics_0.13.0
>>>> ## [10] BiocInstaller_1.17.1
>>>> ##
>>>> ## loaded via a namespace (and not attached):
>>>> ## [1] compiler_3.2.0 tools_3.2.0
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>
--
Laurent Gatto
http://cpu.sysbiol.cam.ac.uk/
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