[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3

[Martin Morgan]

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?


>
> 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.

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
>>>
>


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