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

[Laurent Gatto]

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 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?

> 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. 

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/