[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
Laurent Gatto
lg390 at cam.ac.uk
Tue Nov 4 20:14:08 CET 2014
On 4 November 2014 15:55, Dan Tenenbaum wrote:
> Hi Laurent,
>
> ----- Original Message -----
>> From: "Martin Morgan" <mtmorgan at fredhutch.org>
>> To: "Laurent Gatto" <lg390 at cam.ac.uk>, bioc-devel at r-project.org
>> Sent: Tuesday, November 4, 2014 5:41:04 AM
>> Subject: Re: [Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
>>
>> 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.
>> >
>> > I want to install Homo.sapiens:
>> >
>> >> library("BiocInstaller")
>> > ## Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for
>> > help
>> >> 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/RtmpXYXfis/downloaded_packages’
>> > ## Warning message:
>> > ## In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)
>> > :
>> > ## installation of package ‘Homo.sapiens’ had non-zero exit
>> > status
>> >
>> > GO.db is up-to-date, but let's (successfully) biocLite and load it:
>> >
>> >> biocLite("GO.db")
>> > ## BioC_mirror: http://bioconductor.org
>> > ## Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version
>> > 3.2.0.
>> > ## Installing package(s) 'GO.db'
>> > ## trying URL
>> > 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/GO.db_3.0.0.tar.gz'
>> > ## Content type 'application/x-gzip' length 28747892 bytes (27.4
>> > MB)
>> > ## opened URL
>> > ## ==================================================
>> > ## downloaded 27.4 MB
>> > ##
>> > ## * installing *source* package ‘GO.db’ ...
>> > ## ** R
>> > ## ** inst
>> > ## ** preparing package for lazy loading
>> > ## ** help
>> > ## *** installing help indices
>> > ## ** building package indices
>> > ## ** testing if installed package can be loaded
>> > ## * DONE (GO.db)
>> > ##
>> > ## The downloaded source packages are in
>> > ## ‘/tmp/Rtmprr15y4/downloaded_packages’
>> >> suppressPackageStartupMessages(library("GO.db"))
>> >
>> > Repeating unsuccessful attempt to install Homo.sapiens fails again:
>> >
>> >> 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?
>>
>> It might help to (maybe before biocLite(), to find the source of the
>> problem)
>>
>> biocLite("Homo.sapiens", INSTALL_opts="--no-test-load")
>>
>> and then
>>
>> library(Homo.sapiens)
>>
>> followed by traceback() -- this way you'll at least be able to
>> explore the call
>> stack.
>>
>
>
> Didn't you report this same problem the other day and the solution was
> to update all your packages?
Yes, and that was Go.db that failed. Updating to AnnotationDbi 1.29.1
fixed it.
> Note that both installed.packages() and packageDescription() display
> information about the version of R under which a given package was
> built.
> So that could help narrow things down. It's almost certainly an
> annotation package, because almost all of the ones in our devel
> repository are just copied from our release repository and built under
> R-3.1.x. So we might need to rebuild them under R-devel, at least the
> ones with stale serialized references.
Ok, I guess I will go ahead and hunt all annotation packages.
What is the best way to programmatically get a list of all annotation
packages - biocViews? While thinking about a question that came up on
the support site, I realised that I did not even know if the annotation
packages lived in an svn repo.
Laurent
> Dan
>
>
>
>
>> 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
>> >
>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>> _______________________________________________
>> 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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