[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
Dan Tenenbaum
dtenenba at fredhutch.org
Tue Nov 4 20:18:53 CET 2014
----- Original Message -----
> From: "Laurent Gatto" <lg390 at cam.ac.uk>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Martin Morgan" <mtmorgan at fredhutch.org>, bioc-devel at r-project.org
> Sent: Tuesday, November 4, 2014 11:14:08 AM
> Subject: Re: [Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
>
>
> 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.
>
Actually, the fact that an AnnotationDbi update fixed your earlier issue makes me unsure about whether the "bad" package you have is an annotation package.
But if you still want to know....You can look at http://bioconductor.org/packages/devel/data/annotation/src/contrib/PACKAGES or available.packages() which tells you what repository a package comes from.
Dan
> 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/
>
More information about the Bioc-devel
mailing list