[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Tue Nov 4 21:27:23 CET 2014
Laurent,
If you do
installed.packages()
(note the 'ed') you are told which version of R was used to build the
package. This has sometimes been useful to me in these kind of situations.
Best,
Kasper
On Tue, Nov 4, 2014 at 2:18 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:
>
>
> ----- 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/
> >
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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