[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
Laurent Gatto
lg390 at cam.ac.uk
Wed Nov 5 01:55:12 CET 2014
On 4 November 2014 20:27, Kasper Daniel Hansen wrote:
> 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.
Just to follow up, I got rid of all packages that were built using R <
3.2.0, but no luck:
> ip <- installed.packages()
> table(ip[, "Built"])
3.2.0
911
> 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’
Same also with ChIPpeakAnno/GO.db now.
Will investigate further tomorrow.
Laurent
> 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
>>
--
Laurent Gatto
http://cpu.sysbiol.cam.ac.uk/
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