Hi Laurent,
----- Original Message -----
> From: "Martin Morgan" <mtmor...@fredhutch.org>
> To: "Laurent Gatto" <lg...@cam.ac.uk>, bioc-devel@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?
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.
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@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
> --
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>
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>
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