[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3
Martin Morgan
mtmorgan at fredhutch.org
Tue Nov 4 14:41:04 CET 2014
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.
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
>
> _______________________________________________
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>
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