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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