[Bioc-devel] error: 2 arguments passed to .Internal(ls) which requires 3

[Laurent Gatto]

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?

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