[Bioc-devel] biocValid vs biocLite

[Laurent Gatto]

I am curious as to why biocValid and biocLite do not seem to agree on
the update of certain packages:

> library("BiocInstaller")
> biocValid()
## 
## * 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] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocInstaller_1.17.1
## 
## loaded via a namespace (and not attached):
## [1] compiler_3.2.0 tools_3.2.0   
## 
## * Out-of-date packages
##                                 Package                          
## Homo.sapiens                    "Homo.sapiens"                   
## Mus.musculus                    "Mus.musculus"                   
## qtpaint                         "qtpaint"                        
## SNPlocs.Hsapiens.dbSNP.20090506 "SNPlocs.Hsapiens.dbSNP.20090506"
## SNPlocs.Hsapiens.dbSNP.20120608 "SNPlocs.Hsapiens.dbSNP.20120608"
##                                 LibPath                                             
## Homo.sapiens                    "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2"
## Mus.musculus                    "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2"
## qtpaint                         "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2"
## SNPlocs.Hsapiens.dbSNP.20090506 "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2"
## SNPlocs.Hsapiens.dbSNP.20120608 "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2"
##                                 Installed Built    ReposVer
## Homo.sapiens                    "1.1.2"   "3.1.0"  "1.1.2" 
## Mus.musculus                    "1.1.2"   "3.1.0"  "1.1.2" 
## qtpaint                         "0.9.0"   "2.16.0" "0.9.0" 
## SNPlocs.Hsapiens.dbSNP.20090506 "0.99.8"  "3.0.0"  "0.99.8"
## SNPlocs.Hsapiens.dbSNP.20120608 "0.99.9"  "3.1.0"  "0.99.9"
##                                 Repository                                                        
## Homo.sapiens                    "http://bioconductor.org/packages/3.1/data/annotation/src/contrib"
## Mus.musculus                    "http://bioconductor.org/packages/3.1/data/annotation/src/contrib"
## qtpaint                         "http://cran.ma.imperial.ac.uk/src/contrib"                       
## SNPlocs.Hsapiens.dbSNP.20090506 "http://bioconductor.org/packages/3.1/data/annotation/src/contrib"
## SNPlocs.Hsapiens.dbSNP.20120608 "http://bioconductor.org/packages/3.1/data/annotation/src/contrib"
## 
## update with biocLite()
## 
## * Packages too new for Bioconductor version '3.1'
## 
##               Version  LibPath                                             
## GenomicRanges "1.19.3" "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2"
## 
## downgrade with biocLite("GenomicRanges")
## 
## Error: 5 package(s) out of date; 1 package(s) too new

Even though the installed and repo version are the same, I assume that
biocValid marks the packages above as out-of-data because they have
been built with previous R versions. But, if I run biocLite, no package
gets updated.

> biocLite()
## BioC_mirror: http://bioconductor.org
## Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version 3.2.0.

Running biocValid(fix=TRUE) will initiate a package download/install.

Thank you very much in advance.

Laurent