[Bioc-devel] update.packages query -was stale link to reposTools in BioC FAQ?

Hi Herve

I have been following the thread regarding reposTools and was interestred in the 
update.packages comments near the end of this interchange. In particular:
 >   > update.packages()
 >
 > followed by
 >
 >   > update.packages(getOption("BioC.Repos"))
 >
 > should be equivalent to
 >
 >   > update.packages(rep=biocReposList())
 >
I have R2.4.0 on Windows. They are not equivalent for me.
I run
 > library(Biobase)
 > update.packages()
and I'm prompted to select a CRAN mirror, which I do (Australia VIC has been a 
good mirror for me).
I am not prompted to update any packages.
I run
 > update.packages(getOption("BioC.Repos"))
and I'm not prompted to update any packages.
I run
 > update.packages(rep=biocReposList())
and I'm prompted to update 7 packages; Biostrings, GO, humanCHRLOC, 
humanLLMappings, KEGG, mouseCHRLOC and mouseLLMappings. I responded N for now so 
I can test further.

biocReposList() responds with 6 repositories(5 bioc + 1 cran) as shown below.
getOption("BioC.Repos") responds with NULL.
getOption("repos") responds with the CRAN and CRANextra repositories.

Hence, for me the procedures are not equivalent. Should they be?

NB. I automatically load up biocLite from my .Rprofile in "My Documents" each 
time I start R. It contains:
tryCatch({
     source("http://bioconductor.org/biocLite.R")
}, error=function(e) invisible(NULL),
          warning=function(w) cat("Not connected to the net\n"))

Below is a copy and paste from my Rgui window.
============================
 > library(Biobase)
Loading required package: tools

Welcome to Bioconductor

     Vignettes contain introductory material. To view, type
     'openVignette()' or start with 'help(Biobase)'. For details
     on reading vignettes, see the openVignette help page.

 > sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
"datasets"  "base"

other attached packages:
  Biobase
"1.12.2"
 > ls()
[1] "biocLite" "getBioC"
 > ge<-getOption("BioC.Repos")
 > ge
NULL
 > update.packages()
--- Please select a CRAN mirror for use in this session ---
 > update.packages()
 > update.packages(getOption("BioC.Repos"))
 > update.packages(rep=biocReposList())
Biostrings :
  Version 2.2.0 installed in C:/R/R-2.4.0/library
  Version 2.2.1 available at http://bioconductor.org/packages/1.9/bioc
Update (y/N/c)?  n
GO :
  Version 1.14.0 installed in C:/R/R-2.4.0/library
  Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)?  n
humanCHRLOC :
  Version 1.14.0 installed in C:/R/R-2.4.0/library
  Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)?  n
humanLLMappings :
  Version 1.14.0 installed in C:/R/R-2.4.0/library
  Version 1.14.2 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)?  n
KEGG :
  Version 1.14.0 installed in C:/R/R-2.4.0/library
  Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)?  n
mouseCHRLOC :
  Version 1.14.0 installed in C:/R/R-2.4.0/library
  Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)?  n
mouseLLMappings :
  Version 1.14.0 installed in C:/R/R-2.4.0/library
  Version 1.14.2 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)?  n
 > biocReposList()
                                                   bioc
            "http://bioconductor.org/packages/1.9/bioc"
                                                  aData
"http://bioconductor.org/packages/1.9/data/annotation"
                                                  eData
"http://bioconductor.org/packages/1.9/data/experiment"
                                                     oh
        "http://bioconductor.org/packages/1.9/omegahat"
                                                     mo
       "http://bioconductor.org/packages/1.9/monograph"
                                                   cran
                                "http://cran.fhcrc.org"
 > getOption("BioC.Repos")
NULL
 >
 > getOption("repos")
                                 CRAN                            CRANextra
      "http://cran.ms.unimelb.edu.au" "http://www.stats.ox.ac.uk/pub/RWin"
 >

==============================

cheers,

Keith

========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
=======================

Steven McKinney wrote:

cut ---

I just ran an update using

update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates

Where did you get this code from? Did it work for you?

I tried various combinations of calls to update.packages, looked in the
internals of getBioC, getOption, install.packages, etc.  The
above calls seemed to work best.  Your suggestion below looks better.

I have not yet determined which function set up list item BioC.Repos
in my options, information from anyone who knows this would be appreciated.

getOption("BioC.Repos")

[1] "http://www.bioconductor.org/packages/1.9/bioc"            "http://www.bioconductor.org/packages/1.9/data/annotation"
[3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"       

This should be OK too. The CRAN and monograph repos are missing
compared to biocReposList() but, if you don't have any package
from the monograph repo, then doing (in this order):

  > update.packages()

followed by

  > update.packages(getOption("BioC.Repos"))

should be equivalent to

  > update.packages(rep=biocReposList())

Cheers,

H.

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