[Bioc-devel] update.packages query -was stale link to reposTools in BioC FAQ?
Keith Satterley
keith at wehi.EDU.AU
Thu Nov 9 04:59:34 CET 2006
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
=======================
Herve Pages wrote:
> 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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