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

[Herve Pages]

Hi Keith,

Of course they are not equivalent for you, or for me, or
for anybody who doesn't have the "BioC.Repos" option set like
Steven.

Steven has:
  > getOption("BioC.Repos")
  [1] "http://www.bioconductor.org/packages/1.9/bioc"
  [2] "http://www.bioconductor.org/packages/1.9/data/annotation"
  [3] "http://www.bioconductor.org/packages/1.9/data/experiment"
  [4] "http://www.bioconductor.org/packages/1.9/omegahat"

So in _his_ case (and only if he doesn't have any package from
the monograph repo), this
  > update.packages()
  > update.packages(getOption("BioC.Repos"))
should be equivalent to
  > update.packages(rep=biocReposList())

Anyway, the recommended way to update all BioC + CRAN packages is
to use the latter command.

Cheers,
H.



Keith Satterley wrote:
> 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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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel