[Bioc-devel] How to install a package from bioC devel?

[cstrato]

Dear Jim

Thank you very much, this is what I wanted to know. The following now works:
install.packages("xps",repos="http://www.bioconductor.org/packages/2.2/bioc",type="source")

Best regards
Christian

James W. MacDonald wrote:
> cstrato wrote:
>> Dear Vincent
>>
>> Thank you, but this is not what I want. I would like to install the 
>> package from BioC devel in R-2.6.1.
>>
>> In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html
>> Seth mentioned that it is possible to use install.packages for this 
>> purpose, but I get the error mentioned.
>> Did I make a mistake or is the URL wrong?
>>
>> Best regards
>> Christian
>>
>> Vincent Carey 525-2265 wrote:
>>> biocLite will install the devel version of the package
>>> if invoked from R devel (2.7.0 at this time)
>>>
>>> ---
>>> Vince Carey, PhD
>>> Assoc. Prof Med (Biostatistics)
>>> Harvard Medical School
>>> Channing Laboratory - ph 6175252265 fa 6177311541
>>> 181 Longwood Ave Boston MA 02115 USA
>>> stvjc at channing.harvard.edu
>>>
>>> On Wed, 16 Jan 2008, cstrato wrote:
>>>
>>>  
>>>> Dear all,
>>>>
>>>> How can a user install a package from BioC devel?
>>>>
>>>> I have tried the following:
>>>>
>>>> 1. biocLite:
>>>>  >
>>>> biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps", 
>>>>
>>>> type="source")
>>>> Running biocinstall version 2.1.8 with R version 2.6.1
>>>> Your version of R requires version 2.1 of Bioconductor.
>>>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
>>>> dependencies,  :
>>>>   argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
>>>> Warning message:
>>>> In install.packages(pkgs = pkgs, repos = repos, dependencies =
>>>> dependencies,  :
>>>>   package
>>>> 'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
>>>> available
>>>>
>>>>
>>>> 2. install.package from BioC devel repository:
>>>>  >
>>>> install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") 
>>>>
>
> First, you don't want to state the version. By giving the repository 
> you will automatically get the correct version.
>
>>>> Warning in install.packages("xps_0.4.1.tar.gz", repos =
>>>> "http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
>>>>   argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
>>>> Warning: unable to access index for repository
>>>> http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6 
>>>>
>
> The above should have given you a big hint: What you gave as the 
> repository ended up with 'bin/macosx/universal/contrib/2.6' added on 
> the end. So two things are happening.
>
> First, the repository you are giving is wrong -- install.packages() 
> will add the specific directory to get the package, so remove the 
> src/contrib/ from the end.
>
> Second, you evidently want a source package, but you are not telling 
> install.packages(), so it is trying to get the universal binary. Hint: 
> type="source".
>
> Best,
>
> Jim
>
>
>>>> Warning message:
>>>> package 'xps_0.4.1.tar.gz' is not available
>>>>
>>>>
>>>> 3. download the package and use install.package locally:
>>>>  > 
>>>> install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
>>>> Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",
>>>> repos = NULL) :
>>>>   argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
>>>> Error in gzfile(file, "r") : unable to open connection
>>>> In addition: Warning message:
>>>> In gzfile(file, "r") :
>>>>   cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'
>>>>
>>>> As you see, none of the methods that I have tried works.
>>>> Is the URL of the BioC devel repository correct?
>>>> Why does the local installation not work?
>>>>
>>>> The only installation method that works is:
>>>> R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz
>>>>
>>>>  > sessionInfo()
>>>> R version 2.6.1 (2007-11-26)
>>>> i386-apple-darwin8.10.1
>>>>
>>>> locale:
>>>> C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] rcompgen_0.1-17 tools_2.6.1
>>>>
>>>> Best regards
>>>> Christian
>>>> _._._._._._._._._._._._._._._._
>>>> C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
>>>> V.i.e.n.n.a       A.u.s.t.r.i.a
>>>> e.m.a.i.l:    cstrato at aon.at
>>>> _._._._._._._._._._._._._._._._
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>     
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>>
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