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

[cstrato]

Dear Oleg

As mentioned in my original mail, R CMD INSTALL is the ONLY method that 
worked for me!
However, I want to know why install.packages() does not work, neither 
from an URL nor locally.

Why does install.packages() not work?
What is the correct url to access a package from BioC devel?

Best regards
Christian

Oleg Sklyar wrote:
> Go to the bioconductor web page, download the package, and all the 
> dependencies if required and save them onto a local disk. Then in 
> Linux/UNIX/Mac do 'R CMD INSTALL ThePackage.tar.gz' outside of the R 
> session and in Windows within an R session select in menu 'Install 
> from a local Zip file'. However, please pay attention that those 
> packages might be unsupported, not fully tested and even buggy - they 
> are the development versions. So if you then encounter problems, be 
> warned.
>
> Best,
> Oleg
>
> 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/") 
>>>>
>>>> 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 
>>>>
>>>> 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
>>>>
>>>>     
>>> The information transmitted in this electronic communi...{{dropped:13}}
>>
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