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

[Oleg Sklyar]

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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-- 
Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466