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

[James W. MacDonald]

Note that you might also want to add dependencies=TRUE.

Best,

Jim


cstrato wrote:
> 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
>>>>>
>>>>>     
>>>> The information transmitted in this electronic communi...{{dropped:13}}
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
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>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623