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

[cstrato]

Thank you, I keep this in mind for the future.
In my case I simply wanted to know if my package works as expected when 
a user downloads it.

Best regards
Christian

James W. MacDonald wrote:
> 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}}
>>>>
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>>
>