[R] Can't get installing a package source (.tar.gz) from a web page to work...

[Uwe Ligges]

On 16.09.2011 18:27, Martin Morgan wrote:
> On 09/16/2011 04:21 AM, Søren Højsgaard wrote:
>> Thanks Uwe,
>>
>> The problem, however, is not solved. If I do:
>>
>> download.file("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz",
>>
>> tempdir()) Error in
>> download.file("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz",
>>
>> : cannot open destfile 'c:\temp\RtmpcrQ0WM', reason 'Permission
>> denied'
>>
>>
>> However, if I specify a filename then things are working:
>> download.file("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz",
>>
>> paste(tempdir(),"thisfile",sep="\\")) trying URL
>> 'http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz'
>>
>>
>>
> Content type 'application/x-tar' length 315847 bytes (308 Kb)
>> opened URL downloaded 308 Kb
>>
>> dir(tempdir()) [1] "thisfile"
>>
>> According to to the documentation:
>>
>> "Destfile A character string with the name where the downloaded file
>> is saved. Tilde-expansion is performed."
>
> A little ambiguous, but I guess it is the full path of the downloaded
> file; 'destfile' and not 'destdir'.
>
> Perhaps you mean tempfile() (a file name that can be created in R's
> temporary directory) rather than tempdir() (R's temporary directory).
> Otherwise you are trying to open for writing a location that is an
> in-use directory, and Windows is saying that you can't do that.


Right, I was simply wrong in my suggestion that I had not tested before 
sending it.

Uwe


> Martin
>
>> I read the documentation such that I can specify a directory in which
>> the file is to be put, but I may be wrong; or is it possible that
>> there is a bug somewhere?
>>
>> Best regards Søren
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -----Oprindelig meddelelse----- Fra: Uwe Ligges
>> [mailto:ligges at statistik.tu-dortmund.de] Sendt: 15. september 2011
>> 10:47 Til: Søren Højsgaard Cc: r-help at stat.math.ethz.ch Emne: Re: [R]
>> Can't get installing a package source (.tar.gz) from a web page to
>> work...
>>
>>
>>
>> On 15.09.2011 10:34, Søren Højsgaard wrote:
>>> I have created an R-package with datasets which I want my students
>>> to install (the package is not on CRAN).
>>>
>>> 1) I've put the package on the web in a directory called 'data' and
>>> I thought I could do:
>>>
>>>> install.packages("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz",repos=NULL,type="source")
>>>>
>>>
>>>
>>>>
> Warning: invalid package
> 'http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz'
>
>>> Error: ERROR: no packages specified Warning messages: 1: running
>>> command 'C:/programs/R/current/bin/i386/R CMD INSTALL -l
>>> "C:/programs/R/current/library"
>>> "http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz"'
>>>
>>> had status 1 2: In
>>> install.packages("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz",
>>>
>>> : installation of package
>>> 'http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz'
>>>
>>> had non-zero exit status
>>
>>
>> Right, install.packages assumes a package name or a file path. URLs
>> (or any othr connections) are not supported.
>>
>>
>>> 2) I've then put the package in data/src/contrib/ and try:
>>>
>>>> install.packages('LiSciData_0.0-03.tar.gz',repos='http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/',
>>>>
>>>> type='source')
>>> Warning: unable to access index for repository
>>> http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/src/contrib
>>>
>>>
>>>
> Warning message:
>>> In getDependencies(pkgs, dependencies, available, lib) : package
>>> 'LiSciData_0.0-03.tar.gz' is not available (for R version 2.13.1)
>>
>> If you want to use it as a repository, you have to make such a
>> repository. For a source repository, create subdirs ./src/contrib
>> and put your package there. Afterwards, you can run
>> tools::write_PACKAGES on that directory in order to create PACKAGES
>> and PACKAGES.gz files for that repository.
>>
>>
>>> 3) If I put the package in the Rs working directory then the
>>> following works:
>>>> install.packages("LiSciData_0.0-03.tar.gz",repos=NULL,type="source")
>>
>>>>
>> Right, hence you can also tell your students to:
>>
>> download.file("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz",
>>
>>
>> tempdir()) install.packages(file.path(tempdir(),
>> 'LiSciData_0.0-03.tar.gz'), repos=NULL, type='source')
>>
>> Best wishes, Uee
>>
>>
>>
>>
>>
>>> I would much prefer if it could be done directly from the web in
>>> the spirit of attempt 1) above (because then fewer things can go
>>> wrong for the students). Any hint on what I am doing wrong?
>>> sessionInfo() shown below.
>>>
>>> Regards Søren
>>>
>>>
>>>
>>>> sessionInfo()
>>> R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386
>>> (32-bit) locale: [1] LC_COLLATE=Danish_Denmark.1252
>>> LC_CTYPE=Danish_Denmark.1252 LC_MONETARY=Danish_Denmark.1252
>>> LC_NUMERIC=C LC_TIME=Danish_Denmark.1252
>>> attached base packages: [1] stats graphics grDevices utils
>>> datasets methods base other attached packages: [1] SHDtools_1.0
>>> loaded via a namespace (and not attached): [1] tools_2.13.1
>>> ______________________________________________ R-help at r-project.org
>>> mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
>>> read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>> ______________________________________________ R-help at r-project.org
>> mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
>> read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>