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

[Søren Højsgaard]

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."

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
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