R devel - Nov 2010 - installing dependencies: binary vs source

Hi,

Installing from binaries on Windows:

   > install.packages("multtest")
   Warning: dependency 'Biobase' is not available
   trying URL 
'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip'
   Content type 'application/zip' length 1645590 bytes (1.6 Mb)
   opened URL
   downloaded 1.6 Mb

   package 'multtest' successfully unpacked and MD5 sums checked

   The downloaded packages are in
 
C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpPzRqzb\downloaded_packages

Note the warning that a dependency is missing. But still the package
got installed even though it won't be loadable.

Now installing from source on Windows:

   > install.packages("multtest", type="source")
   Warning: dependency 'Biobase' is not available
   trying URL 'http://cran.fhcrc.org/src/contrib/multtest_2.6.0.tar.gz'
   Content type 'application/x-gzip' length 1457444 bytes (1.4 Mb)
   opened URL
   downloaded 1.4 Mb

   ERROR: dependency 'Biobase' is not available for package
'multtest'
   * removing 'D:/biocbld/bbs-2.7-bioc/R/library/multtest'

   The downloaded packages are in
 
'C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpPzRqzb\downloaded_packages'
   Warning message:
   In install.packages("multtest", type = "source") :
     installation of package 'multtest' had non-zero exit status

Note the warning *and* ERROR.

Is this the intended behavior of install.packages() when installing
from binaries?

Thanks,
H.

PS: Sorry I don't have access to an R-2.13 installation where I can
test this at the moment.

   > sessionInfo()
   R version 2.12.0 (2010-10-15)
   Platform: x86_64-pc-mingw32/x64 (64-bit)

   locale:
   [1] LC_COLLATE=English_United States.1252
   [2] LC_CTYPE=English_United States.1252
   [3] LC_MONETARY=English_United States.1252
   [4] LC_NUMERIC=C
   [5] LC_TIME=English_United States.1252

   attached base packages:
   [1] stats     graphics  grDevices utils     datasets  methods   base


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

On 12.11.2010 01:40, Herv? Pag?s wrote:
> Hi,
>
> Installing from binaries on Windows:
>
>  > install.packages("multtest")
> Warning: dependency 'Biobase' is not available
> trying URL
> 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip'
> Content type 'application/zip' length 1645590 bytes (1.6 Mb)
> opened URL
> downloaded 1.6 Mb
>
> package 'multtest' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>
> C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpPzRqzb\downloaded_packages
>
> Note the warning that a dependency is missing. But still the package
> got installed even though it won't be loadable.
>
> Now installing from source on Windows:
>
>  > install.packages("multtest", type="source")
> Warning: dependency 'Biobase' is not available
> trying URL
'http://cran.fhcrc.org/src/contrib/multtest_2.6.0.tar.gz'
> Content type 'application/x-gzip' length 1457444 bytes (1.4 Mb)
> opened URL
> downloaded 1.4 Mb
>
> ERROR: dependency 'Biobase' is not available for package
'multtest'
> * removing 'D:/biocbld/bbs-2.7-bioc/R/library/multtest'
>
> The downloaded packages are in
>
>
'C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpPzRqzb\downloaded_packages'
> Warning message:
> In install.packages("multtest", type = "source") :
> installation of package 'multtest' had non-zero exit status
>
> Note the warning *and* ERROR.
>
> Is this the intended behavior of install.packages() when installing
> from binaries?

Herv?,

yes, I think so. If you ask to install a package, it is installed unless 
it cannot be installed (as it was the case since R had to load Biobase 
which was unavailable).


Best,
Uwe


> Thanks,
> H.
>
> PS: Sorry I don't have access to an R-2.13 installation where I can
> test this at the moment.
>
>  > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>