From hpages at fhcrc.org  Fri Nov 12 01:40:31 2010
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Thu, 11 Nov 2010 16:40:31 -0800
Subject: [Rd] installing dependencies: binary vs source
Message-ID: <4CDC8CFF.6080303@fhcrc.org>

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



[Rd] installing dependencies: binary vs source
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