[BioC] biocLite() failed to get CRAN package...

[Jenny Drnevich]

Hi everyone,

I just upgraded to R 2.7.0 and used biocLite() to install many 
Bioconductor packages. The base install of biocLite() worked fine, 
but when I used it to install some other packages, at the end I got a 
warning message that "dependency 'XML' is not available" (screen 
output and sessionInfo below). However, I then used the install menu 
on PC and was able to download and install XML from CRAN. So I'm not 
sure what happened that biocLite() wasn't able to get it...

Cheers,
Jenny

 > x <- 
c("affycoretools","convert","made4","plier","simpleaffy","tkWidgets","widgetTools","RWinEdt")
 > biocLite(x)
Running biocinstall version 2.2.7 with R version 2.7.0
Your version of R requires version 2.2 of BioConductor.
also installing the dependencies 'graph', 'RBGL', 'Category', 
'RCurl', 'GOstats', 'biomaRt', 'ade4'

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/graph_1.18.0.zip'
Content type 'application/zip' length 856239 bytes (836 Kb)
opened URL
downloaded 836 Kb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/RBGL_1.16.0.zip'
Content type 'application/zip' length 1074190 bytes (1.0 Mb)
opened URL
downloaded 1.0 Mb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/Category_2.6.0.zip'
Content type 'application/zip' length 643858 bytes (628 Kb)
opened URL
downloaded 628 Kb

trying URL 
'http://bioconductor.org/packages/2.2/extra/bin/windows/contrib/2.7/RCurl_0.8-1.zip'
Content type 'application/zip' length 944881 bytes (922 Kb)
opened URL
downloaded 922 Kb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/GOstats_2.6.0.zip'
Content type 'application/zip' length 2802070 bytes (2.7 Mb)
opened URL
downloaded 2.7 Mb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/biomaRt_1.14.0.zip'
Content type 'application/zip' length 420193 bytes (410 Kb)
opened URL
downloaded 410 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.7/ade4_1.4-7.zip'
Content type 'application/zip' length 3023234 bytes (2.9 Mb)
opened URL
downloaded 2.9 Mb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/affycoretools_1.12.0.zip'
Content type 'application/zip' length 6992261 bytes (6.7 Mb)
opened URL
downloaded 6.7 Mb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/convert_1.16.0.zip'
Content type 'application/zip' length 46834 bytes (45 Kb)
opened URL
downloaded 45 Kb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/made4_1.14.0.zip'
Content type 'application/zip' length 937469 bytes (915 Kb)
opened URL
downloaded 915 Kb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/plier_1.10.0.zip'
Content type 'application/zip' length 47646 bytes (46 Kb)
opened URL
downloaded 46 Kb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/simpleaffy_2.16.0.zip'
Content type 'application/zip' length 802232 bytes (783 Kb)
opened URL
downloaded 783 Kb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/tkWidgets_1.18.0.zip'
Content type 'application/zip' length 503016 bytes (491 Kb)
opened URL
downloaded 491 Kb

trying URL 
'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/widgetTools_1.16.0.zip'
Content type 'application/zip' length 271188 bytes (264 Kb)
opened URL
downloaded 264 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.7/RWinEdt_1.7-9.zip'
Content type 'application/zip' length 397216 bytes (387 Kb)
opened URL
downloaded 387 Kb

package 'graph' successfully unpacked and MD5 sums checked
package 'RBGL' successfully unpacked and MD5 sums checked
package 'Category' successfully unpacked and MD5 sums checked
package 'RCurl' successfully unpacked and MD5 sums checked
package 'GOstats' successfully unpacked and MD5 sums checked
package 'biomaRt' successfully unpacked and MD5 sums checked
package 'ade4' successfully unpacked and MD5 sums checked
package 'affycoretools' successfully unpacked and MD5 sums checked
package 'convert' successfully unpacked and MD5 sums checked
package 'made4' successfully unpacked and MD5 sums checked
package 'plier' successfully unpacked and MD5 sums checked
package 'simpleaffy' successfully unpacked and MD5 sums checked
package 'tkWidgets' successfully unpacked and MD5 sums checked
package 'widgetTools' successfully unpacked and MD5 sums checked
package 'RWinEdt' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\drnevich\Local 
Settings\Temp\RtmpPZtAmS\downloaded_packages
updating HTML package descriptions
Warning message:
dependency 'XML' is not available

 > utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
trying URL 
'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/XML_1.94-0.1.zip'
Content type 'application/zip' length 1659232 bytes (1.6 Mb)
opened URL
downloaded 1.6 Mb

package 'XML' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\drnevich\Local 
Settings\Temp\RtmpPZtAmS\downloaded_packages
updating HTML package descriptions

 >sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

loaded via a namespace (and not attached):
[1] tools_2.7.0



Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu