Today I installed the current R-devel for the first time and all packages
build except "oligo" and a couple packages that depend on it. Below is my
buid output followed by sessionInfo(). Please let me know if I can provide
any other information that might be helpful. Thanks,

Mark

downloaded 696 Kb

Loading required package: utils
* installing *source* package ‘oligo’ ...
** libs
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
 -I/usr/local/include
-I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
 -g -O2 -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:144: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:318: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
 -I/usr/local/include
-I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
 -g -O2 -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
 -I/usr/local/include
-I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
 -g -O2 -c basecontent.c -o basecontent.o
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
 -I/usr/local/include
-I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
 -g -O2 -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
 -I/usr/local/include
-I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
 -g -O2 -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include
 -I/usr/local/include
-I"/home/mkimpel/R_HOME/site-library-2.11.0/preprocessCore/include"   -fpic
 -g -O2 -c trimmed.c -o trimmed.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o oligo.so ParserXYS.o
baseProfile.o basecontent.o rma2.o rma_common.o trimmed.o
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Error in setMethod("pmSequence", "FeatureSet", function(object)
pmSequence(getPD(object))) :
  no existing definition for function "pmSequence"
Error : unable to load R code in package 'oligo'
ERROR: lazy loading failed for package ‘oligo’
* removing ‘/home/mkimpel/R_HOME/site-library-2.11.0/oligo’

The downloaded packages are in
‘/tmp/RtmpTF8R6F/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'oligo' had non-zero exit status
> sessionInfo()
R version 2.11.0 Under development (unstable) (2009-12-03 r50653)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] Biobase_2.7.0

loaded via a namespace (and not attached):
[1] tools_2.11.0

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please

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