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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier
Package 12/238HostnameOSArchBUILDCHECKBUILD BIN

affyPLM

1.13.5

Ben Bolstad
Last Changed Date: 2007-06-05 12:44:17 -0700
Last Changed Rev: 25196
lamb1 Linux (SUSE 10.1) x86_64 [ OK ] WARNINGS 
wellington Linux (SUSE 9.2) i686  OK  WARNINGS 
churchill Solaris 2.9 sparc  OK  WARNINGS 
lemming Windows Server 2003 (32-bit) x64  ERROR skippedskipped
Package: affyPLM
Version: 1.13.5
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD build affyPLM
RetCode: 0
Time: 196.8 seconds
Status: OK
PackageFile: affyPLM_1.13.5.tar.gz

Command output

* checking for file 'affyPLM/DESCRIPTION' ... OK
* preparing 'affyPLM':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* installing the package to re-build vignettes
* Installing *source* package 'affyPLM' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c avg_log.c -o avg_log.o
avg_log.c: In function 'AverageLog_threestep':
avg_log.c:64: warning: implicit declaration of function 'AverageLog'
avg_log.c: In function 'AverageLog_PLM':
avg_log.c:80: warning: implicit declaration of function 'averagelog_no_copy'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c biweight.c -o biweight.o
biweight.c: In function 'TukeyBiweight_threestep':
biweight.c:66: warning: implicit declaration of function 'TukeyBiweight'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c log_avg.c -o log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c median_logPM.c -o median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c medianPM.c -o medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function 'qnorm_probeset_c':
qnorm_probeset.c:154: warning: implicit declaration of function 'AverageLog_noSE'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:99: warning: 'rlmPLM_alloc_space' defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60: warning: unused variable 'i'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o
R_rlm_interfaces.c: In function 'R_wrlm_rma_default_model':
R_rlm_interfaces.c:197: warning: implicit declaration of function 'rlm_wfit_anova'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm_threestep.o log_avg.o matrix_functions.o median_logPM.o medianPM.o medianpolish.o nthLargestPM.o PLM_modelmatrix.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rma_background2.o rma_common.o rma_PLM.o rmaPLM_pseudo.o R_rlm_interfaces.o SCAB.o scaling.o threestep.o threestep_common.o threestep_PLM.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -lgfortran -lm -L/home/biocbuild/bbs-2.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.1-bioc/R/lib -lRblas  -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Loading required package: affyio
Loading required package: preprocessCore
Loading required package: affydata
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
Creating a new generic function for "weights" in "affyPLM"
Creating a new generic function for "summary" in "affyPLM"
Creating a new generic function for "resid" in "affyPLM"
Creating a new generic function for "residuals" in "affyPLM"
** help
Note: unmatched right brace in 'threestep' on or after line 33
 >>> Building/Updating help pages for package 'affyPLM'
     Formats: text html latex example 
  MAplot                            text    html    latex
  PLMset-class                      text    html    latex   example
  PLMset2exprSet                    text    html    latex   example
  ReadRMAExpress                    text    html    latex
  affyPLM-internal                  text    html    latex
  bg.correct.LESN                   text    html    latex   example
  fitPLM                            text    html    latex   example
  normalize.exprSet                 text    html    latex   example
  normalize.quantiles.probeset      text    html    latex
  normalize.scaling                 text    html    latex   example
  preprocess                        text    html    latex   example
  pseudo                            text    html    latex   example
  rmaPLM                            text    html    latex   example
  threestep                         text    html    latex   example
  threestepPLM                      text    html    latex   example
** building package indices ...
* DONE (affyPLM)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'affyPLM_1.13.5.tar.gz'