Package: affyPLM

Version: 1.13.5

Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD build affyPLM

RetCode: 1

Time: 15.5 seconds

Status: ERROR

PackageFile: None

* 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 R.css in D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst392433624


---------- Making package affyPLM ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making LESN.d from LESN.c
making PLM_modelmatrix.d from PLM_modelmatrix.c
making R_rlm_interfaces.d from R_rlm_interfaces.c
making SCAB.d from SCAB.c
making avg_log.d from avg_log.c
making biweight.d from biweight.c
making chipbackground.d from chipbackground.c
making common_types.d from common_types.c
making do_PLMrlm.d from do_PLMrlm.c
making do_PLMrma.d from do_PLMrma.c
making do_PLMthreestep.d from do_PLMthreestep.c
making idealmismatch.d from idealmismatch.c
making lm_threestep.d from lm_threestep.c
making log_avg.d from log_avg.c
making matrix_functions.d from matrix_functions.c
making medianPM.d from medianPM.c
making median_logPM.d from median_logPM.c
making medianpolish.d from medianpolish.c
making nthLargestPM.d from nthLargestPM.c
making preprocess.d from preprocess.c
making psi_fns.d from psi_fns.c
making qnorm_probeset.d from qnorm_probeset.c
making read_rmaexpress.d from read_rmaexpress.c
making rlm_PLM.d from rlm_PLM.c
making rlm_threestep.d from rlm_threestep.c
making rmaPLM_pseudo.d from rmaPLM_pseudo.c
making rma_PLM.d from rma_PLM.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
making scaling.d from scaling.c
making threestep.d from threestep.c
making threestep_PLM.d from threestep_PLM.c
making threestep_common.d from threestep_common.c
making threestep_summary.d from threestep_summary.c
making threestep_summary_methods.d from threestep_summary_methods.c
making transfns.d from transfns.c
making weightedkerneldensity.d from weightedkerneldensity.c
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c LESN.c -o LESN.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -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  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c SCAB.c -o SCAB.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -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  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c biweight.c -o biweight.o
biweight.c: In function `TukeyBiweight_threestep':
biweight.c:66: warning: implicit declaration of function `TukeyBiweight'
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c chipbackground.c -o chipbackground.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c common_types.c -o common_types.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c do_PLMrlm.c -o do_PLMrlm.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c do_PLMrma.c -o do_PLMrma.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c idealmismatch.c -o idealmismatch.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c lm_threestep.c -o lm_threestep.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c log_avg.c -o log_avg.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c matrix_functions.c -o matrix_functions.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c medianPM.c -o medianPM.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c median_logPM.c -o median_logPM.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c medianpolish.c -o medianpolish.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c nthLargestPM.c -o nthLargestPM.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c preprocess.c -o preprocess.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c psi_fns.c -o psi_fns.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -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  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c read_rmaexpress.c -o read_rmaexpress.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:99: warning: 'rlmPLM_alloc_space' defined but not used
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rlm_threestep.c -o rlm_threestep.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rma_PLM.c -o rma_PLM.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rma_background2.c -o rma_background2.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rma_common.c -o rma_common.o
rma_common.c: In function `median':
rma_common.c:60: warning: unused variable `i'
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c scaling.c -o scaling.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c threestep.c -o threestep.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c threestep_PLM.c -o threestep_PLM.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c threestep_common.c -o threestep_common.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c threestep_summary.c -o threestep_summary.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c transfns.c -o transfns.o
gcc  -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c weightedkerneldensity.c -o weightedkerneldensity.o
windres -I d:/biocbld/bbs-2.1-bioc/R/include  -i affyPLM_res.rc -o affyPLM_res.o
gcc  -shared -s  -o affyPLM.dll affyPLM.def LESN.o PLM_modelmatrix.o R_rlm_interfaces.o SCAB.o avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o log_avg.o matrix_functions.o medianPM.o median_logPM.o medianpolish.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_background2.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o affyPLM_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin -lg2c -Ld:/biocbld/bbs-2.1-bioc/R/bin -lRlapack -Ld:/biocbld/bbs-2.1-bioc/R/bin -lRblas  -Ld:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -lz   -lR
preprocess.o:preprocess.c:(.text+0x2055): undefined reference to `R_qnorm_robust_weights'
preprocess.o:preprocess.c:(.text+0x207e): undefined reference to `R_qnorm_robust_weights'
preprocess.o:preprocess.c:(.text+0x20d1): undefined reference to `R_qnorm_robust_weights'
rmaPLM_pseudo.o:rmaPLM_pseudo.c:(.text+0x2a): undefined reference to `med_abs'
rmaPLM_pseudo.o:rmaPLM_pseudo.c:(.text+0xd5): undefined reference to `med_abs'
collect2: ld returned 1 exit status
make[3]: *** [affyPLM.dll] Error 1
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-affyPLM] Error 2
*** Installation of affyPLM failed ***

Removing 'D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst392433624/affyPLM'
 ERROR
Installation failed.
Removing 'D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst392433624'