affyPLM 1.44.0
Ben Bolstad
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affyPLM | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | [ OK ] | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/affyPLM_1.44.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch affyPLM_1.44.0.tar.gz && rm affyPLM_1.44.0.tar.gz
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install for i386
* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'affyPLM' ...
** libs
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c: In function 'do_PLM_rlm':
do_PLMrlm.c:620:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c: In function 'do_PLMrma':
do_PLMrma.c:209:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c: In function 'do_PLMthreestep':
do_PLMthreestep.c:118:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c idealmismatch.c -o idealmismatch.o
idealmismatch.c: In function 'IdealMM_correct_single':
idealmismatch.c:71:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
idealmismatch.c: In function 'SpecificBiweightCorrect_single':
idealmismatch.c:183:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c preprocess.c -o preprocess.o
preprocess.c: In function 'pp_background':
preprocess.c:158:7: warning: variable 'which_lesn' set but not used [-Wunused-but-set-variable]
preprocess.c: In function 'pp_bothstages':
preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function 'qnorm_probeset_c':
qnorm_probeset.c:110:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function 'R_rlm_PLMset_c':
rlm_PLM.c:1481:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep.c -o threestep.o
threestep.c: In function 'threestep_summary':
threestep.c:82:15: warning: variable 'MM' set but not used [-Wunused-but-set-variable]
threestep.c: In function 'R_threestep_c':
threestep.c:193:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep_summary.c -o threestep_summary.o
threestep_summary.c: In function 'do_3summary':
threestep_summary.c:73:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c transfns.c -o transfns.o
gcc -m32 -shared -s -static-libgcc -o affyPLM.dll tmp.def LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.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_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -LE:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lgfortran -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lRblas -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/affyPLM/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'summary' from package 'base' in package 'affyPLM'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'affyPLM' ...
** libs
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c: In function 'do_PLM_rlm':
do_PLMrlm.c:620:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c: In function 'do_PLMrma':
do_PLMrma.c:209:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c: In function 'do_PLMthreestep':
do_PLMthreestep.c:118:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c idealmismatch.c -o idealmismatch.o
idealmismatch.c: In function 'IdealMM_correct_single':
idealmismatch.c:71:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
idealmismatch.c: In function 'SpecificBiweightCorrect_single':
idealmismatch.c:183:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c preprocess.c -o preprocess.o
preprocess.c: In function 'pp_background':
preprocess.c:158:7: warning: variable 'which_lesn' set but not used [-Wunused-but-set-variable]
preprocess.c: In function 'pp_bothstages':
preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function 'qnorm_probeset_c':
qnorm_probeset.c:110:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function 'R_rlm_PLMset_c':
rlm_PLM.c:1481:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep.c -o threestep.o
threestep.c: In function 'threestep_summary':
threestep.c:82:15: warning: variable 'MM' set but not used [-Wunused-but-set-variable]
threestep.c: In function 'R_threestep_c':
threestep.c:193:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep_summary.c -o threestep_summary.o
threestep_summary.c: In function 'do_3summary':
threestep_summary.c:73:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"E:/biocbld/bbs-3.1-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c transfns.c -o transfns.o
gcc -m64 -shared -s -static-libgcc -o affyPLM.dll tmp.def LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.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_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -LE:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lgfortran -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lRlapack -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lRblas -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/affyPLM/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (affyPLM)