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This page was generated on 2019-10-16 12:18:59 -0400 (Wed, 16 Oct 2019).
Package 34/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
affyPLM 1.60.0 Ben Bolstad
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | [ OK ] | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: affyPLM |
Version: 1.60.0 |
Command: rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyPLM.buildbin-libdir affyPLM_1.60.0.tar.gz |
StartedAt: 2019-10-16 08:39:31 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 08:41:00 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 88.1 seconds |
RetCode: 0 |
Status: OK |
PackageFile: affyPLM_1.60.0.zip |
PackageFileSize: 2.725 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyPLM.buildbin-libdir affyPLM_1.60.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'affyPLM' ... ** using staged installation ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LESN.c -o LESN.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_avg_log.c -o PLM_avg_log.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_biweight.c -o PLM_biweight.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_log_avg.c -o PLM_log_avg.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_medianPM.c -o PLM_medianPM.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_median_logPM.c -o PLM_median_logPM.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_medianpolish.c -o PLM_medianpolish.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PLM_modelmatrix.c -o PLM_modelmatrix.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SCAB.c -o SCAB.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c common_types.c -o common_types.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ idealmismatch.c: In function 'SpecificBiweightCorrect_single': idealmismatch.c:183:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable] int first_ind; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c lm_threestep.c -o lm_threestep.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c matrix_functions.c -o matrix_functions.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c nthLargestPM.c -o nthLargestPM.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int which_lesn; ^ preprocess.c: In function 'pp_bothstages': preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable] int rows,cols; ^ preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] int rows,cols; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c psi_fns.c -o psi_fns.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_rmaexpress.c -o read_rmaexpress.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int rows,cols; ^ rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] int rows,cols; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rlm_threestep.c -o rlm_threestep.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rma_PLM.c -o rma_PLM.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int i; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c scaling.c -o scaling.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] double *PM,*MM; ^ threestep.c: In function 'R_threestep_c': threestep.c:193:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable] int rows,cols; ^ threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] int rows,cols; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c threestep_PLM.c -o threestep_PLM.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c threestep_common.c -o threestep_common.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c threestep_summary_methods.c -o threestep_summary_methods.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c transfns.c -o transfns.o C:/Rtools/mingw_32/bin/gcc -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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/affyPLM.buildbin-libdir/00LOCK-affyPLM/00new/affyPLM/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'affyPLM' finding HTML links ... done MAplot html PLMset-class html PLMset2exprSet html ReadRMAExpress html affyPLM-internal html bg.correct.LESN html fitPLM html normalize.exprSet html normalize.quantiles.probeset html normalize.scaling html preprocess html pseudo html rmaPLM html threestep html threestepPLM html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'affyPLM' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LESN.c -o LESN.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_avg_log.c -o PLM_avg_log.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_biweight.c -o PLM_biweight.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_log_avg.c -o PLM_log_avg.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_medianPM.c -o PLM_medianPM.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_median_logPM.c -o PLM_median_logPM.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_medianpolish.c -o PLM_medianpolish.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PLM_modelmatrix.c -o PLM_modelmatrix.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SCAB.c -o SCAB.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c common_types.c -o common_types.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ idealmismatch.c: In function 'SpecificBiweightCorrect_single': idealmismatch.c:183:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable] int first_ind; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c lm_threestep.c -o lm_threestep.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c matrix_functions.c -o matrix_functions.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c nthLargestPM.c -o nthLargestPM.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int which_lesn; ^ preprocess.c: In function 'pp_bothstages': preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable] int rows,cols; ^ preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] int rows,cols; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c psi_fns.c -o psi_fns.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_rmaexpress.c -o read_rmaexpress.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int rows,cols; ^ rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] int rows,cols; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rlm_threestep.c -o rlm_threestep.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rma_PLM.c -o rma_PLM.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int i; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c scaling.c -o scaling.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] double *PM,*MM; ^ threestep.c: In function 'R_threestep_c': threestep.c:193:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable] int rows,cols; ^ threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] int rows,cols; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c threestep_PLM.c -o threestep_PLM.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c threestep_common.c -o threestep_common.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int first_ind; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c threestep_summary_methods.c -o threestep_summary_methods.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c transfns.c -o transfns.o C:/Rtools/mingw_64/bin/gcc -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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'affyPLM' as affyPLM_1.60.0.zip * DONE (affyPLM)