* installing *source* package 'affyPLM' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' make[1]: Entering directory '/tmp/RtmpotNrme/R.INSTALL191bc67583178/affyPLM/src' gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LESN.c -o LESN.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PLM_avg_log.c -o PLM_avg_log.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PLM_biweight.c -o PLM_biweight.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PLM_log_avg.c -o PLM_log_avg.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PLM_medianPM.c -o PLM_medianPM.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PLM_median_logPM.c -o PLM_median_logPM.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PLM_medianpolish.c -o PLM_medianpolish.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PLM_modelmatrix.c -o PLM_modelmatrix.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SCAB.c -o SCAB.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c common_types.c -o common_types.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 620 | int first_ind; | ^~~~~~~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 209 | int first_ind; | ^~~~~~~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 118 | int first_ind; | ^~~~~~~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 71 | 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] 183 | int first_ind; | ^~~~~~~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lm_threestep.c -o lm_threestep.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrix_functions.c -o matrix_functions.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nthLargestPM.c -o nthLargestPM.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 158 | int which_lesn; | ^~~~~~~~~~ preprocess.c: In function 'pp_bothstages': preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable] 677 | int rows,cols; | ^~~~ preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] 677 | int rows,cols; | ^~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c psi_fns.c -o psi_fns.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 110 | int first_ind; | ^~~~~~~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_rmaexpress.c -o read_rmaexpress.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 1481 | int rows,cols; | ^~~~ rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] 1481 | int rows,cols; | ^~~~ rlm_PLM.c: In function 'rlm_PLMset_nameoutput': rlm_PLM.c:870:32: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=] 870 | snprintf(tmp_str2,9,"%d",j+1); | ^~ rlm_PLM.c:870:31: note: directive argument in the range [1, 2147483647] 870 | snprintf(tmp_str2,9,"%d",j+1); | ^~~~ rlm_PLM.c:870:11: note: 'snprintf' output between 2 and 11 bytes into a destination of size 9 870 | snprintf(tmp_str2,9,"%d",j+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rlm_PLM.c:868:32: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=] 868 | snprintf(tmp_str2,9,"%d",j+2); | ^~ rlm_PLM.c:868:31: note: directive argument in the range [2, 2147483647] 868 | snprintf(tmp_str2,9,"%d",j+2); | ^~~~ rlm_PLM.c:868:11: note: 'snprintf' output between 2 and 11 bytes into a destination of size 9 868 | snprintf(tmp_str2,9,"%d",j+2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm_threestep.c -o rlm_threestep.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rma_PLM.c -o rma_PLM.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 60 | int i; | ^ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scaling.c -o scaling.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 82 | 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] 193 | int rows,cols; | ^~~~ threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable] 193 | int rows,cols; | ^~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c threestep_PLM.c -o threestep_PLM.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c threestep_common.c -o threestep_common.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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] 73 | int first_ind; | ^~~~~~~~~ gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c threestep_summary_methods.c -o threestep_summary_methods.o gcc -I"C:/r_packages/pkgbuild/lib/zlibbioc/include" -I"C:/r_packages/rinst/include" -DNDEBUG -DHAVE_ZLIB -I'C:/r_packages/pkgbuild/lib/preprocessCore/include' -I"C:/r_packages/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transfns.c -o transfns.o 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:/r_packages/pkgbuild/lib/zlibbioc/libs/x64 -lzlib1bioc -lgfortran -lm -lquadmath -LC:/r_packages/rinst/bin/x64 -lRlapack -LC:/r_packages/rinst/bin/x64 -lRblas -LC:/r_packages/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/r_packages/x86_64-w64-mingw32.static.posix/lib -LC:/r_packages/rinst/bin/x64 -lR make[1]: Leaving directory '/tmp/RtmpotNrme/R.INSTALL191bc67583178/affyPLM/src' installing to C:/r_packages/pkgbuild/lib/00LOCK-affyPLM/00new/affyPLM/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * MD5 sums packaged installation of 'affyPLM' as affyPLM_1.79.0.zip * DONE (affyPLM)