############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL preprocessCore ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'preprocessCore' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_colSummarize.c -o R_colSummarize.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_plmd_interfaces.c -o R_plmd_interfaces.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_plmr_interfaces.c -o R_plmr_interfaces.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_rlm_interfaces.c -o R_rlm_interfaces.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_subColSummarize.c -o R_subColSummarize.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_medianpolish': R_subrcModel_interfaces.c:207:11: warning: unused variable 'se' [-Wunused-variable] 207 | double *se; | ^~ R_subrcModel_interfaces.c:206:11: warning: unused variable 'weights' [-Wunused-variable] 206 | double *weights; | ^~~~~~~ R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable] 165 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable] 165 | double *results, *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable] 165 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_plm': R_subrcModel_interfaces.c:532:10: warning: unused variable 'scale' [-Wunused-variable] 532 | double scale=-1.0; | ^~~~~ R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable] 485 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable] 485 | double *results, *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable] 485 | double *results, *buffer, *buffer2; | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c avg.c -o avg.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c avg_log.c -o avg_log.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biweight.c -o biweight.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lm.c -o lm.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c log_avg.c -o log_avg.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c log_median.c -o log_median.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrix_functions.c -o matrix_functions.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c median.c -o median.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c median_log.c -o median_log.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c medianpolish.c -o medianpolish.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plmd.c -o plmd.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plmr.c -o plmr.o plmr.c:279:13: warning: 'XTWX_R_inv' defined but not used [-Wunused-function] 279 | static void XTWX_R_inv(int *rows, int *cols, double *xtwx){ | ^~~~~~~~~~ plmr.c:152:13: warning: 'XTWX_R' defined but not used [-Wunused-function] 152 | static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){ | ^~~~~~ plmr.c:82:13: warning: 'XTWY_R' defined but not used [-Wunused-function] 82 | static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){ | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c psi_fns.c -o psi_fns.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qnorm.c -o qnorm.o qnorm.c: In function 'qnorm_c_determine_target_l': qnorm.c:1910:7: warning: unused variable 'non_na' [-Wunused-variable] 1910 | int non_na; | ^~~~~~ qnorm.c:1905:12: warning: unused variable 'j' [-Wunused-variable] 1905 | size_t i,j,row_mean_ind; | ^ qnorm.c: In function 'qnorm_c_determine_target_via_subset_l': qnorm.c:2509:7: warning: unused variable 'non_na' [-Wunused-variable] 2509 | int non_na; | ^~~~~~ qnorm.c:2504:12: warning: unused variable 'j' [-Wunused-variable] 2504 | size_t i,j,row_mean_ind; | ^ qnorm.c: In function 'using_target_via_subset_part1': qnorm.c:2725:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable] 2725 | size_t i,j,ind,target_ind; | ^~~ qnorm.c: In function 'using_target_via_subset_part2': qnorm.c:2824:11: warning: unused variable 'datvec' [-Wunused-variable] 2824 | double *datvec; | ^~~~~~ qnorm.c:2823:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] 2823 | double *sample_percentiles; | ^~~~~~~~~~~~~~~~~~ qnorm.c: In function 'using_target_via_subset': qnorm.c:2973:11: warning: unused variable 'datvec' [-Wunused-variable] 2973 | double *datvec; | ^~~~~~ qnorm.c:2972:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] 2972 | double *sample_percentiles; | ^~~~~~~~~~~~~~~~~~ qnorm.c:2968:7: warning: unused variable 'non_na' [-Wunused-variable] 2968 | int non_na = 0; | ^~~~~~ qnorm.c:2967:7: warning: unused variable 'targetnon_na' [-Wunused-variable] 2967 | int targetnon_na = targetrows; | ^~~~~~~~~~~~ qnorm.c:2965:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable] 2965 | double target_ind_double,target_ind_double_floor; | ^~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:2965:10: warning: unused variable 'target_ind_double' [-Wunused-variable] 2965 | double target_ind_double,target_ind_double_floor; | ^~~~~~~~~~~~~~~~~ qnorm.c:2964:10: warning: unused variable 'samplepercentile' [-Wunused-variable] 2964 | double samplepercentile; | ^~~~~~~~~~~~~~~~ qnorm.c:2963:11: warning: unused variable 'ranks' [-Wunused-variable] 2963 | double *ranks = (double *)Calloc((rows),double); | ^~~~~ qnorm.c:2961:11: warning: unused variable 'row_mean' [-Wunused-variable] 2961 | double *row_mean = target; | ^~~~~~~~ qnorm.c:2959:14: warning: unused variable 'dimat' [-Wunused-variable] 2959 | dataitem **dimat; | ^~~~~ qnorm.c:2957:18: warning: unused variable 'target_ind' [-Wunused-variable] 2957 | size_t i,j,ind,target_ind; | ^~~~~~~~~~ qnorm.c:2957:14: warning: unused variable 'ind' [-Wunused-variable] 2957 | size_t i,j,ind,target_ind; | ^~~ qnorm.c:2957:12: warning: unused variable 'j' [-Wunused-variable] 2957 | size_t i,j,ind,target_ind; | ^ qnorm.c: In function 'R_qnorm_using_target': qnorm.c:2115:3: warning: 'target_rows' may be used uninitialized [-Wmaybe-uninitialized] 2115 | qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:2083:10: note: 'target_rows' was declared here 2083 | size_t target_rows, target_cols; | ^~~~~~~~~~~ qnorm.c: In function 'R_qnorm_using_target_via_subset': qnorm.c:3242:3: warning: 'target_rows' may be used uninitialized [-Wmaybe-uninitialized] 3242 | qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:3209:10: note: 'target_rows' was declared here 3209 | size_t target_rows, target_cols; | ^~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm.c -o rlm.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm_anova.c -o rlm_anova.o rlm_anova.c: In function 'rlm_fit_anova_given_probe_effects_engine': rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable] 1235 | double endprobe; | ^~~~~~~~ rlm_anova.c: In function 'rlm_compute_se_anova_given_probe_effects': rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^~~~~~~~~~~ rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^ rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^~ rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable] 1419 | double scale=0.0; | ^~~~~ rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable] 1418 | double Kappa=0.0; /* A correction factor */ | ^~~~~ rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable] 1417 | double sumderivpsi=0.0; /* sum of psi'(r_i) */ | ^~~~~~~~~~~ rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable] 1415 | double sumpsi2=0.0; /* sum of psi(r_i)^2 */ | ^~~~~~~ rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable] 1414 | double k1 = psi_k; /* was 1.345; */ | ^~ rlm_anova.c: In function 'rlm_wfit_anova_given_probe_effects_engine': rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable] 1505 | double endprobe; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm_se.c -o rlm_se.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rma_background4.c -o rma_background4.o rma_background4.c: In function 'R_rma_bg_correct': rma_background4.c:509:12: warning: 'PMcopy' may be used uninitialized [-Wmaybe-uninitialized] 509 | return PMcopy; | ^~~~~~ rma_background4.c:482:13: note: 'PMcopy' was declared here 482 | SEXP dim1,PMcopy; | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -shared -s -static-libgcc -o preprocessCore.dll tmp.def R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-preprocessCore/00new/preprocessCore/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 * DONE (preprocessCore)