############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/preprocessCore_1.54.0.tar.gz && rm -rf preprocessCore.buildbin-libdir && mkdir preprocessCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=preprocessCore.buildbin-libdir preprocessCore_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL preprocessCore_1.54.0.zip && rm preprocessCore_1.54.0.tar.gz preprocessCore_1.54.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 131k 100 131k 0 0 684k 0 --:--:-- --:--:-- --:--:-- 690k install for i386 * installing *source* package 'preprocessCore' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_colSummarize.c -o R_colSummarize.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_plmd_interfaces.c -o R_plmd_interfaces.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_plmr_interfaces.c -o R_plmr_interfaces.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_rlm_interfaces.c -o R_rlm_interfaces.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_subColSummarize.c -o R_subColSummarize.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -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] double *se; ^~ R_subrcModel_interfaces.c:206:11: warning: unused variable 'weights' [-Wunused-variable] double *weights; ^~~~~~~ R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~~ R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~ R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable] 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] double scale=-1.0; ^~~~~ R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~~ R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~ R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c avg.c -o avg.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c avg_log.c -o avg_log.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c biweight.c -o biweight.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lm.c -o lm.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c log_avg.c -o log_avg.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c log_median.c -o log_median.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix_functions.c -o matrix_functions.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c median.c -o median.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c median_log.c -o median_log.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c medianpolish.c -o medianpolish.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c plmd.c -o plmd.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c plmr.c -o plmr.o plmr.c:279:13: warning: 'XTWX_R_inv' defined but not used [-Wunused-function] static void XTWX_R_inv(int *rows, int *cols, double *xtwx){ ^~~~~~~~~~ plmr.c:152:13: warning: 'XTWX_R' defined but not used [-Wunused-function] 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] static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){ ^~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c psi_fns.c -o psi_fns.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qnorm.c -o qnorm.o qnorm.c: In function 'qnorm_c_determine_target_l': qnorm.c:1908:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^~~~~~ qnorm.c:1903:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c: In function 'qnorm_c_determine_target_via_subset_l': qnorm.c:2507:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^~~~~~ qnorm.c:2502:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c: In function 'using_target_via_subset_part1': qnorm.c:2723:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable] size_t i,j,ind,target_ind; ^~~ qnorm.c: In function 'using_target_via_subset_part2': qnorm.c:2822:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^~~~~~ qnorm.c:2821:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^~~~~~~~~~~~~~~~~~ qnorm.c: In function 'using_target_via_subset': qnorm.c:2971:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^~~~~~ qnorm.c:2970:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^~~~~~~~~~~~~~~~~~ qnorm.c:2966:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na = 0; ^~~~~~ qnorm.c:2965:7: warning: unused variable 'targetnon_na' [-Wunused-variable] int targetnon_na = targetrows; ^~~~~~~~~~~~ qnorm.c:2963:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:2963:10: warning: unused variable 'target_ind_double' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^~~~~~~~~~~~~~~~~ qnorm.c:2962:10: warning: unused variable 'samplepercentile' [-Wunused-variable] double samplepercentile; ^~~~~~~~~~~~~~~~ qnorm.c:2961:11: warning: unused variable 'ranks' [-Wunused-variable] double *ranks = (double *)Calloc((rows),double); ^~~~~ qnorm.c:2959:11: warning: unused variable 'row_mean' [-Wunused-variable] double *row_mean = target; ^~~~~~~~ qnorm.c:2957:14: warning: unused variable 'dimat' [-Wunused-variable] dataitem **dimat; ^~~~~ qnorm.c:2955:18: warning: unused variable 'target_ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^~~~~~~~~~ qnorm.c:2955:14: warning: unused variable 'ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^~~ qnorm.c:2955:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c: In function 'R_qnorm_using_target': qnorm.c:2113:3: warning: 'target_rows' may be used uninitialized in this function [-Wmaybe-uninitialized] qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnorm.c: In function 'R_qnorm_using_target_via_subset': qnorm.c:3240:3: warning: 'target_rows' may be used uninitialized in this function [-Wmaybe-uninitialized] qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rlm.c -o rlm.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -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] 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] double vs=0.0,m,varderivpsi=0.0; ^~~~~~~~~~~ rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^~ rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable] double scale=0.0; ^~~~~ rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable] double Kappa=0.0; /* A correction factor */ ^~~~~ rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable] double sumderivpsi=0.0; /* sum of psi'(r_i) */ ^~~~~~~~~~~ rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable] double sumpsi2=0.0; /* sum of psi(r_i)^2 */ ^~~~~~~ rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable] 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] double endprobe; ^~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rlm_se.c -o rlm_se.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -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 in this function [-Wmaybe-uninitialized] return PMcopy; ^~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c weightedkerneldensity.c -o weightedkerneldensity.o C:/rtools40/mingw32/bin/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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/preprocessCore.buildbin-libdir/00LOCK-preprocessCore/00new/preprocessCore/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'preprocessCore' finding HTML links ... done colSummarize html normalize.quantiles html normalize.quantiles.in.blocks html normalize.quantiles.robust html normalize.quantiles.target html rcModelPLMd html rcModelPLMr html rcModels html rma.background.correct html subColSummarize html subrcModels html ** 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 install for x64 * installing *source* package 'preprocessCore' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_colSummarize.c -o R_colSummarize.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_plmd_interfaces.c -o R_plmd_interfaces.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_plmr_interfaces.c -o R_plmr_interfaces.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_rlm_interfaces.c -o R_rlm_interfaces.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_subColSummarize.c -o R_subColSummarize.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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] double *se; ^~ R_subrcModel_interfaces.c:206:11: warning: unused variable 'weights' [-Wunused-variable] double *weights; ^~~~~~~ R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~~ R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~ R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable] 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] double scale=-1.0; ^~~~~ R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~~ R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~ R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable] double *results, *buffer, *buffer2; ^~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c avg.c -o avg.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c avg_log.c -o avg_log.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c biweight.c -o biweight.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lm.c -o lm.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c log_avg.c -o log_avg.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c log_median.c -o log_median.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix_functions.c -o matrix_functions.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c median.c -o median.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c median_log.c -o median_log.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c medianpolish.c -o medianpolish.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c plmd.c -o plmd.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c plmr.c -o plmr.o plmr.c:279:13: warning: 'XTWX_R_inv' defined but not used [-Wunused-function] static void XTWX_R_inv(int *rows, int *cols, double *xtwx){ ^~~~~~~~~~ plmr.c:152:13: warning: 'XTWX_R' defined but not used [-Wunused-function] 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] static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){ ^~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c psi_fns.c -o psi_fns.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qnorm.c -o qnorm.o qnorm.c: In function 'qnorm_c_determine_target_l': qnorm.c:1908:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^~~~~~ qnorm.c:1903:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c: In function 'qnorm_c_determine_target_via_subset_l': qnorm.c:2507:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^~~~~~ qnorm.c:2502:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c: In function 'using_target_via_subset_part1': qnorm.c:2723:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable] size_t i,j,ind,target_ind; ^~~ qnorm.c: In function 'using_target_via_subset_part2': qnorm.c:2822:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^~~~~~ qnorm.c:2821:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^~~~~~~~~~~~~~~~~~ qnorm.c: In function 'using_target_via_subset': qnorm.c:2971:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^~~~~~ qnorm.c:2970:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^~~~~~~~~~~~~~~~~~ qnorm.c:2966:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na = 0; ^~~~~~ qnorm.c:2965:7: warning: unused variable 'targetnon_na' [-Wunused-variable] int targetnon_na = targetrows; ^~~~~~~~~~~~ qnorm.c:2963:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:2963:10: warning: unused variable 'target_ind_double' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^~~~~~~~~~~~~~~~~ qnorm.c:2962:10: warning: unused variable 'samplepercentile' [-Wunused-variable] double samplepercentile; ^~~~~~~~~~~~~~~~ qnorm.c:2961:11: warning: unused variable 'ranks' [-Wunused-variable] double *ranks = (double *)Calloc((rows),double); ^~~~~ qnorm.c:2959:11: warning: unused variable 'row_mean' [-Wunused-variable] double *row_mean = target; ^~~~~~~~ qnorm.c:2957:14: warning: unused variable 'dimat' [-Wunused-variable] dataitem **dimat; ^~~~~ qnorm.c:2955:18: warning: unused variable 'target_ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^~~~~~~~~~ qnorm.c:2955:14: warning: unused variable 'ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^~~ qnorm.c:2955:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c: In function 'R_qnorm_using_target': qnorm.c:2113:3: warning: 'target_rows' may be used uninitialized in this function [-Wmaybe-uninitialized] qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnorm.c: In function 'R_qnorm_using_target_via_subset': qnorm.c:3240:3: warning: 'target_rows' may be used uninitialized in this function [-Wmaybe-uninitialized] qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rlm.c -o rlm.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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] 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] double vs=0.0,m,varderivpsi=0.0; ^~~~~~~~~~~ rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^~ rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable] double scale=0.0; ^~~~~ rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable] double Kappa=0.0; /* A correction factor */ ^~~~~ rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable] double sumderivpsi=0.0; /* sum of psi'(r_i) */ ^~~~~~~~~~~ rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable] double sumpsi2=0.0; /* sum of psi(r_i)^2 */ ^~~~~~~ rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable] 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] double endprobe; ^~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rlm_se.c -o rlm_se.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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 in this function [-Wmaybe-uninitialized] return PMcopy; ^~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c weightedkerneldensity.c -o weightedkerneldensity.o C:/rtools40/mingw64/bin/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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/preprocessCore.buildbin-libdir/preprocessCore/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'preprocessCore' as preprocessCore_1.54.0.zip * DONE (preprocessCore) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'preprocessCore' successfully unpacked and MD5 sums checked