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This page was generated on 2021-10-15 15:06:16 -0400 (Fri, 15 Oct 2021).

INSTALL results for preprocessCore on tokay2

To the developers/maintainers of the preprocessCore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preprocessCore.git to
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raw results

Package 1429/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.54.0  (landing page)
Ben Bolstad
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/preprocessCore
git_branch: RELEASE_3_13
git_last_commit: 66a30ca
git_last_commit_date: 2021-05-19 11:32:55 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: preprocessCore
Version: 1.54.0
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
StartedAt: 2021-10-14 07:05:05 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 07:06:58 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 112.5 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


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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