BioC 3.4: CHECK report for preprocessCore on moscato1

Package: preprocessCore

Version: 1.35.0

Command: rm -rf preprocessCore.buildbin-libdir preprocessCore.Rcheck && mkdir preprocessCore.buildbin-libdir preprocessCore.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=preprocessCore.buildbin-libdir preprocessCore_1.35.0.tar.gz >preprocessCore.Rcheck\00install.out 2>&1 && cp preprocessCore.Rcheck\00install.out preprocessCore-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=preprocessCore.buildbin-libdir --install="check:preprocessCore-install.out" --force-multiarch --no-vignettes --timings preprocessCore_1.35.0.tar.gz

StartedAt: 2016-09-20 14:11:43 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 14:12:44 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 61.6 seconds

RetCode: 0

Status:  OK

CheckDir: preprocessCore.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   rm -rf preprocessCore.buildbin-libdir preprocessCore.Rcheck && mkdir preprocessCore.buildbin-libdir preprocessCore.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=preprocessCore.buildbin-libdir preprocessCore_1.35.0.tar.gz >preprocessCore.Rcheck\00install.out 2>&1 && cp preprocessCore.Rcheck\00install.out preprocessCore-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=preprocessCore.buildbin-libdir --install="check:preprocessCore-install.out" --force-multiarch --no-vignettes --timings preprocessCore_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/preprocessCore.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '1.35.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'preprocessCore' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/preprocessCore.buildbin-libdir/preprocessCore/libs/i386/preprocessCore.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'PLMdtest.R'
  Running 'qnormtest.R'
 OK
** running tests for arch 'x64' ...
  Running 'PLMdtest.R'
  Running 'qnormtest.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/preprocessCore.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'preprocessCore' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_colSummarize.c -o R_colSummarize.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_subColSummarize.c -o R_subColSummarize.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_medianpolish':
R_subrcModel_interfaces.c:190:11: warning: unused variable 'se' [-Wunused-variable]
   double *se;
           ^
R_subrcModel_interfaces.c:189:11: warning: unused variable 'weights' [-Wunused-variable]
   double *weights;
           ^
R_subrcModel_interfaces.c:154:30: warning: unused variable 'buffer2' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                              ^
R_subrcModel_interfaces.c:154:21: warning: unused variable 'buffer' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                     ^
R_subrcModel_interfaces.c:154:11: warning: unused variable 'results' [-Wunused-variable]
   double *results, *buffer, *buffer2;
           ^
R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_plm':
R_subrcModel_interfaces.c:510:10: warning: unused variable 'scale' [-Wunused-variable]
   double scale=-1.0;
          ^
R_subrcModel_interfaces.c:469:30: warning: unused variable 'buffer2' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                              ^
R_subrcModel_interfaces.c:469:21: warning: unused variable 'buffer' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                     ^
R_subrcModel_interfaces.c:469:11: warning: unused variable 'results' [-Wunused-variable]
   double *results, *buffer, *buffer2;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c avg.c -o avg.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c avg_log.c -o avg_log.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c biweight.c -o biweight.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c lm.c -o lm.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c log_avg.c -o log_avg.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c log_median.c -o log_median.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c median.c -o median.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c median_log.c -o median_log.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c medianpolish.c -o medianpolish.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c plmd.c -o plmd.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c plmr.c -o plmr.o
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){
             ^
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:279:13: warning: 'XTWX_R_inv' defined but not used [-Wunused-function]
 static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
             ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c qnorm.c -o qnorm.o
qnorm.c: In function 'qnorm_c_determine_target_l':
qnorm.c:1887:7: warning: unused variable 'non_na' [-Wunused-variable]
   int non_na;
       ^
qnorm.c:1882:12: 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:2481:7: warning: unused variable 'non_na' [-Wunused-variable]
   int non_na;
       ^
qnorm.c:2476:12: warning: unused variable 'j' [-Wunused-variable]
   size_t i,j,row_mean_ind;
            ^
qnorm.c: In function 'using_target_via_subset_part1':
qnorm.c:2692:14: 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:2791:11: warning: unused variable 'datvec' [-Wunused-variable]
   double *datvec;
           ^
qnorm.c:2790:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
   double *sample_percentiles;
           ^
qnorm.c: In function 'using_target_via_subset':
qnorm.c:2940:11: warning: unused variable 'datvec' [-Wunused-variable]
   double *datvec;
           ^
qnorm.c:2939:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
   double *sample_percentiles;
           ^
qnorm.c:2935:7: warning: unused variable 'non_na' [-Wunused-variable]
   int non_na = 0;
       ^
qnorm.c:2934:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
   int targetnon_na = targetrows;
       ^
qnorm.c:2932:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
   double target_ind_double,target_ind_double_floor;
                            ^
qnorm.c:2932:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
   double target_ind_double,target_ind_double_floor;
          ^
qnorm.c:2931:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
   double samplepercentile;
          ^
qnorm.c:2930:11: warning: unused variable 'ranks' [-Wunused-variable]
   double *ranks = (double *)Calloc((rows),double);
           ^
qnorm.c:2928:11: warning: unused variable 'row_mean' [-Wunused-variable]
   double *row_mean = target;
           ^
qnorm.c:2926:14: warning: unused variable 'dimat' [-Wunused-variable]
   dataitem **dimat;
              ^
qnorm.c:2924:18: warning: unused variable 'target_ind' [-Wunused-variable]
   size_t i,j,ind,target_ind;
                  ^
qnorm.c:2924:14: warning: unused variable 'ind' [-Wunused-variable]
   size_t i,j,ind,target_ind;
              ^
qnorm.c:2924:12: warning: unused variable 'j' [-Wunused-variable]
   size_t i,j,ind,target_ind;
            ^
qnorm.c: In function 'R_qnorm_using_target':
qnorm.c:2055:10: warning: 'target_rows' may be used uninitialized in this function [-Wmaybe-uninitialized]
   size_t target_rows, target_cols;
          ^
qnorm.c: In function 'R_qnorm_using_target_via_subset':
qnorm.c:3205:3: 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:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rlm.c -o rlm.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rlm_se.c -o rlm_se.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_background4.c -o rma_background4.o
rma_background4.c: In function 'R_rma_bg_correct':
rma_background4.c:465:13: warning: 'PMcopy' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SEXP dim1,PMcopy;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c weightedkerneldensity.c -o weightedkerneldensity.o
weightedkerneldensity.c: In function 'IQR':
weightedkerneldensity.c:750:14: warning: variable 'high_i' set but not used [-Wunused-but-set-variable]
   int low_i, high_i;
              ^
weightedkerneldensity.c:750:7: warning: variable 'low_i' set but not used [-Wunused-but-set-variable]
   int low_i, high_i;
       ^
C:/Rtools/mingw_32/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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/preprocessCore.buildbin-libdir/preprocessCore/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'preprocessCore' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_colSummarize.c -o R_colSummarize.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_subColSummarize.c -o R_subColSummarize.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_medianpolish':
R_subrcModel_interfaces.c:190:11: warning: unused variable 'se' [-Wunused-variable]
   double *se;
           ^
R_subrcModel_interfaces.c:189:11: warning: unused variable 'weights' [-Wunused-variable]
   double *weights;
           ^
R_subrcModel_interfaces.c:154:30: warning: unused variable 'buffer2' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                              ^
R_subrcModel_interfaces.c:154:21: warning: unused variable 'buffer' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                     ^
R_subrcModel_interfaces.c:154:11: warning: unused variable 'results' [-Wunused-variable]
   double *results, *buffer, *buffer2;
           ^
R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_plm':
R_subrcModel_interfaces.c:510:10: warning: unused variable 'scale' [-Wunused-variable]
   double scale=-1.0;
          ^
R_subrcModel_interfaces.c:469:30: warning: unused variable 'buffer2' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                              ^
R_subrcModel_interfaces.c:469:21: warning: unused variable 'buffer' [-Wunused-variable]
   double *results, *buffer, *buffer2;
                     ^
R_subrcModel_interfaces.c:469:11: warning: unused variable 'results' [-Wunused-variable]
   double *results, *buffer, *buffer2;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c avg.c -o avg.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c avg_log.c -o avg_log.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c biweight.c -o biweight.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c lm.c -o lm.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c log_avg.c -o log_avg.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c log_median.c -o log_median.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c median.c -o median.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c median_log.c -o median_log.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c medianpolish.c -o medianpolish.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c plmd.c -o plmd.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c plmr.c -o plmr.o
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){
             ^
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:279:13: warning: 'XTWX_R_inv' defined but not used [-Wunused-function]
 static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
             ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c qnorm.c -o qnorm.o
qnorm.c: In function 'qnorm_c_determine_target_l':
qnorm.c:1887:7: warning: unused variable 'non_na' [-Wunused-variable]
   int non_na;
       ^
qnorm.c:1882:12: 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:2481:7: warning: unused variable 'non_na' [-Wunused-variable]
   int non_na;
       ^
qnorm.c:2476:12: warning: unused variable 'j' [-Wunused-variable]
   size_t i,j,row_mean_ind;
            ^
qnorm.c: In function 'using_target_via_subset_part1':
qnorm.c:2692:14: 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:2791:11: warning: unused variable 'datvec' [-Wunused-variable]
   double *datvec;
           ^
qnorm.c:2790:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
   double *sample_percentiles;
           ^
qnorm.c: In function 'using_target_via_subset':
qnorm.c:2940:11: warning: unused variable 'datvec' [-Wunused-variable]
   double *datvec;
           ^
qnorm.c:2939:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
   double *sample_percentiles;
           ^
qnorm.c:2935:7: warning: unused variable 'non_na' [-Wunused-variable]
   int non_na = 0;
       ^
qnorm.c:2934:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
   int targetnon_na = targetrows;
       ^
qnorm.c:2932:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
   double target_ind_double,target_ind_double_floor;
                            ^
qnorm.c:2932:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
   double target_ind_double,target_ind_double_floor;
          ^
qnorm.c:2931:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
   double samplepercentile;
          ^
qnorm.c:2930:11: warning: unused variable 'ranks' [-Wunused-variable]
   double *ranks = (double *)Calloc((rows),double);
           ^
qnorm.c:2928:11: warning: unused variable 'row_mean' [-Wunused-variable]
   double *row_mean = target;
           ^
qnorm.c:2926:14: warning: unused variable 'dimat' [-Wunused-variable]
   dataitem **dimat;
              ^
qnorm.c:2924:18: warning: unused variable 'target_ind' [-Wunused-variable]
   size_t i,j,ind,target_ind;
                  ^
qnorm.c:2924:14: warning: unused variable 'ind' [-Wunused-variable]
   size_t i,j,ind,target_ind;
              ^
qnorm.c:2924:12: warning: unused variable 'j' [-Wunused-variable]
   size_t i,j,ind,target_ind;
            ^
qnorm.c: In function 'R_qnorm_using_target':
qnorm.c:2087:3: 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:3205:3: 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:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rlm.c -o rlm.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rlm_se.c -o rlm_se.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_background4.c -o rma_background4.o
rma_background4.c: In function 'R_rma_bg_correct':
rma_background4.c:465:13: warning: 'PMcopy' may be used uninitialized in this function [-Wmaybe-uninitialized]
   SEXP dim1,PMcopy;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c weightedkerneldensity.c -o weightedkerneldensity.o
weightedkerneldensity.c: In function 'IQR':
weightedkerneldensity.c:750:14: warning: variable 'high_i' set but not used [-Wunused-but-set-variable]
   int low_i, high_i;
              ^
weightedkerneldensity.c:750:7: warning: variable 'low_i' set but not used [-Wunused-but-set-variable]
   int low_i, high_i;
       ^
C:/Rtools/mingw_64/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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/preprocessCore.buildbin-libdir/preprocessCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'preprocessCore' as preprocessCore_1.35.0.zip
* DONE (preprocessCore)

name	user	system	elapsed
colSummarize	0	0	0
normalize.quantiles.in.blocks	0.03	0.00	0.03
rcModelPLMd	0.02	0.00	0.02
rcModelPLMr	0.03	0.00	0.03
rcModels	0.02	0.00	0.02
subColSummarize	0	0	0
subrcModels	0	0	0

name	user	system	elapsed
colSummarize	0	0	0
normalize.quantiles.in.blocks	0.01	0.02	0.03
rcModelPLMd	0.02	0.00	0.02
rcModelPLMr	0.04	0.00	0.05
rcModels	0.02	0.00	0.01
subColSummarize	0	0	0
subrcModels	0.02	0.00	0.02