Multiple platform build/check report for BioC 3.20 - INSTALL results for preprocessCore on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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INSTALL results for preprocessCore on palomino8

To the developers/maintainers of the preprocessCore package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preprocessCore.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: preprocessCore
Version: 1.68.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL preprocessCore
StartedAt: 2024-12-19 15:25:11 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 15:26:15 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 63.2 seconds
RetCode: 0
Status: OK
Command output

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###
### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL preprocessCore
###
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* 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) 13.3.0'
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 *)R_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)