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This page was generated on 2025-08-04 12:07 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1602/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.71.2  (landing page)
Ben Bolstad
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/preprocessCore
git_branch: devel
git_last_commit: d53376a
git_last_commit_date: 2025-06-20 10:10:46 -0400 (Fri, 20 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK 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: 1.71.2
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preprocessCore.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings preprocessCore_1.71.2.tar.gz
StartedAt: 2025-08-04 05:26:09 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 05:26:42 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 33.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: preprocessCore.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preprocessCore.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings preprocessCore_1.71.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '1.71.2'
* 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
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... WARNING
checkRd: (-1) colSummarize.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (7) normalize.quantiles.Rd:47: Invalid email address: bmbolstad.com
checkRd: (7) rma.background.correct.Rd:35: Invalid email address: bmbolstad.com
checkRd: (-1) subColSummarize.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:61-63: Lost braces in \itemize; meant \describe ?
* 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 shell scripts ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/preprocessCore/libs/x64/preprocessCore.dll':
  Found '_exit', possibly from '_exit' (C)
  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 use Fortran I/O
nor system RNGs nor [v]sprintf. 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'PLMdtest.R'
  Running 'qnormtest.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck/00check.log'
for details.


Installation output

preprocessCore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'preprocessCore' ...
** this is package 'preprocessCore' version '1.71.2'
** using staged installation

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


** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_colSummarize.c -o R_colSummarize.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_subColSummarize.c -o R_subColSummarize.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -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:222:11: warning: unused variable 'se' [-Wunused-variable]
  222 |   double *se;
      |           ^~
R_subrcModel_interfaces.c:221:11: warning: unused variable 'weights' [-Wunused-variable]
  221 |   double *weights;
      |           ^~~~~~~
R_subrcModel_interfaces.c:177:30: warning: unused variable 'buffer2' [-Wunused-variable]
  177 |   double *results, *buffer, *buffer2;
      |                              ^~~~~~~
R_subrcModel_interfaces.c:177:21: warning: unused variable 'buffer' [-Wunused-variable]
  177 |   double *results, *buffer, *buffer2;
      |                     ^~~~~~
R_subrcModel_interfaces.c:177:11: warning: unused variable 'results' [-Wunused-variable]
  177 |   double *results, *buffer, *buffer2;
      |           ^~~~~~~
R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_plm':
R_subrcModel_interfaces.c:552:10: warning: unused variable 'scale' [-Wunused-variable]
  552 |   double scale=-1.0;
      |          ^~~~~
R_subrcModel_interfaces.c:502:30: warning: unused variable 'buffer2' [-Wunused-variable]
  502 |   double *results, *buffer, *buffer2;
      |                              ^~~~~~~
R_subrcModel_interfaces.c:502:21: warning: unused variable 'buffer' [-Wunused-variable]
  502 |   double *results, *buffer, *buffer2;
      |                     ^~~~~~
R_subrcModel_interfaces.c:502:11: warning: unused variable 'results' [-Wunused-variable]
  502 |   double *results, *buffer, *buffer2;
      |           ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c avg.c -o avg.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c avg_log.c -o avg_log.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c biweight.c -o biweight.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c init_package.c -o init_package.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c lm.c -o lm.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c log_avg.c -o log_avg.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c log_median.c -o log_median.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c matrix_functions.c -o matrix_functions.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c median.c -o median.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c median_log.c -o median_log.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c medianpolish.c -o medianpolish.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c plmd.c -o plmd.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -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-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c psi_fns.c -o psi_fns.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c qnorm.c -o qnorm.o
qnorm.c: In function 'qnorm_c_determine_target_l':
qnorm.c:1931:7: warning: unused variable 'non_na' [-Wunused-variable]
 1931 |   int non_na;
      |       ^~~~~~
qnorm.c:1926:12: warning: unused variable 'j' [-Wunused-variable]
 1926 |   size_t i,j,row_mean_ind;
      |            ^
qnorm.c: In function 'qnorm_c_determine_target_via_subset_l':
qnorm.c:2533:7: warning: unused variable 'non_na' [-Wunused-variable]
 2533 |   int non_na;
      |       ^~~~~~
qnorm.c:2528:12: warning: unused variable 'j' [-Wunused-variable]
 2528 |   size_t i,j,row_mean_ind;
      |            ^
qnorm.c: In function 'using_target_via_subset_part1':
qnorm.c:2752:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable]
 2752 |   size_t i,j,ind,target_ind;
      |              ^~~
qnorm.c: In function 'using_target_via_subset_part2':
qnorm.c:2851:11: warning: unused variable 'datvec' [-Wunused-variable]
 2851 |   double *datvec;
      |           ^~~~~~
qnorm.c:2850:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
 2850 |   double *sample_percentiles;
      |           ^~~~~~~~~~~~~~~~~~
qnorm.c: In function 'using_target_via_subset':
qnorm.c:3000:11: warning: unused variable 'datvec' [-Wunused-variable]
 3000 |   double *datvec;
      |           ^~~~~~
qnorm.c:2999:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
 2999 |   double *sample_percentiles;
      |           ^~~~~~~~~~~~~~~~~~
qnorm.c:2995:7: warning: unused variable 'non_na' [-Wunused-variable]
 2995 |   int non_na = 0;
      |       ^~~~~~
qnorm.c:2994:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
 2994 |   int targetnon_na = targetrows;
      |       ^~~~~~~~~~~~
qnorm.c:2992:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
 2992 |   double target_ind_double,target_ind_double_floor;
      |                            ^~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2992:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
 2992 |   double target_ind_double,target_ind_double_floor;
      |          ^~~~~~~~~~~~~~~~~
qnorm.c:2991:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
 2991 |   double samplepercentile;
      |          ^~~~~~~~~~~~~~~~
qnorm.c:2990:11: warning: unused variable 'ranks' [-Wunused-variable]
 2990 |   double *ranks = (double *)R_Calloc((rows),double);
      |           ^~~~~
qnorm.c:2988:11: warning: unused variable 'row_mean' [-Wunused-variable]
 2988 |   double *row_mean = target;
      |           ^~~~~~~~
qnorm.c:2986:14: warning: unused variable 'dimat' [-Wunused-variable]
 2986 |   dataitem **dimat;
      |              ^~~~~
qnorm.c:2984:18: warning: unused variable 'target_ind' [-Wunused-variable]
 2984 |   size_t i,j,ind,target_ind;
      |                  ^~~~~~~~~~
qnorm.c:2984:14: warning: unused variable 'ind' [-Wunused-variable]
 2984 |   size_t i,j,ind,target_ind;
      |              ^~~
qnorm.c:2984:12: warning: unused variable 'j' [-Wunused-variable]
 2984 |   size_t i,j,ind,target_ind;
      |            ^
qnorm.c: In function 'R_qnorm_using_target':
qnorm.c:2139:3: warning: 'target_rows' may be used uninitialized [-Wmaybe-uninitialized]
 2139 |   qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2107:10: note: 'target_rows' was declared here
 2107 |   size_t target_rows, target_cols;
      |          ^~~~~~~~~~~
qnorm.c: In function 'R_qnorm_using_target_via_subset':
qnorm.c:3272:3: warning: 'target_rows' may be used uninitialized [-Wmaybe-uninitialized]
 3272 |   qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:3239:10: note: 'target_rows' was declared here
 3239 |   size_t target_rows, target_cols;
      |          ^~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c rlm.c -o rlm.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -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-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c rlm_se.c -o rlm_se.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c rma_background4.c -o rma_background4.o
rma_background4.c: In function 'R_rma_bg_correct':
rma_background4.c:527:12: warning: 'PMcopy' may be used uninitialized [-Wmaybe-uninitialized]
  527 |     return PMcopy;
      |            ^~~~~~
rma_background4.c:500:13: note: 'PMcopy' was declared here
  500 |   SEXP dim1,PMcopy;
      |             ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c rma_common.c -o rma_common.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -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-3.22-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-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)

Tests output

preprocessCore.Rcheck/tests/PLMdtest.Rout


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> 
> library(preprocessCore)
> 
> 
> values <- rnorm(100)
> group.labels <- sample(0:4,replace=TRUE, 100)
> 
> results <- double(10000)
> ngroups <- 2
> 
> 
> for (i in 1:10000){
+        values <- rnorm(100,sd=1)
+        values <- values/sd(values)
+        group.labels <- sample(0:(ngroups-1),replace=TRUE, 100)
+        blah <- .C("R_split_test",as.double(values), as.integer(100), as.integer(ngroups), as.integer(group.labels),double(1))
+        results[i] <- blah[[5]]
+ }
> 
> plot(sort(results),qchisq(0:9999/10000,ngroups-1))
> lm(qchisq(0:9999/10000,ngroups-1) ~ sort(results))

Call:
lm(formula = qchisq(0:9999/10000, ngroups - 1) ~ sort(results))

Coefficients:
  (Intercept)  sort(results)  
      0.01466        0.97621  

> 
> 
> 
> boxplot(values ~ group.labels,ylim=c(-2,2))
> 
> 
> 
> sc <- median(abs(resid(lm(values ~ 1))))/0.6745
> sum((resid(lm(values ~ 1))/sc)^2)/2
[1] 47.68782
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 47.45315
> 
> 
> values <- rnorm(100)
> group.labels <- sample(0:4,replace=TRUE, 100)
> values[group.labels == 1] <- values[group.labels == 1] + 0.4
> 
> 
> blah <- .C("R_split_test",as.double(values), as.integer(100), as.integer(5), as.integer(group.labels),double(1))
> 
> boxplot(values ~ group.labels,ylim=c(-2,2))
> 
> 
> 
> library(preprocessCore)
> 
> .C("R_test_get_design_matrix",as.integer(4),as.integer(5))
1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 
1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 
1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 
1.00 0.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 
0.00 1.00 0.00 0.00 0.00 1.00 0.00 0.00 
0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 
0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 
0.00 1.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 
0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 
0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00 
0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 
0.00 0.00 1.00 0.00 0.00 -1.00 -1.00 -1.00 
0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 
0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00 
0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 
0.00 0.00 0.00 1.00 0.00 -1.00 -1.00 -1.00 
0.00 0.00 0.00 0.00 1.00 1.00 0.00 0.00 
0.00 0.00 0.00 0.00 1.00 0.00 1.00 0.00 
0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00 
0.00 0.00 0.00 0.00 1.00 -1.00 -1.00 -1.00 

1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 
1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 
1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 
1.00 0.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00 
0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 
0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 
0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 
0.00 1.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00 
0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 0.00 
0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 
0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 
0.00 0.00 1.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00 
0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 0.00 
0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00 
0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 
0.00 0.00 0.00 1.00 0.00 -1.00 -1.00 -1.00 -1.00 
0.00 0.00 0.00 0.00 1.00 1.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00 
0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 
0.00 0.00 0.00 0.00 1.00 -1.00 -1.00 -1.00 -1.00 

1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 
1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 
1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 
1.00 0.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00 -1.00 
0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 
0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 
0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 
0.00 1.00 0.00 0.00 0.00 -1.00 -1.00 -1.00 -1.00 -1.00 
0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 
0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 
0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 
0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 
0.00 0.00 0.00 1.00 0.00 1.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00 0.00 
0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 
0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00 1.00 
0.00 0.00 0.00 0.00 1.00 1.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 1.00 0.00 0.00 1.00 0.00 0.00 
0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 0.00 
0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 
[[1]]
[1] 4

[[2]]
[1] 5

> 
> 
> 
> chips <- as.factor(rep(c(1,2,3,4,5,6),c(5,5,5,5,5,5)))
> probes <- rep(c(1,3,4,5,6),6)
>        
> probes[c(1,6,11)] <- 2
> ##probes[24 + c(8,16,24)] <- 10
> probes <- as.factor(probes)
> 
> 
> model.matrix(~ -1 + probes)%*%contr.sum(6)
   [,1] [,2] [,3] [,4] [,5]
1     0    1    0    0    0
2     0    0    1    0    0
3     0    0    0    1    0
4     0    0    0    0    1
5    -1   -1   -1   -1   -1
6     0    1    0    0    0
7     0    0    1    0    0
8     0    0    0    1    0
9     0    0    0    0    1
10   -1   -1   -1   -1   -1
11    0    1    0    0    0
12    0    0    1    0    0
13    0    0    0    1    0
14    0    0    0    0    1
15   -1   -1   -1   -1   -1
16    1    0    0    0    0
17    0    0    1    0    0
18    0    0    0    1    0
19    0    0    0    0    1
20   -1   -1   -1   -1   -1
21    1    0    0    0    0
22    0    0    1    0    0
23    0    0    0    1    0
24    0    0    0    0    1
25   -1   -1   -1   -1   -1
26    1    0    0    0    0
27    0    0    1    0    0
28    0    0    0    1    0
29    0    0    0    0    1
30   -1   -1   -1   -1   -1
> 
> 
> probes <- rep(c(1,3,4,5,6),6)
>        
> probes[c(1,6,11)] <- 2
> probes[c(20,25,30)] <- 7
> probes <- as.factor(probes)
> model.matrix(~ -1 + probes)%*%contr.sum(7)
   [,1] [,2] [,3] [,4] [,5] [,6]
1     0    1    0    0    0    0
2     0    0    1    0    0    0
3     0    0    0    1    0    0
4     0    0    0    0    1    0
5     0    0    0    0    0    1
6     0    1    0    0    0    0
7     0    0    1    0    0    0
8     0    0    0    1    0    0
9     0    0    0    0    1    0
10    0    0    0    0    0    1
11    0    1    0    0    0    0
12    0    0    1    0    0    0
13    0    0    0    1    0    0
14    0    0    0    0    1    0
15    0    0    0    0    0    1
16    1    0    0    0    0    0
17    0    0    1    0    0    0
18    0    0    0    1    0    0
19    0    0    0    0    1    0
20   -1   -1   -1   -1   -1   -1
21    1    0    0    0    0    0
22    0    0    1    0    0    0
23    0    0    0    1    0    0
24    0    0    0    0    1    0
25   -1   -1   -1   -1   -1   -1
26    1    0    0    0    0    0
27    0    0    1    0    0    0
28    0    0    0    1    0    0
29    0    0    0    0    1    0
30   -1   -1   -1   -1   -1   -1
> 
> 
> 
> 
> probes <- rep(c(1,3,4,5,6),6)
>        
> probes[c(1,6,11)] <- 2
> probes[c(5,10,15)] <- 7
> probes <- as.factor(probes)
> model.matrix(~ -1 + probes)%*%contr.sum(7)
   [,1] [,2] [,3] [,4] [,5] [,6]
1     0    1    0    0    0    0
2     0    0    1    0    0    0
3     0    0    0    1    0    0
4     0    0    0    0    1    0
5    -1   -1   -1   -1   -1   -1
6     0    1    0    0    0    0
7     0    0    1    0    0    0
8     0    0    0    1    0    0
9     0    0    0    0    1    0
10   -1   -1   -1   -1   -1   -1
11    0    1    0    0    0    0
12    0    0    1    0    0    0
13    0    0    0    1    0    0
14    0    0    0    0    1    0
15   -1   -1   -1   -1   -1   -1
16    1    0    0    0    0    0
17    0    0    1    0    0    0
18    0    0    0    1    0    0
19    0    0    0    0    1    0
20    0    0    0    0    0    1
21    1    0    0    0    0    0
22    0    0    1    0    0    0
23    0    0    0    1    0    0
24    0    0    0    0    1    0
25    0    0    0    0    0    1
26    1    0    0    0    0    0
27    0    0    1    0    0    0
28    0    0    0    1    0    0
29    0    0    0    0    1    0
30    0    0    0    0    0    1
> 
> 
> 
> probes <- rep(c(1,3,4,5,6),6)
>        
> probes[c(1,6,11)] <- 2
> probes[1+c(1,6,11)] <- 8
> probes[2+c(1,6,11)] <- 9
> probes[3+c(1,6,11)] <- 10
> probes[c(5,10,15)] <- 7
> probes <- as.factor(probes)
> model.matrix(~ -1 + probes)%*%contr.sum(10)
   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
1     0    1    0    0    0    0    0    0    0
2     0    0    0    0    0    0    0    1    0
3     0    0    0    0    0    0    0    0    1
4    -1   -1   -1   -1   -1   -1   -1   -1   -1
5     0    0    0    0    0    0    1    0    0
6     0    1    0    0    0    0    0    0    0
7     0    0    0    0    0    0    0    1    0
8     0    0    0    0    0    0    0    0    1
9    -1   -1   -1   -1   -1   -1   -1   -1   -1
10    0    0    0    0    0    0    1    0    0
11    0    1    0    0    0    0    0    0    0
12    0    0    0    0    0    0    0    1    0
13    0    0    0    0    0    0    0    0    1
14   -1   -1   -1   -1   -1   -1   -1   -1   -1
15    0    0    0    0    0    0    1    0    0
16    1    0    0    0    0    0    0    0    0
17    0    0    1    0    0    0    0    0    0
18    0    0    0    1    0    0    0    0    0
19    0    0    0    0    1    0    0    0    0
20    0    0    0    0    0    1    0    0    0
21    1    0    0    0    0    0    0    0    0
22    0    0    1    0    0    0    0    0    0
23    0    0    0    1    0    0    0    0    0
24    0    0    0    0    1    0    0    0    0
25    0    0    0    0    0    1    0    0    0
26    1    0    0    0    0    0    0    0    0
27    0    0    1    0    0    0    0    0    0
28    0    0    0    1    0    0    0    0    0
29    0    0    0    0    1    0    0    0    0
30    0    0    0    0    0    1    0    0    0
> 
> 
> 
> 
> 
> 
> 
> 
> 
> true.probes <- c(4,3,2,1,-1,-2,-3,-4)
> 
> true.chips  <- c(8,9,10,11,12,13)
> 
> 
> y <- outer(true.probes,true.chips,"+")
> 
> 
> 
> estimate.coefficients <- function(y){
+ 
+ 
+ colmean <- apply(y,2,mean)
+ 
+ y <- sweep(y,2,FUN="-",colmean)
+ 
+ rowmean <- apply(y,1,mean)
+ y <- sweep(y,1,FUN="-",rowmean)
+ 
+ 
+ list(y,colmean,rowmean)
+ }
> estimate.coefficients(y)
[[1]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0
[8,]    0    0    0    0    0    0

[[2]]
[1]  8  9 10 11 12 13

[[3]]
[1]  4  3  2  1 -1 -2 -3 -4

> 
> 
> 
> y <- outer(true.probes,true.chips,"+")
> 
> 
> estimate.coefficients(y)
[[1]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0
[8,]    0    0    0    0    0    0

[[2]]
[1]  8  9 10 11 12 13

[[3]]
[1]  4  3  2  1 -1 -2 -3 -4

> 
> 
> 
> 
> y2 <- sweep(y,2,FUN="-",apply(y,2,mean))
> 
> 
> 
> c(3.875, 2.875,  1.875,  0.875,
+  -1.125, -2.125, -3.125, -4, -2.25)
[1]  3.875  2.875  1.875  0.875 -1.125 -2.125 -3.125 -4.000 -2.250
> 
> 
> 
> 
> cp <- rep(c(1,2,3,4,5,6),rep(8,6))
> pr <- rep(c(1,2,3,4,5,6,7,8),6)
> 
> 
> pr[c(32,40,48)] <- 9
> 
> 
> 
> 
> true.probes <- c(4,3,2,1,-1,-2,-3,-4)
> 
> true.chips  <- c(8,9,10,11,12,10)
> 
> 
> y <- outer(true.probes,true.chips,"+") + rnorm(48,0,0.1)
> 
> y[8,4:6] <- c(11,12,10)+2 + rnorm(3,0,0.1)
> 
> 
> lm(as.vector(y) ~  -1 + as.factor(cp) + C(as.factor(pr),"contr.sum"))

Call:
lm(formula = as.vector(y) ~ -1 + as.factor(cp) + C(as.factor(pr), 
    "contr.sum"))

Coefficients:
                as.factor(cp)1                  as.factor(cp)2  
                        8.2358                          9.2073  
                as.factor(cp)3                  as.factor(cp)4  
                       10.2112                         11.2100  
                as.factor(cp)5                  as.factor(cp)6  
                       12.1928                         10.2301  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                        3.7531                          2.7397  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                        1.8209                          0.8494  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                       -1.2677                         -2.2538  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                       -3.1628                         -4.3331  

> 
> 
> matplot(y,type="l")
> matplot(matrix(fitted( lm(as.vector(y) ~  -1 + as.factor(cp) +
+ C(as.factor(pr),"contr.sum"))),ncol=6),type="l")
> 
> 
> library(preprocessCore)
> true.probes <- c(4,3,2,1,-1,-2,-3,-4)
> 
> true.chips  <- c(8,9,10,11,12,10)
> 
> y <- outer(true.probes,true.chips,"+") + rnorm(48,0,0.25)
> 
> y[8,4:6] <- c(11,12,10)+ 2.5 + rnorm(3,0,0.25)
> y[5,4:6] <- c(11,12,10)+-2.5 + rnorm(3,0,0.25)
> 
> 
> 
> ###.C("plmd_fit_R", as.double(y), as.integer(8), as.integer(6),
> ###		as.integer(2), as.integer(c(1,1,1,2,2,2) - 1),
> ###		double(6 +2*8),
> ###		double(48),
> ###		double(48))
> 
> ###matplot(matrix(.C("plmd_fit_R", as.double(y), as.integer(8), as.integer(6),
> ###		as.integer(2), as.integer(c(1,1,1,2,2,2) - 1),
> ###		double(6 +2*8),
> ###		double(48),
> ###		double(48))[[7]],ncol=6))
> ###		
> 
> 
> ##.Call("R_plmd_model",y,0,1.3345,as.integer(c(1,1,1,2,2,2) - 1),as.integer(2))
> rcModelPLM(y)
$Estimates
 [1]  8.3674960  9.3085588 10.3169486 11.3184476 12.3608379 10.2710539
 [7]  3.7507929  2.6509559  1.5448883  0.7271974 -2.0694501 -2.3067911
[13] -3.3494776 -0.9481158

$Weights
          [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
[1,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[2,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[3,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[4,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[5,] 1.0000000 0.8974171 0.4064908 0.6722867 0.6045769 1.0000000
[6,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8,] 0.1140974 0.1134357 0.1342130 0.1231175 0.1125980 0.1249719

$Residuals
            [,1]        [,2]       [,3]         [,4]        [,5]       [,6]
[1,]  0.22677245 -0.11305986 -0.1042906  0.164508379  0.18057362 -0.3545040
[2,]  0.10084444 -0.06235982  0.2543282  0.008420513 -0.15618447 -0.1450489
[3,] -0.13275723 -0.24884958  0.1439212  0.041009318  0.02516515  0.1715112
[4,] -0.05133846  0.22554288 -0.2183863  0.084156373 -0.31404474  0.2740702
[5,]  0.37570556  0.44350292  0.9787997 -0.591406571 -0.65767296 -0.3763771
[6,]  0.21935645  0.11990477 -0.2382464 -0.332142077  0.08561904  0.1455082
[7,] -0.34080904  0.07858250  0.1625697  0.033869317  0.17871286 -0.1129254
[8,] -3.48626868 -3.50655116 -2.9637144  3.230839946  3.53267701  3.1828412

$StdErrors
 [1] 0.2173713 0.2187790 0.2257415 0.2216910 0.2232544 0.2169061 0.2230948
 [8] 0.2230948 0.2230948 0.2230948 0.2487682 0.2230948 0.2230948 0.5693101

$Scale
[1] 0.2957449

> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
 [1]  8.024300  8.968514 10.117063 11.006597 12.079803  9.983647  4.055361
 [8]  2.944859  1.838791  1.027080 -1.175739 -2.317838 -2.005123 -3.055575
[15] -3.972585  2.660768

$Weights
     [,1] [,2]      [,3]      [,4]      [,5]      [,6]
[1,]    1    1 1.0000000 1.0000000 1.0000000 0.8278236
[2,]    1    1 1.0000000 1.0000000 1.0000000 1.0000000
[3,]    1    1 1.0000000 1.0000000 1.0000000 1.0000000
[4,]    1    1 0.9664624 1.0000000 0.9243043 1.0000000
[5,]    1    1 1.0000000 1.0000000 1.0000000 1.0000000
[6,]    1    1 0.9049324 0.9556908 1.0000000 1.0000000
[7,]    1    1 1.0000000 1.0000000 1.0000000 1.0000000
[8,]    1    1 1.0000000 1.0000000 1.0000000 1.0000000

$Residuals
             [,1]        [,2]        [,3]        [,4]        [,5]       [,6]
[1,]  0.265399670 -0.07758354 -0.20897329  0.17179033  0.15704019 -0.3716653
[2,]  0.150136984 -0.01621816  0.16031087  0.02636779 -0.16905257 -0.1515449
[3,] -0.083464685 -0.20270793  0.04990383  0.05895660  0.01229705  0.1650151
[4,] -0.008025297  0.26570515 -0.31838304  0.09612427 -0.33289222  0.2615948
[5,] -0.174810247 -0.11016378  0.28497403 -0.03116812 -0.12824989  0.1594180
[6,]  0.260883742  0.15828117 -0.34002899 -0.32196005  0.06498569  0.1312469
[7,] -0.291516495  0.12472415  0.06855236  0.05181660  0.16584476 -0.1194214
[8,] -0.118603672 -0.14203705  0.26064072 -0.06619320  0.20482848 -0.1386353

$StdErrors
 [1] 0.08636739 0.08636739 0.10222487 0.09333611 0.09333611 0.09342858
 [7] 0.10276252 0.09373056 0.09373056 0.11418086 0.13394628 0.13419922
[13] 0.11418086 0.09373056 0.13394628 0.00000000

$WasSplit
[1] 0 0 0 0 1 0 0 1

> 
> ###R_plmd_model(SEXP Y, SEXP PsiCode, SEXP PsiK, SEXP Groups, SEXP Ngroups)
> 
> 
> 
> 
> 
> pr[seq(3,48,8)][1:3] <- 10
> 
> y[seq(3,48,8)][1:3] <- c(8,9,10) -3 + rnorm(3,0,0.1)
> lm(as.vector(y) ~  -1 + as.factor(cp) + C(as.factor(pr),"contr.sum"))

Call:
lm(formula = as.vector(y) ~ -1 + as.factor(cp) + C(as.factor(pr), 
    "contr.sum"))

Coefficients:
                as.factor(cp)1                  as.factor(cp)2  
                         8.009                           8.974  
                as.factor(cp)3                  as.factor(cp)4  
                        10.081                          10.774  
                as.factor(cp)5                  as.factor(cp)6  
                        11.846                           9.745  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                         4.170                           3.070  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                         2.153                           1.146  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                        -1.621                          -1.888  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                        -2.930                          -3.957  
C(as.factor(pr), "contr.sum")9  
                         2.896  

> 
> 
> proc.time()
   user  system elapsed 
   1.64    0.15    1.76 

preprocessCore.Rcheck/tests/qnormtest.Rout


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(preprocessCore)
> 
> err.tol <- 10^-8
> 
> x <- matrix(c(100,15,200,250,110,16.5,220,275,120,18,240,300),ncol=3)
> x
     [,1]  [,2] [,3]
[1,]  100 110.0  120
[2,]   15  16.5   18
[3,]  200 220.0  240
[4,]  250 275.0  300
> normalize.quantiles(x)
      [,1]  [,2]  [,3]
[1,] 110.0 110.0 110.0
[2,]  16.5  16.5  16.5
[3,] 220.0 220.0 220.0
[4,] 275.0 275.0 275.0
> 
> x.norm.truth <- matrix(rep(c(110.0,16.5,220,275.0),3),ncol=3)
> 
> if (all(abs(x.norm.truth - normalize.quantiles(x)) < err.tol) != TRUE){
+ 	stop("Disagreement in normalize.quantiles(x)")
+ }
> 
> normalize.quantiles.determine.target(x)
[1]  16.5 110.0 220.0 275.0
> 
> x.norm.target.truth <- c(16.5,110.0,220.0,275.0)
> 
> if (all(abs(x.norm.target.truth - normalize.quantiles.determine.target(x)) < err.tol) != TRUE){
+ 	stop("Disagreement in normalize.quantiles.determine.target(x)")
+ }
> 
> 
> y <- x
> y[2,2] <- NA
> y
     [,1] [,2] [,3]
[1,]  100  110  120
[2,]   15   NA   18
[3,]  200  220  240
[4,]  250  275  300
> normalize.quantiles(y)
          [,1]      [,2]      [,3]
[1,] 134.44444  47.66667 134.44444
[2,]  47.66667        NA  47.66667
[3,] 226.11111 180.27778 226.11111
[4,] 275.00000 275.00000 275.00000
> 
> y.norm.target.truth <- c(47.6666666666667,134.4444444444444,226.1111111111111,275.0000000000000)
> 
> y.norm.truth <- matrix(c(134.4444444444444,  47.6666666666667, 134.4444444444444,
+                          47.6666666666667,                NA,  47.6666666666667,
+                         226.1111111111111, 180.2777777777778, 226.1111111111111,
+                         275.0000000000000, 275.0000000000000, 275.0000000000000),byrow=TRUE,ncol=3)
> 
> 
> if (all(abs(y.norm.truth - normalize.quantiles(y)) < err.tol,na.rm=TRUE) != TRUE){
+ 	stop("Disagreement in normalize.quantiles(y)")
+ }
> 
> 
> 
> if (all(abs(y.norm.target.truth - normalize.quantiles.determine.target(y)) < err.tol) != TRUE){
+ 	stop("Disagreement in normalize.quantiles.determine.target(y)")
+ }
> 
> 
> 
> if (all(abs(normalize.quantiles.use.target(y,y.norm.target.truth) - y.norm.truth) < err.tol,na.rm=TRUE) != TRUE){
+ 		stop("Disagreement in normalize.quantiles.use.target(y)")
+ }
> 
> 
> x <- matrix(c(100,15,200,250,110,16.5,220,275,120,18,240,300),ncol=3)
> rownames(x) <- letters[1:4]
> colnames(x) <- LETTERS[1:3]
> y <- normalize.quantiles(x, keep.names = TRUE)
> if(!all(colnames(x)==colnames(y))){
+     stop("Disagreement between initial and final column names despite keep.names=TRUE")
+ }
> if(!all(rownames(x)==rownames(y))){
+     stop("Disagreement between initial and final row names despite keep.names=TRUE")
+ }
> 
> proc.time()
   user  system elapsed 
   0.18    0.04    0.25 

Example timings

preprocessCore.Rcheck/preprocessCore-Ex.timings

nameusersystemelapsed
colSummarize0.000.020.02
normalize.quantiles.in.blocks0.030.000.04
rcModelPLMd0.020.010.03
rcModelPLMr0.030.000.03
rcModels0.000.020.02
subColSummarize000
subrcModels0.020.000.02