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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:07 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 1602/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preprocessCore 1.71.2 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| 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 |
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###
### 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
###
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* 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.
preprocessCore.Rcheck/00install.out
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###
### 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)
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
preprocessCore.Rcheck/preprocessCore-Ex.timings
| name | user | system | elapsed | |
| colSummarize | 0.00 | 0.02 | 0.02 | |
| normalize.quantiles.in.blocks | 0.03 | 0.00 | 0.04 | |
| rcModelPLMd | 0.02 | 0.01 | 0.03 | |
| rcModelPLMr | 0.03 | 0.00 | 0.03 | |
| rcModels | 0.00 | 0.02 | 0.02 | |
| subColSummarize | 0 | 0 | 0 | |
| subrcModels | 0.02 | 0.00 | 0.02 | |