Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1558/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
preprocessCore 1.67.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.67.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preprocessCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings preprocessCore_1.67.0.tar.gz |
StartedAt: 2024-07-16 02:51:57 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 02:52:26 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 28.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: preprocessCore.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preprocessCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings preprocessCore_1.67.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/preprocessCore.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * 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 '1.67.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'preprocessCore' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Found a 'configure.in' file: 'configure.ac' has long been preferred. * 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 'C:/Users/biocbuild/bbs-3.20-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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/preprocessCore.Rcheck/00check.log' for details.
preprocessCore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL preprocessCore ### ############################################################################## ############################################################################## * installing to library 'C:/Users/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) 13.2.0' gcc -I"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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 *)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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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"C:/Users/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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LC:/Users/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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/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)
preprocessCore.Rcheck/tests/PLMdtest.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 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) 0.02291 0.94782 > > > > 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] 49.97033 > sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2 [1] 49.9615 > > > 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 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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 8.2151 9.1880 as.factor(cp)3 as.factor(cp)4 10.3001 11.2177 as.factor(cp)5 as.factor(cp)6 12.2024 10.1942 C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2 3.7679 2.7660 C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4 1.7707 0.7763 C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6 -1.2338 -2.2055 C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8 -3.1761 -4.1837 > > > 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] 8.2418722 9.2542159 10.1863253 11.4159904 12.2830641 10.5004098 [7] 3.6445000 2.6213683 1.6618115 0.8101747 -2.1395045 -1.9729783 [13] -3.4577281 -1.1676438 $Weights [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0.52384601 1.0000000 1.0000000 1.0000000 1.00000000 0.7336940 [2,] 1.00000000 1.0000000 1.0000000 1.0000000 1.00000000 1.0000000 [3,] 1.00000000 1.0000000 1.0000000 1.0000000 1.00000000 1.0000000 [4,] 1.00000000 1.0000000 1.0000000 1.0000000 1.00000000 1.0000000 [5,] 0.33452956 0.2335182 0.9829847 0.2914306 0.42930880 0.5059178 [6,] 1.00000000 1.0000000 1.0000000 1.0000000 1.00000000 0.9486194 [7,] 1.00000000 1.0000000 1.0000000 1.0000000 1.00000000 1.0000000 [8,] 0.09638358 0.1102677 0.1155455 0.1088892 0.09819336 0.1140627 $Residuals [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0.67627828 0.01877070 -0.062981265 0.11161636 -0.067584388 -0.48260866 [2,] -0.08886339 0.01069691 -0.001110967 -0.13447739 -0.005070288 0.21882513 [3,] -0.09237576 -0.01008751 -0.237741841 0.01655936 0.097054124 0.22659162 [4,] -0.11297359 -0.13966372 0.235816804 0.09682101 0.016567533 -0.09656803 [5,] 1.05888102 1.51690631 0.360332096 -1.21551708 -0.825146789 -0.70005733 [6,] -0.09057522 -0.07947629 -0.124005540 -0.22558074 0.165234411 0.37359911 [7,] 0.03052777 0.19976887 0.190056704 0.13507195 -0.206187138 -0.34923815 [8,] -3.67523696 -3.21249086 -3.065759863 3.25310686 3.607459081 3.10570171 $StdErrors [1] 0.2364642 0.2299626 0.2167675 0.2287446 0.2264196 0.2289775 0.2362101 [8] 0.2244571 0.2244571 0.2244571 0.3075595 0.2251700 0.2244571 0.5973580 $Scale [1] 0.2633737 > rcModelPLMd(y,c(1,1,1,2,2,2)) $Estimates [1] 7.860802 8.992100 9.874593 11.065321 12.031667 10.218417 3.938433 [8] 2.927865 1.968308 1.116671 -0.699591 -2.758392 -1.683056 -3.116005 [15] -4.143365 2.449132 $Weights [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0.3236061 1.0000000 1.0000000 1 1.0000000 0.4995489 [2,] 1.0000000 1.0000000 1.0000000 1 1.0000000 1.0000000 [3,] 1.0000000 1.0000000 1.0000000 1 1.0000000 1.0000000 [4,] 1.0000000 1.0000000 1.0000000 1 1.0000000 1.0000000 [5,] 1.0000000 0.7284309 0.3217493 1 1.0000000 1.0000000 [6,] 1.0000000 1.0000000 1.0000000 1 1.0000000 0.6755616 [7,] 1.0000000 1.0000000 1.0000000 1 0.8332179 0.6041064 [8,] 0.7757651 1.0000000 1.0000000 1 1.0000000 1.0000000 $Residuals [,1] [,2] [,3] [,4] [,5] [,6] [1,] 7.634157e-01 -0.01304614 -0.045181506 0.16835305 -0.11012012 -0.4945486 [2,] -1.428956e-02 -0.03368348 0.004125248 -0.09030425 -0.06016956 0.1943216 [3,] -1.780192e-02 -0.05446789 -0.232505626 0.06073250 0.04195485 0.2020881 [4,] -3.839976e-02 -0.18404410 0.241053019 0.14099415 -0.03853174 -0.1210716 [5,] 3.763332e-05 0.33910870 -0.767848913 -0.24596032 0.04513756 0.2008228 [6,] 5.721864e-04 -0.10728311 -0.102195759 -0.16483404 0.12670870 0.3656691 [7,] 6.987475e-02 0.12016162 0.160066062 0.14401823 -0.29651327 -0.4089685 [8,] -3.184460e-01 0.02534585 0.221693451 -0.01299932 0.24208048 -0.2290812 $StdErrors [1] 0.09521682 0.08807855 0.08807855 0.08190208 0.08855203 0.10652306 [7] 0.10776619 0.08856548 0.08856548 0.08856548 0.21553868 0.12660106 [13] 0.09604806 0.10710850 0.15203525 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 8.004 9.061 as.factor(cp)3 as.factor(cp)4 9.903 10.759 as.factor(cp)5 as.factor(cp)6 11.719 9.876 C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2 4.103 3.048 C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4 2.390 1.237 C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6 -1.680 -1.543 C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8 -3.031 -4.247 C(as.factor(pr), "contr.sum")9 2.770 > > > proc.time() user system elapsed 1.28 0.17 1.42
preprocessCore.Rcheck/tests/qnormtest.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 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 0.14 0.06 0.18
preprocessCore.Rcheck/preprocessCore-Ex.timings
name | user | system | elapsed | |
colSummarize | 0 | 0 | 0 | |
normalize.quantiles.in.blocks | 0.00 | 0.03 | 0.03 | |
rcModelPLMd | 0.00 | 0.02 | 0.02 | |
rcModelPLMr | 0.03 | 0.00 | 0.03 | |
rcModels | 0.00 | 0.01 | 0.02 | |
subColSummarize | 0 | 0 | 0 | |
subrcModels | 0.00 | 0.02 | 0.01 | |