| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-22 11:36:01 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 1602/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preprocessCore 1.66.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | 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 | see weekly results here | ||||||||||||
|
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: 1.66.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preprocessCore.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings preprocessCore_1.66.0.tar.gz |
| StartedAt: 2024-05-22 05:13:56 -0400 (Wed, 22 May 2024) |
| EndedAt: 2024-05-22 05:14:28 -0400 (Wed, 22 May 2024) |
| EllapsedTime: 31.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: preprocessCore.Rcheck |
| Warnings: 1 |
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### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preprocessCore.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings preprocessCore_1.66.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/preprocessCore.Rcheck'
* using R version 4.4.0 (2024-04-24 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 '1.66.0'
* 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 'F:/biocbuild/bbs-3.19-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
'F:/biocbuild/bbs-3.19-bioc/meat/preprocessCore.Rcheck/00check.log'
for details.
preprocessCore.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL preprocessCore
###
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* installing to library 'F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_colSummarize.c -o R_colSummarize.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_subColSummarize.c -o R_subColSummarize.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_medianpolish':
R_subrcModel_interfaces.c:207:11: warning: unused variable 'se' [-Wunused-variable]
207 | double *se;
| ^~
R_subrcModel_interfaces.c:206:11: warning: unused variable 'weights' [-Wunused-variable]
206 | double *weights;
| ^~~~~~~
R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable]
165 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable]
165 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable]
165 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_plm':
R_subrcModel_interfaces.c:532:10: warning: unused variable 'scale' [-Wunused-variable]
532 | double scale=-1.0;
| ^~~~~
R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable]
485 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable]
485 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable]
485 | double *results, *buffer, *buffer2;
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c avg.c -o avg.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c avg_log.c -o avg_log.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biweight.c -o biweight.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lm.c -o lm.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c log_avg.c -o log_avg.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c log_median.c -o log_median.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrix_functions.c -o matrix_functions.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c median.c -o median.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c median_log.c -o median_log.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c medianpolish.c -o medianpolish.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plmd.c -o plmd.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plmr.c -o plmr.o
plmr.c:279:13: warning: 'XTWX_R_inv' defined but not used [-Wunused-function]
279 | static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
| ^~~~~~~~~~
plmr.c:152:13: warning: 'XTWX_R' defined but not used [-Wunused-function]
152 | static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){
| ^~~~~~
plmr.c:82:13: warning: 'XTWY_R' defined but not used [-Wunused-function]
82 | static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c psi_fns.c -o psi_fns.o
gcc -I"F:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm.c -o rlm.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm_anova.c -o rlm_anova.o
rlm_anova.c: In function 'rlm_fit_anova_given_probe_effects_engine':
rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable]
1235 | double endprobe;
| ^~~~~~~~
rlm_anova.c: In function 'rlm_compute_se_anova_given_probe_effects':
rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable]
1426 | double vs=0.0,m,varderivpsi=0.0;
| ^~~~~~~~~~~
rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable]
1426 | double vs=0.0,m,varderivpsi=0.0;
| ^
rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable]
1426 | double vs=0.0,m,varderivpsi=0.0;
| ^~
rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable]
1419 | double scale=0.0;
| ^~~~~
rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
1418 | double Kappa=0.0; /* A correction factor */
| ^~~~~
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
1417 | double sumderivpsi=0.0; /* sum of psi'(r_i) */
| ^~~~~~~~~~~
rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable]
1415 | double sumpsi2=0.0; /* sum of psi(r_i)^2 */
| ^~~~~~~
rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable]
1414 | double k1 = psi_k; /* was 1.345; */
| ^~
rlm_anova.c: In function 'rlm_wfit_anova_given_probe_effects_engine':
rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable]
1505 | double endprobe;
| ^~~~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm_se.c -o rlm_se.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rma_background4.c -o rma_background4.o
rma_background4.c: In function 'R_rma_bg_correct':
rma_background4.c:509:12: warning: 'PMcopy' may be used uninitialized [-Wmaybe-uninitialized]
509 | return PMcopy;
| ^~~~~~
rma_background4.c:482:13: note: 'PMcopy' was declared here
482 | SEXP dim1,PMcopy;
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -shared -s -static-libgcc -o preprocessCore.dll tmp.def R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
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)
-0.001714 0.988184
>
>
>
> 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] 41.34336
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 40.67247
>
>
> 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
8.2692 9.2305
as.factor(cp)3 as.factor(cp)4
10.1856 11.2384
as.factor(cp)5 as.factor(cp)6
12.1897 10.2836
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
3.7627 2.7616
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
1.7519 0.7776
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.2131 -2.2019
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-3.1999 -4.1933
>
>
> 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] 8.3292393 9.0789637 10.2280262 11.3377307 12.3505601 10.2535927
[7] 3.5861846 2.7317033 1.7402214 0.6091956 -2.0580650 -2.4641465
[13] -3.1385502 -1.0065431
$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 0.6154596 1.0000000 1.0000000 1.0000000
[4,] 1.0000000 1.0000000 1.0000000 0.5037303 1.0000000 1.0000000
[5,] 0.4753503 0.4340428 0.4062613 0.6834032 0.3668416 0.3473574
[6,] 0.5406355 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8,] 0.1140088 0.1192603 0.1134387 0.1086287 0.1148463 0.1238138
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.01329413 0.17107330 0.108216984 0.15020439 -0.3273437 -0.11544513
[2,] -0.22754809 0.19699242 0.161629409 -0.31008358 0.1672031 0.01180673
[3,] 0.05472527 0.12531750 -0.577719202 0.08885961 0.1849728 -0.09831237
[4,] -0.01131267 -0.16828265 0.002840915 0.70575807 -0.1035543 -0.07520301
[5,] 0.74778857 0.81885801 0.874751184 -0.52001936 -0.9689144 -1.02326191
[6,] 0.65759154 -0.08930674 -0.073736683 -0.17544827 -0.1021301 0.08510439
[7,] -0.18471686 -0.23578226 0.156677455 -0.10909926 0.1808620 0.19205890
[8,] -3.11748536 -2.98029587 -3.133347065 3.27204604 3.0948161 2.87066610
$StdErrors
[1] 0.2257573 0.2190278 0.2258825 0.2227824 0.2205509 0.2205400 0.2180267
[8] 0.2180267 0.2237775 0.2258904 0.3007073 0.2250975 0.2180267 0.5616930
$Scale
[1] 0.2641292
> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
[1] 7.9761031 8.7821391 9.9387752 11.1029833 12.0446532 9.8937601
[7] 3.9142249 3.0705516 2.0772494 0.9032603 -0.9311952 -2.6107415
[13] -2.1937644 -2.8318652 -3.7705153 2.3727953
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.0000000 1.0000000 1.0000000 1.0000000 0.6321848 1.0000000
[2,] 1.0000000 1.0000000 1.0000000 0.5330793 1.0000000 1.0000000
[3,] 1.0000000 1.0000000 0.3531128 1.0000000 1.0000000 1.0000000
[4,] 1.0000000 1.0000000 1.0000000 0.3416924 1.0000000 1.0000000
[5,] 1.0000000 1.0000000 1.0000000 0.8267767 1.0000000 1.0000000
[6,] 0.2983274 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[7,] 1.0000000 0.8991394 1.0000000 1.0000000 1.0000000 0.9006362
[8,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
$Residuals
[,1] [,2] [,3] [,4] [,5]
[1,] 0.0383900657 0.13985760 0.069427640 0.05691147 -0.34947699
[2,] -0.2132602135 0.15496866 0.112032004 -0.41418456 0.13426173
[3,] 0.0708335066 0.08511411 -0.625496242 -0.01342100 0.15385181
[4,] 0.0477588438 -0.16552276 -0.001972845 0.64644073 -0.09171206
[5,] -0.0259450476 -0.01118724 0.037132289 0.26740445 -0.11033096
[6,] 0.7403456460 -0.06286427 -0.054867854 -0.21108301 -0.06660520
[7,] -0.1382655942 -0.24564263 0.139243441 -0.18103685 0.18008405
[8,] -0.0003769546 0.08050089 -0.080123939 0.12745499 0.02138466
[,6]
[1,] -0.083652754
[2,] 0.032791052
[3,] -0.075507686
[4,] -0.009435049
[5,] -0.110752796
[6,] 0.174554944
[7,] 0.245206607
[8,] -0.148839647
$StdErrors
[1] 0.07358415 0.07353613 0.07358415 0.08853592 0.07318110 0.07317708
[7] 0.08120682 0.08040142 0.08097583 0.08040142 0.10535659 0.12796326
[13] 0.08097583 0.09066455 0.10535659 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
8.062 8.811
as.factor(cp)3 as.factor(cp)4
9.986 10.880
as.factor(cp)5 as.factor(cp)6
11.770 9.639
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
3.991 3.137
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
2.350 1.073
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.665 -2.009
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-2.733 -3.824
C(as.factor(pr), "contr.sum")9
2.624
>
>
> proc.time()
user system elapsed
1.65 0.23 1.86
preprocessCore.Rcheck/tests/qnormtest.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
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
0.20 0.09 0.26
preprocessCore.Rcheck/preprocessCore-Ex.timings
| name | user | system | elapsed | |
| colSummarize | 0.02 | 0.00 | 0.02 | |
| normalize.quantiles.in.blocks | 0.03 | 0.00 | 0.04 | |
| rcModelPLMd | 0.02 | 0.00 | 0.02 | |
| rcModelPLMr | 0.05 | 0.00 | 0.04 | |
| rcModels | 0.00 | 0.02 | 0.02 | |
| subColSummarize | 0 | 0 | 0 | |
| subrcModels | 0.01 | 0.00 | 0.01 | |