Ben Bolstad
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 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 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1638/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preprocessCore 1.71.2 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preprocessCore_1.71.2.tar.gz |
| StartedAt: 2025-10-24 23:25:50 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 23:26:18 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 27.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: preprocessCore.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preprocessCore_1.71.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘preprocessCore’ can be installed ... WARNING
Found the following significant warnings:
qnorm.c:614:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
qnorm.c:635:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
qnorm.c:2029:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
qnorm.c:2632:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 is not available
* 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: 2 WARNINGs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.
preprocessCore.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘preprocessCore’ ...
** this is package ‘preprocessCore’ version ‘1.71.2’
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch x86_64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to enable C11 features... none needed
checking how to run the C preprocessor... clang -arch x86_64 -E
checking for library containing pthread_create... none required
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for stdlib.h... (cached) yes
checking if PTHREAD_STACK_MIN is defined... yes
checking if __pthread_get_minstack can be used... no
configure: Enabling threading for preprocessCore
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_colSummarize.c -o R_colSummarize.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c:133:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:131:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:127:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:125:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:309:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:307:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:301:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:303:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:482:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:480:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:488:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:486:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:666:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:668:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:660:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:662:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:839:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:841:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:845:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:847:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1027:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1025:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1019:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:1021:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1203:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1205:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1197:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:1199:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1380:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1382:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1374:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:1376:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1564:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1562:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1558:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1556:21: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
double *results, *buffer, *buffer2;
^
R_subColSummarize.c:1556:30: warning: variable 'buffer2' set but not used [-Wunused-but-set-variable]
double *results, *buffer, *buffer2;
^
R_subColSummarize.c:1739:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subColSummarize.c:1739:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subColSummarize.c:1747:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1745:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1741:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1703:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function]
static void *subColSummarize_medianpolish_group(void *data){
^
43 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:87:11: warning: unused variable 'buffer' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:102:11: warning: unused variable 'weights' [-Wunused-variable]
double *weights;
^
R_subrcModel_interfaces.c:103:11: warning: unused variable 'se' [-Wunused-variable]
double *se;
^
R_subrcModel_interfaces.c:87:20: warning: unused variable 'buffer2' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:177:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:179:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subrcModel_interfaces.c:183:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subrcModel_interfaces.c:177:11: warning: unused variable 'results' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:185:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subrcModel_interfaces.c:177:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:392:11: warning: unused variable 'buffer' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:392:20: warning: unused variable 'buffer2' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:413:10: warning: unused variable 'scale' [-Wunused-variable]
double scale=-1.0;
^
R_subrcModel_interfaces.c:508:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subrcModel_interfaces.c:510:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subrcModel_interfaces.c:502:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:502:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:502:11: warning: unused variable 'results' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:504:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
19 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c avg.c -o avg.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c avg_log.c -o avg_log.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c biweight.c -o biweight.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c lm.c -o lm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c log_avg.c -o log_avg.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c log_median.c -o log_median.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c median.c -o median.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c median_log.c -o median_log.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c medianpolish.c -o medianpolish.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c plmd.c -o plmd.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c plmr.c -o plmr.o
plmr.c:82:13: warning: unused function 'XTWY_R' [-Wunused-function]
static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){
^
plmr.c:152:13: warning: unused function 'XTWX_R' [-Wunused-function]
static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){
^
plmr.c:279:13: warning: unused function 'XTWX_R_inv' [-Wunused-function]
static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c psi_fns.c -o psi_fns.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c qnorm.c -o qnorm.o
qnorm.c:614:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
i, returnCode, *((int *) status));
^
qnorm.c:635:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
i, returnCode, *((int *) status));
^
qnorm.c:2029:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
i, returnCode, *((int *) status));
^
qnorm.c:1926:12: warning: unused variable 'j' [-Wunused-variable]
size_t i,j,row_mean_ind;
^
qnorm.c:1931:7: warning: unused variable 'non_na' [-Wunused-variable]
int non_na;
^
qnorm.c:2126:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (isMatrix(target)){
^~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:977:19: note: expanded from macro 'isMatrix'
#define isMatrix Rf_isMatrix
^
qnorm.c:2139:55: note: uninitialized use occurs here
qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
^~~~~~~~~~~
qnorm.c:2126:10: note: remove the 'if' if its condition is always true
} else if (isMatrix(target)){
^~~~~~~~~~~~~~~~~~~~~
qnorm.c:2107:21: note: initialize the variable 'target_rows' to silence this warning
size_t target_rows, target_cols;
^
= 0
qnorm.c:2632:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
i, returnCode, *((int *) status));
^
qnorm.c:2528:12: warning: unused variable 'j' [-Wunused-variable]
size_t i,j,row_mean_ind;
^
qnorm.c:2533:7: warning: unused variable 'non_na' [-Wunused-variable]
int non_na;
^
qnorm.c:2752:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable]
size_t i,j,ind,target_ind;
^
qnorm.c:2850:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
double *sample_percentiles;
^
qnorm.c:2851:11: warning: unused variable 'datvec' [-Wunused-variable]
double *datvec;
^
qnorm.c:2984:12: warning: unused variable 'j' [-Wunused-variable]
size_t i,j,ind,target_ind;
^
qnorm.c:2984:14: warning: unused variable 'ind' [-Wunused-variable]
size_t i,j,ind,target_ind;
^
qnorm.c:2984:18: warning: unused variable 'target_ind' [-Wunused-variable]
size_t i,j,ind,target_ind;
^
qnorm.c:2986:14: warning: unused variable 'dimat' [-Wunused-variable]
dataitem **dimat;
^
qnorm.c:2988:11: warning: unused variable 'row_mean' [-Wunused-variable]
double *row_mean = target;
^
qnorm.c:2990:11: warning: unused variable 'ranks' [-Wunused-variable]
double *ranks = (double *)R_Calloc((rows),double);
^
qnorm.c:2991:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
double samplepercentile;
^
qnorm.c:2992:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
double target_ind_double,target_ind_double_floor;
^
qnorm.c:2992:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
double target_ind_double,target_ind_double_floor;
^
qnorm.c:2994:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
int targetnon_na = targetrows;
^
qnorm.c:2995:7: warning: unused variable 'non_na' [-Wunused-variable]
int non_na = 0;
^
qnorm.c:2999:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
double *sample_percentiles;
^
qnorm.c:3000:11: warning: unused variable 'datvec' [-Wunused-variable]
double *datvec;
^
qnorm.c:3258:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (isMatrix(target)){
^~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:977:19: note: expanded from macro 'isMatrix'
#define isMatrix Rf_isMatrix
^
qnorm.c:3272:77: note: uninitialized use occurs here
qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
^~~~~~~~~~~
qnorm.c:3258:10: note: remove the 'if' if its condition is always true
} else if (isMatrix(target)){
^~~~~~~~~~~~~~~~~~~~~
qnorm.c:3239:21: note: initialize the variable 'target_rows' to silence this warning
size_t target_rows, target_cols;
^
= 0
26 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rlm.c -o rlm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rlm_anova.c -o rlm_anova.o
rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable]
double endprobe;
^
rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable]
double scale=0.0;
^
rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable]
double sumpsi2=0.0; /* sum of psi(r_i)^2 */
^
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
double sumderivpsi=0.0; /* sum of psi'(r_i) */
^
rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
double Kappa=0.0; /* A correction factor */
^
rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable]
double vs=0.0,m,varderivpsi=0.0;
^
rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable]
double k1 = psi_k; /* was 1.345; */
^
rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable]
double vs=0.0,m,varderivpsi=0.0;
^
rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable]
double vs=0.0,m,varderivpsi=0.0;
^
rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable]
double endprobe;
^
10 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rlm_se.c -o rlm_se.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rma_background4.c -o rma_background4.o
rma_background4.c:369:10: warning: unused variable 'j' [-Wunused-variable]
size_t j;
^
rma_background4.c:370:10: warning: unused variable 'param' [-Wunused-variable]
double param[3];
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rma_common.c -o rma_common.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o preprocessCore.so 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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-preprocessCore/00new/preprocessCore/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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)
0.03251 0.90739
>
>
>
> 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] 65.38318
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 64.5809
>
>
> 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
8.2297 9.2495
as.factor(cp)3 as.factor(cp)4
10.2214 11.2350
as.factor(cp)5 as.factor(cp)6
12.2450 10.2629
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
3.7117 2.7714
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
1.7675 0.7312
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.1495 -2.2449
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-3.1878 -4.2684
>
>
> 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] 8.4348520 9.4842851 10.4080009 11.2677277 12.3303771 10.3307829
[7] 3.5891055 2.6119043 1.6478885 0.9131835 -2.1261656 -2.3204807
[13] -3.2957709 -1.0196646
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.0000000 1.0000000 1.00000000 1.00000000 1.00000000 1.00000000
[2,] 1.0000000 1.0000000 1.00000000 1.00000000 1.00000000 1.00000000
[3,] 1.0000000 1.0000000 1.00000000 1.00000000 1.00000000 1.00000000
[4,] 1.0000000 1.0000000 1.00000000 1.00000000 1.00000000 1.00000000
[5,] 0.4714191 0.3912649 0.60570119 0.52030446 0.44736275 0.47077295
[6,] 1.0000000 1.0000000 0.79494912 1.00000000 1.00000000 1.00000000
[7,] 1.0000000 1.0000000 1.00000000 1.00000000 0.98477623 0.80889169
[8,] 0.0934676 0.0814599 0.09241574 0.08202917 0.08849466 0.09695802
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.05776453 -0.09020717 -0.042145602 0.12593496 -0.083262809 0.03191609
[2,] -0.01739209 0.19708797 0.005711199 -0.16444397 0.049254148 -0.07021725
[3,] -0.08778389 0.05480210 0.004893005 0.05231801 0.004566786 -0.02879601
[4,] -0.16322226 -0.10388516 0.214882914 -0.15204580 0.140494902 0.06377540
[5,] 0.61843118 0.74512935 0.481386603 -0.56038493 -0.651630795 -0.61935068
[6,] 0.11534925 0.19358166 -0.366659058 0.09052773 0.180272726 -0.28825607
[7,] 0.09530166 -0.25136526 0.108108651 0.04772755 -0.295877402 0.36049379
[8,] -3.11934282 -3.57914873 -3.154779670 3.55425129 3.294691781 3.00698143
$StdErrors
[1] 0.1964663 0.1983688 0.1970257 0.1962478 0.1972793 0.1987399 0.1955805
[8] 0.1955805 0.1955805 0.1955805 0.2595082 0.1981380 0.1981146 0.5628725
$Scale
[1] 0.2168574
> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
[1] 8.139907 9.174169 10.106619 10.991119 12.032366 9.990821 3.892610
[8] 2.912320 1.951393 1.209869 -1.209035 -2.431760 -1.969961 -2.980632
[15] -3.947895 2.573093
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[2,] 1 0.8640556 1.0000000 0.9491171 1.0000000 1.0000000
[3,] 1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[4,] 1 1.0000000 0.8136762 1.0000000 1.0000000 1.0000000
[5,] 1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[6,] 1 1.0000000 0.4297080 1.0000000 1.0000000 0.5979060
[7,] 1 0.6968606 1.0000000 1.0000000 0.5708255 0.4637249
[8,] 1 0.5242511 1.0000000 0.7505089 1.0000000 0.7267449
$Residuals
[,1] [,2] [,3] [,4] [,5]
[1,] 0.049205537 -0.08359556 -0.044267734 0.099039665 -8.875614e-02
[2,] -0.022862252 0.20678841 0.006677899 -0.188250433 4.684965e-02
[3,] -0.096342883 0.06141370 0.002770873 0.025422717 -9.265407e-04
[4,] -0.164962436 -0.09045474 0.219579598 -0.172122274 1.418204e-01
[5,] -0.003753685 0.13811508 -0.134361398 0.021818733 -4.802516e-02
[6,] 0.059774788 0.15317779 -0.415796662 0.016616967 1.277639e-01
[7,] 0.075107943 -0.25638839 0.094351793 0.009197533 -3.130055e-01
[8,] 0.103832987 -0.34080233 0.074833002 0.238102909 -5.463181e-05
[,6]
[1,] 0.068374231
[2,] -0.030670278
[3,] 0.007662132
[4,] 0.107052358
[5,] 0.026206427
[6,] -0.298813401
[7,] 0.385317205
[8,] -0.245813516
$StdErrors
[1] 0.06147021 0.07951568 0.07275046 0.07219143 0.06589906 0.07956447
[7] 0.06722460 0.08082620 0.06722460 0.07375016 0.09485545 0.09507679
[13] 0.08134331 0.09366932 0.11440860 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
8.140 9.100
as.factor(cp)3 as.factor(cp)4
10.082 10.770
as.factor(cp)5 as.factor(cp)6
11.789 9.766
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
4.024 3.047
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
2.192 1.348
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.689 -1.898
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-2.850 -3.969
C(as.factor(pr), "contr.sum")9
2.800
>
>
> proc.time()
user system elapsed
1.549 0.130 1.677
preprocessCore.Rcheck/tests/qnormtest.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
0.192 0.076 0.262
preprocessCore.Rcheck/preprocessCore-Ex.timings
| name | user | system | elapsed | |
| colSummarize | 0.001 | 0.002 | 0.003 | |
| normalize.quantiles.in.blocks | 0.035 | 0.002 | 0.037 | |
| rcModelPLMd | 0.013 | 0.003 | 0.017 | |
| rcModelPLMr | 0.032 | 0.006 | 0.039 | |
| rcModels | 0.004 | 0.008 | 0.012 | |
| subColSummarize | 0.004 | 0.002 | 0.005 | |
| subrcModels | 0.006 | 0.011 | 0.016 | |