Ben Bolstad
| Snapshot Date: 2026-03-31 13:45 -0400 (Tue, 31 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/preprocessCore |
| git_branch: RELEASE_3_22 |
| git_last_commit: f8fc99a |
| git_last_commit_date: 2025-10-29 09:42:06 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-01 11:57 -0400 (Wed, 01 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4896 |
| 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 1.72.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| See other builds for preprocessCore in R Universe. | ||||||||||||||
|
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: 1.72.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings preprocessCore_1.72.0.tar.gz |
| StartedAt: 2026-04-01 02:45:30 -0400 (Wed, 01 Apr 2026) |
| EndedAt: 2026-04-01 02:45:47 -0400 (Wed, 01 Apr 2026) |
| EllapsedTime: 17.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: preprocessCore.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings preprocessCore_1.72.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.72.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘preprocessCore’ can be installed ... WARNING
Found the following significant warnings:
qnorm.c:613:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
qnorm.c:634:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
qnorm.c:2028:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
qnorm.c:2631:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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
‘/home/biocbuild/bbs-3.22-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.
preprocessCore.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL preprocessCore
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘preprocessCore’ ...
** this is package ‘preprocessCore’ version ‘1.72.0’
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc -std=gnu2x
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 gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -std=gnu2x -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... yes
configure: Enabling threading for preprocessCore
configure: Using __pthread_get_minstack
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_colSummarize.c -o R_colSummarize.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c: In function ‘R_subColSummarize_avg_log’:
R_subColSummarize.c:133:9: warning: unused variable ‘j’ [-Wunused-variable]
133 | int i,j;
| ^
R_subColSummarize.c:131:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
131 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:127:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
127 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:125:21: warning: unused variable ‘buffer’ [-Wunused-variable]
125 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_log_avg’:
R_subColSummarize.c:309:9: warning: unused variable ‘j’ [-Wunused-variable]
309 | int i,j;
| ^
R_subColSummarize.c:307:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
307 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:303:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
303 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:301:21: warning: unused variable ‘buffer’ [-Wunused-variable]
301 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_avg’:
R_subColSummarize.c:488:9: warning: unused variable ‘j’ [-Wunused-variable]
488 | int i,j;
| ^
R_subColSummarize.c:486:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
486 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:482:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
482 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:480:21: warning: unused variable ‘buffer’ [-Wunused-variable]
480 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_biweight_log’:
R_subColSummarize.c:668:9: warning: unused variable ‘j’ [-Wunused-variable]
668 | int i,j;
| ^
R_subColSummarize.c:666:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
666 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:662:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
662 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:660:21: warning: unused variable ‘buffer’ [-Wunused-variable]
660 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_biweight’:
R_subColSummarize.c:847:9: warning: unused variable ‘j’ [-Wunused-variable]
847 | int i,j;
| ^
R_subColSummarize.c:845:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
845 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:841:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
841 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:839:21: warning: unused variable ‘buffer’ [-Wunused-variable]
839 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_median_log’:
R_subColSummarize.c:1027:9: warning: unused variable ‘j’ [-Wunused-variable]
1027 | int i,j;
| ^
R_subColSummarize.c:1025:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1025 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1021:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1021 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1019:21: warning: unused variable ‘buffer’ [-Wunused-variable]
1019 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_log_median’:
R_subColSummarize.c:1205:9: warning: unused variable ‘j’ [-Wunused-variable]
1205 | int i,j;
| ^
R_subColSummarize.c:1203:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1203 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1199:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1199 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1197:21: warning: unused variable ‘buffer’ [-Wunused-variable]
1197 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_median’:
R_subColSummarize.c:1382:9: warning: unused variable ‘j’ [-Wunused-variable]
1382 | int i,j;
| ^
R_subColSummarize.c:1380:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1380 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1376:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1376 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1374:21: warning: unused variable ‘buffer’ [-Wunused-variable]
1374 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish_log’:
R_subColSummarize.c:1564:9: warning: unused variable ‘j’ [-Wunused-variable]
1564 | int i,j;
| ^
R_subColSummarize.c:1562:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1562 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1558:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1558 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1556:30: warning: variable ‘buffer2’ set but not used [-Wunused-but-set-variable]
1556 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subColSummarize.c:1556:21: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable]
1556 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish’:
R_subColSummarize.c:1747:9: warning: unused variable ‘j’ [-Wunused-variable]
1747 | int i,j;
| ^
R_subColSummarize.c:1745:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1745 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1741:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1741 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1739:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
1739 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subColSummarize.c:1739:21: warning: unused variable ‘buffer’ [-Wunused-variable]
1739 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subColSummarize.c: At top level:
R_subColSummarize.c:1703:14: warning: ‘subColSummarize_medianpolish_group’ defined but not used [-Wunused-function]
1703 | static void *subColSummarize_medianpolish_group(void *data){
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c: In function ‘sub_rcModelSummarize_medianpolish_group’:
R_subrcModel_interfaces.c:103:11: warning: unused variable ‘se’ [-Wunused-variable]
103 | double *se;
| ^~
R_subrcModel_interfaces.c:102:11: warning: unused variable ‘weights’ [-Wunused-variable]
102 | double *weights;
| ^~~~~~~
R_subrcModel_interfaces.c:87:20: warning: unused variable ‘buffer2’ [-Wunused-variable]
87 | double *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:87:11: warning: unused variable ‘buffer’ [-Wunused-variable]
87 | double *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_medianpolish’:
R_subrcModel_interfaces.c:185:9: warning: unused variable ‘j’ [-Wunused-variable]
185 | int i,j;
| ^
R_subrcModel_interfaces.c:183:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
183 | int ncur_rows;
| ^~~~~~~~~
R_subrcModel_interfaces.c:179:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
179 | int *cur_rows;
| ^~~~~~~~
R_subrcModel_interfaces.c:177:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
177 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:177:21: warning: unused variable ‘buffer’ [-Wunused-variable]
177 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c:177:11: warning: unused variable ‘results’ [-Wunused-variable]
177 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c: In function ‘sub_rcModelSummarize_plm_group’:
R_subrcModel_interfaces.c:413:10: warning: unused variable ‘scale’ [-Wunused-variable]
413 | double scale=-1.0;
| ^~~~~
R_subrcModel_interfaces.c:392:20: warning: unused variable ‘buffer2’ [-Wunused-variable]
392 | double *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:392:11: warning: unused variable ‘buffer’ [-Wunused-variable]
392 | double *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_plm’:
R_subrcModel_interfaces.c:510:9: warning: unused variable ‘j’ [-Wunused-variable]
510 | int i,j;
| ^
R_subrcModel_interfaces.c:508:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
508 | int ncur_rows;
| ^~~~~~~~~
R_subrcModel_interfaces.c:504:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
504 | int *cur_rows;
| ^~~~~~~~
R_subrcModel_interfaces.c:502:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
502 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:502:21: warning: unused variable ‘buffer’ [-Wunused-variable]
502 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c:502:11: warning: unused variable ‘results’ [-Wunused-variable]
502 | double *results, *buffer, *buffer2;
| ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c avg.c -o avg.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c avg_log.c -o avg_log.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c biweight.c -o biweight.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c lm.c -o lm.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c log_avg.c -o log_avg.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c log_median.c -o log_median.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c median.c -o median.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c median_log.c -o median_log.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c medianpolish.c -o medianpolish.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c plmd.c -o plmd.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c psi_fns.c -o psi_fns.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c qnorm.c -o qnorm.o
qnorm.c: In function ‘qnorm_c_l’:
qnorm.c:613:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
613 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
614 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c:634:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
634 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
635 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c: In function ‘qnorm_c_determine_target_l’:
qnorm.c:2028:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
2028 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
2029 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c:1931:7: warning: unused variable ‘non_na’ [-Wunused-variable]
1931 | int non_na;
| ^~~~~~
qnorm.c:1926:12: warning: unused variable ‘j’ [-Wunused-variable]
1926 | size_t i,j,row_mean_ind;
| ^
qnorm.c: In function ‘qnorm_c_determine_target_via_subset_l’:
qnorm.c:2631:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
2631 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
2632 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c:2533:7: warning: unused variable ‘non_na’ [-Wunused-variable]
2533 | int non_na;
| ^~~~~~
qnorm.c:2528:12: warning: unused variable ‘j’ [-Wunused-variable]
2528 | size_t i,j,row_mean_ind;
| ^
qnorm.c: In function ‘using_target_via_subset_part1’:
qnorm.c:2752:14: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
2752 | size_t i,j,ind,target_ind;
| ^~~
qnorm.c: In function ‘using_target_via_subset_part2’:
qnorm.c:2851:11: warning: unused variable ‘datvec’ [-Wunused-variable]
2851 | double *datvec;
| ^~~~~~
qnorm.c:2850:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
2850 | double *sample_percentiles;
| ^~~~~~~~~~~~~~~~~~
qnorm.c: In function ‘using_target_via_subset’:
qnorm.c:3000:11: warning: unused variable ‘datvec’ [-Wunused-variable]
3000 | double *datvec;
| ^~~~~~
qnorm.c:2999:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
2999 | double *sample_percentiles;
| ^~~~~~~~~~~~~~~~~~
qnorm.c:2995:7: warning: unused variable ‘non_na’ [-Wunused-variable]
2995 | int non_na = 0;
| ^~~~~~
qnorm.c:2994:7: warning: unused variable ‘targetnon_na’ [-Wunused-variable]
2994 | int targetnon_na = targetrows;
| ^~~~~~~~~~~~
qnorm.c:2992:28: warning: unused variable ‘target_ind_double_floor’ [-Wunused-variable]
2992 | double target_ind_double,target_ind_double_floor;
| ^~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2992:10: warning: unused variable ‘target_ind_double’ [-Wunused-variable]
2992 | double target_ind_double,target_ind_double_floor;
| ^~~~~~~~~~~~~~~~~
qnorm.c:2991:10: warning: unused variable ‘samplepercentile’ [-Wunused-variable]
2991 | double samplepercentile;
| ^~~~~~~~~~~~~~~~
qnorm.c:2990:11: warning: unused variable ‘ranks’ [-Wunused-variable]
2990 | double *ranks = (double *)R_Calloc((rows),double);
| ^~~~~
qnorm.c:2988:11: warning: unused variable ‘row_mean’ [-Wunused-variable]
2988 | double *row_mean = target;
| ^~~~~~~~
qnorm.c:2986:14: warning: unused variable ‘dimat’ [-Wunused-variable]
2986 | dataitem **dimat;
| ^~~~~
qnorm.c:2984:18: warning: unused variable ‘target_ind’ [-Wunused-variable]
2984 | size_t i,j,ind,target_ind;
| ^~~~~~~~~~
qnorm.c:2984:14: warning: unused variable ‘ind’ [-Wunused-variable]
2984 | size_t i,j,ind,target_ind;
| ^~~
qnorm.c:2984:12: warning: unused variable ‘j’ [-Wunused-variable]
2984 | size_t i,j,ind,target_ind;
| ^
qnorm.c: In function ‘R_qnorm_using_target’:
qnorm.c:2139:3: warning: ‘target_rows’ may be used uninitialized [-Wmaybe-uninitialized]
2139 | qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2107:10: note: ‘target_rows’ was declared here
2107 | size_t target_rows, target_cols;
| ^~~~~~~~~~~
qnorm.c: In function ‘R_qnorm_using_target_via_subset’:
qnorm.c:3272:3: warning: ‘target_rows’ may be used uninitialized [-Wmaybe-uninitialized]
3272 | qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:3239:10: note: ‘target_rows’ was declared here
3239 | size_t target_rows, target_cols;
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rlm.c -o rlm.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rlm_se.c -o rlm_se.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rma_background4.c -o rma_background4.o
rma_background4.c: In function ‘rma_bg_correct’:
rma_background4.c:370:10: warning: unused variable ‘param’ [-Wunused-variable]
370 | double param[3];
| ^~~~~
rma_background4.c:369:10: warning: unused variable ‘j’ [-Wunused-variable]
369 | size_t j;
| ^
rma_background4.c: In function ‘R_rma_bg_correct’:
rma_background4.c:527:12: warning: ‘PMcopy’ may be used uninitialized [-Wmaybe-uninitialized]
527 | return PMcopy;
| ^~~~~~
rma_background4.c:500:13: note: ‘PMcopy’ was declared here
500 | SEXP dim1,PMcopy;
| ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rma_common.c -o rma_common.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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)
0.01337 0.96381
>
>
>
> 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] 43.84073
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 43.82665
>
>
> 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
8.2376 9.2128
as.factor(cp)3 as.factor(cp)4
10.2466 11.2658
as.factor(cp)5 as.factor(cp)6
12.2385 10.2147
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
3.8030 2.8219
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
1.7372 0.7172
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.2296 -2.2697
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-3.1842 -4.1676
>
>
> 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] 8.2047875 9.3218842 10.3650371 11.4118710 12.3059672 10.4645514
[7] 3.6846904 2.6010681 1.7237986 0.7769332 -2.0863830 -2.3861779
[13] -3.4194274 -0.8945019
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
[2,] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
[3,] 0.84854845 1.00000000 1.00000000 0.94087151 1.00000000 1.00000000
[4,] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
[5,] 0.28454745 0.32556072 0.35886092 0.36075966 0.33670007 0.27420783
[6,] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
[7,] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
[8,] 0.08589852 0.07838165 0.08920447 0.08244272 0.08384309 0.08655402
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.245014161 0.040554224 0.1034168 -0.19266382 0.01345246 0.28025454
[2,] -0.004096191 0.124933158 0.1174082 0.13994972 -0.09596736 -0.28222755
[3,] 0.334625757 0.057653484 -0.1420184 -0.30131894 0.14927913 -0.06535798
[4,] 0.092778150 0.037938567 -0.1594955 0.27172593 -0.12204768 -0.12089946
[5,] 0.997233061 0.871519203 0.7906433 -0.78644166 -0.84275280 -1.03480700
[6,] -0.077619750 -0.005996256 -0.1424588 -0.01615595 0.11518619 0.12704461
[7,] -0.050015630 -0.255069213 0.2231636 0.08061301 -0.05988875 0.06119699
[8,] -3.303185223 -3.620061414 -3.1808586 3.44178278 3.38418986 3.27819579
$StdErrors
[1] 0.2097908 0.2073054 0.2060719 0.2071450 0.2067931 0.2079450 0.2042360
[8] 0.2042360 0.2068361 0.2042360 0.3201148 0.2042360 0.2042360 0.5972001
$Scale
[1] 0.2108801
> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
[1] 7.9286358 8.9982793 10.0761230 11.1492755 12.0164426 10.1277018
[7] 3.9712278 2.9056913 2.0334139 1.0655792 -0.9036943 -2.6780603
[13] -2.0899045 -3.1201770 -3.9539537 2.7698775
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.7826456 1.0000000 1.0000000 0.9228105 1 0.6047770
[2,] 1.0000000 1.0000000 1.0000000 1.0000000 1 0.7996062
[3,] 0.6638061 1.0000000 1.0000000 0.5738700 1 1.0000000
[4,] 1.0000000 1.0000000 1.0000000 0.8137206 1 1.0000000
[5,] 1.0000000 1.0000000 1.0000000 1.0000000 1 1.0000000
[6,] 1.0000000 1.0000000 1.0000000 1.0000000 1 1.0000000
[7,] 1.0000000 0.8665337 0.9392442 1.0000000 1 1.0000000
[8,] 1.0000000 0.8435499 1.0000000 1.0000000 1 1.0000000
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.25539995 0.07762164 0.1057934 -0.21660581 0.016439609 0.33056668
[2,] -0.03256769 0.14391487 0.1016992 0.09792202 -0.111065916 -0.25000111
[3,] 0.30116207 0.07164300 -0.1627197 -0.34833882 0.129188379 -0.03812373
[4,] 0.08028381 0.07289743 -0.1592274 0.24567539 -0.121169088 -0.07269586
[5,] 0.09069598 0.01243532 -0.1031313 0.06783107 0.038449065 -0.10628014
[6,] -0.09774147 0.02133523 -0.1498181 -0.04983386 0.108437413 0.16762083
[7,] -0.07311437 -0.23071475 0.2128273 0.04395807 -0.069614554 0.09879619
[8,] 0.03241819 -0.23700480 0.1675072 0.03999888 0.009335093 -0.04933397
$StdErrors
[1] 0.07676445 0.07697646 0.07064017 0.08616155 0.06507966 0.07745341
[7] 0.09980976 0.07758078 0.08645736 0.07736368 0.10146622 0.10261685
[13] 0.07092027 0.08782579 0.12333940 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
7.932 9.005
as.factor(cp)3 as.factor(cp)4
10.116 10.879
as.factor(cp)5 as.factor(cp)6
11.761 9.883
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
4.101 3.017
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
2.204 1.193
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.671 -1.970
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-3.003 -3.983
C(as.factor(pr), "contr.sum")9
3.026
>
>
> proc.time()
user system elapsed
1.539 0.044 1.571
preprocessCore.Rcheck/tests/qnormtest.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
0.150 0.037 0.175
preprocessCore.Rcheck/preprocessCore-Ex.timings
| name | user | system | elapsed | |
| colSummarize | 0.001 | 0.000 | 0.001 | |
| normalize.quantiles.in.blocks | 0.032 | 0.000 | 0.032 | |
| rcModelPLMd | 0.014 | 0.000 | 0.015 | |
| rcModelPLMr | 0.030 | 0.001 | 0.032 | |
| rcModels | 0.004 | 0.000 | 0.004 | |
| subColSummarize | 0.003 | 0.000 | 0.003 | |
| subrcModels | 0.003 | 0.002 | 0.005 | |