Ben Bolstad
| Snapshot Date: 2025-11-04 13:40 -0500 (Tue, 04 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/preprocessCore |
| git_branch: devel |
| git_last_commit: bb678ea |
| git_last_commit_date: 2025-10-29 09:42:06 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 1614/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preprocessCore 1.73.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
|
To the developers/maintainers of the preprocessCore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preprocessCore.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: preprocessCore |
| Version: 1.73.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings preprocessCore_1.73.0.tar.gz |
| StartedAt: 2025-11-05 02:34:09 -0500 (Wed, 05 Nov 2025) |
| EndedAt: 2025-11-05 02:34:27 -0500 (Wed, 05 Nov 2025) |
| EllapsedTime: 18.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: preprocessCore.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings preprocessCore_1.73.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/preprocessCore.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.73.0’
* 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-3.23-bioc/meat/preprocessCore.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 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 ... INFO
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
See
‘/home/biocbuild/bbs-3.23-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-3.23-bioc/R/bin/R CMD INSTALL preprocessCore
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘preprocessCore’ ...
** this is package ‘preprocessCore’ version ‘1.73.0’
** 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) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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)
-0.007002 0.980159
>
>
>
> 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] 50.81082
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 50.7946
>
>
> 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
8.2313 9.2362
as.factor(cp)3 as.factor(cp)4
10.2240 11.2702
as.factor(cp)5 as.factor(cp)6
12.2222 10.1805
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
3.7364 2.7993
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
1.7653 0.7969
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.2730 -2.2438
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-3.1886 -4.1787
>
>
> 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] 8.4248687 9.3554923 10.2240708 11.2818767 12.4498659 10.3762528
[7] 3.6656072 2.8688898 1.4792998 0.7126841 -2.0700196 -2.2926710
[13] -3.4144196 -0.9493705
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.00000000 0.6593881 1.00000000 1.00000000 1.00000000 1.00000000
[2,] 0.36777047 1.0000000 1.00000000 1.00000000 1.00000000 1.00000000
[3,] 1.00000000 0.6421969 1.00000000 1.00000000 1.00000000 1.00000000
[4,] 1.00000000 1.0000000 1.00000000 1.00000000 1.00000000 1.00000000
[5,] 0.22322037 0.2969607 0.30879037 0.21746197 0.22178219 0.44024996
[6,] 1.00000000 1.0000000 1.00000000 1.00000000 0.98235351 1.00000000
[7,] 1.00000000 1.0000000 1.00000000 1.00000000 1.00000000 1.00000000
[8,] 0.06505337 0.0701864 0.07403076 0.07182226 0.07419221 0.06349911
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.07046076 -0.35619521 0.07272534 -0.008140680 0.20332394 -0.103498467
[2,] -0.63872666 -0.01939378 0.06038531 0.027803391 0.08782709 0.078282791
[3,] 0.08610915 0.36553884 -0.11769344 -0.103741083 -0.02012206 -0.079300461
[4,] -0.07968044 0.06298668 0.03977921 0.117831029 -0.15074258 0.009826103
[5,] 1.05173815 0.79062567 0.76041479 -1.079729789 -1.05856233 -0.533316149
[6,] 0.13118870 0.05534728 -0.17467240 0.008998016 -0.23874230 0.213667747
[7,] 0.02687074 -0.09879391 0.11946952 -0.042754915 0.11419880 -0.118990231
[8,] -3.60955156 -3.34549108 -3.17168539 3.269243060 3.16494699 3.697767204
$StdErrors
[1] 0.2026400 0.2011196 0.1914959 0.1934517 0.1934379 0.1896846 0.1933909
[8] 0.1974311 0.1936140 0.1894652 0.3101290 0.1896527 0.1894652 0.5952365
$Scale
[1] 0.1745919
> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
[1] 8.1175227 9.0363106 9.9269239 10.9430581 12.0946161 10.1389814
[7] 3.9686361 3.1831090 1.7818120 1.0218531 -0.8945352 -2.6863941
[13] -1.9842041 -3.1052506 -4.0055222 2.7204960
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.0000000 0.6219514 1 1 0.827549 1.0000000
[2,] 0.3275669 1.0000000 1 1 1.000000 1.0000000
[3,] 1.0000000 0.5533009 1 1 1.000000 1.0000000
[4,] 1.0000000 1.0000000 1 1 1.000000 1.0000000
[5,] 1.0000000 1.0000000 1 1 1.000000 0.6601781
[6,] 1.0000000 1.0000000 1 1 1.000000 1.0000000
[7,] 1.0000000 1.0000000 1 1 1.000000 1.0000000
[8,] 0.8593860 1.0000000 1 1 1.000000 0.7974990
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.07477780 -0.34004252 0.06684329 0.02764891 0.25554484 -0.169255975
[2,] -0.64559988 -0.01443135 0.04331300 0.05240273 0.12885773 0.001335025
[3,] 0.09094294 0.38220828 -0.12305874 -0.06743475 0.03261558 -0.144541225
[4,] -0.08150350 0.07299926 0.02775705 0.14748051 -0.10466179 -0.062071516
[5,] 0.18359976 -0.06567707 -0.11792269 -0.12453674 -0.08693798 0.320329798
[6,] 0.13006779 0.06606202 -0.18599240 0.03934966 -0.19195936 0.142472288
[7,] 0.02504767 -0.08878133 0.10744736 -0.01310543 0.16027959 -0.190887851
[8,] -0.24605394 0.02984219 0.18161314 -0.06180488 -0.14966965 0.265172162
$StdErrors
[1] 0.07615610 0.07632732 0.06477154 0.06427027 0.06954255 0.07600025
[7] 0.08617107 0.07648644 0.07692799 0.07035981 0.10012923 0.12028206
[13] 0.07035981 0.07035981 0.12153570 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
8.053 9.015
as.factor(cp)3 as.factor(cp)4
9.950 10.674
as.factor(cp)5 as.factor(cp)6
11.831 9.890
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
4.095 3.251
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
1.982 1.163
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.632 -1.843
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-2.965 -3.996
C(as.factor(pr), "contr.sum")9
2.999
>
>
> proc.time()
user system elapsed
1.566 0.079 1.630
preprocessCore.Rcheck/tests/qnormtest.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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
0.174 0.036 0.194
preprocessCore.Rcheck/preprocessCore-Ex.timings
| name | user | system | elapsed | |
| colSummarize | 0.000 | 0.002 | 0.003 | |
| normalize.quantiles.in.blocks | 0.033 | 0.002 | 0.035 | |
| rcModelPLMd | 0.015 | 0.003 | 0.018 | |
| rcModelPLMr | 0.029 | 0.003 | 0.033 | |
| rcModels | 0.004 | 0.007 | 0.012 | |
| subColSummarize | 0.003 | 0.002 | 0.005 | |
| subrcModels | 0.006 | 0.011 | 0.017 | |