| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-04-04 12:34 -0400 (Fri, 04 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 871 |
| 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 156/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| preprocessCore 1.69.0 (landing page) Ben Bolstad
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
|
To the developers/maintainers of the preprocessCore package: - 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: 1.69.0 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings preprocessCore_1.69.0.tar.gz |
| StartedAt: 2025-04-04 12:31:19 -0400 (Fri, 04 Apr 2025) |
| EndedAt: 2025-04-04 12:31:33 -0400 (Fri, 04 Apr 2025) |
| EllapsedTime: 13.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: preprocessCore.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings preprocessCore_1.69.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/preprocessCore.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.69.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
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:595:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
qnorm.c:616:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
qnorm.c:2004:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
qnorm.c:2604:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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 ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking Rd \usage sections ... WARNING
Fatal error: cannot create 'R_TempDir'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Fatal error: cannot create 'R_TempDir'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking for unstated dependencies in examples ... WARNING
Fatal error: cannot create 'R_TempDir'
* 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 ... NOTE
Fatal error: cannot create 'R_TempDir'
* 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
Fatal error: cannot create 'R_TempDir'
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘PLMdtest.R’
Running ‘qnormtest.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 4 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/preprocessCore.Rcheck/00check.log’
for details.
preprocessCore.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################
* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘preprocessCore’ ...
** this is package ‘preprocessCore’ version ‘1.69.0’
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... gcc
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for library containing pthread_create... none required
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking if PTHREAD_STACK_MIN is defined... yes
checking if R is using flexiblas... flexiblas not found. preprocessCore threading will not be disabled
configure: Enabling threading for preprocessCore
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 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c R_colSummarize.c -o R_colSummarize.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=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:117:9: warning: unused variable ‘j’ [-Wunused-variable]
117 | int i,j;
| ^
R_subColSummarize.c:115:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
115 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:111:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
111 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:109:21: warning: unused variable ‘buffer’ [-Wunused-variable]
109 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_log_avg’:
R_subColSummarize.c:290:9: warning: unused variable ‘j’ [-Wunused-variable]
290 | int i,j;
| ^
R_subColSummarize.c:288:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
288 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:284:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
284 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:282:21: warning: unused variable ‘buffer’ [-Wunused-variable]
282 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_avg’:
R_subColSummarize.c:466:9: warning: unused variable ‘j’ [-Wunused-variable]
466 | int i,j;
| ^
R_subColSummarize.c:464:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
464 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:460:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
460 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:458:21: warning: unused variable ‘buffer’ [-Wunused-variable]
458 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_biweight_log’:
R_subColSummarize.c:643:9: warning: unused variable ‘j’ [-Wunused-variable]
643 | int i,j;
| ^
R_subColSummarize.c:641:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
641 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:637:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
637 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:635:21: warning: unused variable ‘buffer’ [-Wunused-variable]
635 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_biweight’:
R_subColSummarize.c:819:9: warning: unused variable ‘j’ [-Wunused-variable]
819 | int i,j;
| ^
R_subColSummarize.c:817:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
817 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:813:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
813 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:811:21: warning: unused variable ‘buffer’ [-Wunused-variable]
811 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_median_log’:
R_subColSummarize.c:996:9: warning: unused variable ‘j’ [-Wunused-variable]
996 | int i,j;
| ^
R_subColSummarize.c:994:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
994 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:990:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
990 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:988:21: warning: unused variable ‘buffer’ [-Wunused-variable]
988 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_log_median’:
R_subColSummarize.c:1171:9: warning: unused variable ‘j’ [-Wunused-variable]
1171 | int i,j;
| ^
R_subColSummarize.c:1169:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1169 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1165:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1165 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1163:21: warning: unused variable ‘buffer’ [-Wunused-variable]
1163 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_median’:
R_subColSummarize.c:1345:9: warning: unused variable ‘j’ [-Wunused-variable]
1345 | int i,j;
| ^
R_subColSummarize.c:1343:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1343 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1339:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1339 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1337:21: warning: unused variable ‘buffer’ [-Wunused-variable]
1337 | double *results, *buffer;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish_log’:
R_subColSummarize.c:1524:9: warning: unused variable ‘j’ [-Wunused-variable]
1524 | int i,j;
| ^
R_subColSummarize.c:1522:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1522 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1518:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1518 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1516:30: warning: variable ‘buffer2’ set but not used [-Wunused-but-set-variable]
1516 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subColSummarize.c:1516:21: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable]
1516 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish’:
R_subColSummarize.c:1704:9: warning: unused variable ‘j’ [-Wunused-variable]
1704 | int i,j;
| ^
R_subColSummarize.c:1702:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
1702 | int ncur_rows;
| ^~~~~~~~~
R_subColSummarize.c:1698:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
1698 | int *cur_rows;
| ^~~~~~~~
R_subColSummarize.c:1696:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
1696 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subColSummarize.c:1696:21: warning: unused variable ‘buffer’ [-Wunused-variable]
1696 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subColSummarize.c: At top level:
R_subColSummarize.c:1660:14: warning: ‘subColSummarize_medianpolish_group’ defined but not used [-Wunused-function]
1660 | static void *subColSummarize_medianpolish_group(void *data){
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=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:91:11: warning: unused variable ‘se’ [-Wunused-variable]
91 | double *se;
| ^~
R_subrcModel_interfaces.c:90:11: warning: unused variable ‘weights’ [-Wunused-variable]
90 | double *weights;
| ^~~~~~~
R_subrcModel_interfaces.c:75:20: warning: unused variable ‘buffer2’ [-Wunused-variable]
75 | double *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:75:11: warning: unused variable ‘buffer’ [-Wunused-variable]
75 | double *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_medianpolish’:
R_subrcModel_interfaces.c:173:9: warning: unused variable ‘j’ [-Wunused-variable]
173 | int i,j;
| ^
R_subrcModel_interfaces.c:171:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
171 | int ncur_rows;
| ^~~~~~~~~
R_subrcModel_interfaces.c:167:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
167 | int *cur_rows;
| ^~~~~~~~
R_subrcModel_interfaces.c:165:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
165 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:165:21: warning: unused variable ‘buffer’ [-Wunused-variable]
165 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c:165:11: warning: unused variable ‘results’ [-Wunused-variable]
165 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c: In function ‘sub_rcModelSummarize_plm_group’:
R_subrcModel_interfaces.c:398:10: warning: unused variable ‘scale’ [-Wunused-variable]
398 | double scale=-1.0;
| ^~~~~
R_subrcModel_interfaces.c:377:20: warning: unused variable ‘buffer2’ [-Wunused-variable]
377 | double *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:377:11: warning: unused variable ‘buffer’ [-Wunused-variable]
377 | double *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_plm’:
R_subrcModel_interfaces.c:493:9: warning: unused variable ‘j’ [-Wunused-variable]
493 | int i,j;
| ^
R_subrcModel_interfaces.c:491:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
491 | int ncur_rows;
| ^~~~~~~~~
R_subrcModel_interfaces.c:487:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
487 | int *cur_rows;
| ^~~~~~~~
R_subrcModel_interfaces.c:485:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
485 | double *results, *buffer, *buffer2;
| ^~~~~~~
R_subrcModel_interfaces.c:485:21: warning: unused variable ‘buffer’ [-Wunused-variable]
485 | double *results, *buffer, *buffer2;
| ^~~~~~
R_subrcModel_interfaces.c:485:11: warning: unused variable ‘results’ [-Wunused-variable]
485 | double *results, *buffer, *buffer2;
| ^~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c avg.c -o avg.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c avg_log.c -o avg_log.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c biweight.c -o biweight.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c lm.c -o lm.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c log_avg.c -o log_avg.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c log_median.c -o log_median.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c median.c -o median.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c median_log.c -o median_log.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c medianpolish.c -o medianpolish.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c plmd.c -o plmd.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=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 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c psi_fns.c -o psi_fns.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c qnorm.c -o qnorm.o
qnorm.c: In function ‘qnorm_c_l’:
qnorm.c:595:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
595 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
596 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c:616:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
616 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
617 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c: In function ‘qnorm_c_determine_target_l’:
qnorm.c:2004:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
2004 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
2005 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c:1910:7: warning: unused variable ‘non_na’ [-Wunused-variable]
1910 | int non_na;
| ^~~~~~
qnorm.c:1905:12: warning: unused variable ‘j’ [-Wunused-variable]
1905 | size_t i,j,row_mean_ind;
| ^
qnorm.c: In function ‘qnorm_c_determine_target_via_subset_l’:
qnorm.c:2604:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
2604 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n",
| ~^
| |
| int
| %ld
2605 | i, returnCode, *((int *) status));
| ~
| |
| size_t {aka long unsigned int}
qnorm.c:2509:7: warning: unused variable ‘non_na’ [-Wunused-variable]
2509 | int non_na;
| ^~~~~~
qnorm.c:2504:12: warning: unused variable ‘j’ [-Wunused-variable]
2504 | size_t i,j,row_mean_ind;
| ^
qnorm.c: In function ‘using_target_via_subset_part1’:
qnorm.c:2725:14: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
2725 | size_t i,j,ind,target_ind;
| ^~~
qnorm.c: In function ‘using_target_via_subset_part2’:
qnorm.c:2824:11: warning: unused variable ‘datvec’ [-Wunused-variable]
2824 | double *datvec;
| ^~~~~~
qnorm.c:2823:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
2823 | double *sample_percentiles;
| ^~~~~~~~~~~~~~~~~~
qnorm.c: In function ‘using_target_via_subset’:
qnorm.c:2973:11: warning: unused variable ‘datvec’ [-Wunused-variable]
2973 | double *datvec;
| ^~~~~~
qnorm.c:2972:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
2972 | double *sample_percentiles;
| ^~~~~~~~~~~~~~~~~~
qnorm.c:2968:7: warning: unused variable ‘non_na’ [-Wunused-variable]
2968 | int non_na = 0;
| ^~~~~~
qnorm.c:2967:7: warning: unused variable ‘targetnon_na’ [-Wunused-variable]
2967 | int targetnon_na = targetrows;
| ^~~~~~~~~~~~
qnorm.c:2965:28: warning: unused variable ‘target_ind_double_floor’ [-Wunused-variable]
2965 | double target_ind_double,target_ind_double_floor;
| ^~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2965:10: warning: unused variable ‘target_ind_double’ [-Wunused-variable]
2965 | double target_ind_double,target_ind_double_floor;
| ^~~~~~~~~~~~~~~~~
qnorm.c:2964:10: warning: unused variable ‘samplepercentile’ [-Wunused-variable]
2964 | double samplepercentile;
| ^~~~~~~~~~~~~~~~
qnorm.c:2963:11: warning: unused variable ‘ranks’ [-Wunused-variable]
2963 | double *ranks = (double *)R_Calloc((rows),double);
| ^~~~~
qnorm.c:2961:11: warning: unused variable ‘row_mean’ [-Wunused-variable]
2961 | double *row_mean = target;
| ^~~~~~~~
qnorm.c:2959:14: warning: unused variable ‘dimat’ [-Wunused-variable]
2959 | dataitem **dimat;
| ^~~~~
qnorm.c:2957:18: warning: unused variable ‘target_ind’ [-Wunused-variable]
2957 | size_t i,j,ind,target_ind;
| ^~~~~~~~~~
qnorm.c:2957:14: warning: unused variable ‘ind’ [-Wunused-variable]
2957 | size_t i,j,ind,target_ind;
| ^~~
qnorm.c:2957:12: warning: unused variable ‘j’ [-Wunused-variable]
2957 | size_t i,j,ind,target_ind;
| ^
qnorm.c: In function ‘R_qnorm_using_target’:
qnorm.c:2115:3: warning: ‘target_rows’ may be used uninitialized [-Wmaybe-uninitialized]
2115 | qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2083:10: note: ‘target_rows’ was declared here
2083 | size_t target_rows, target_cols;
| ^~~~~~~~~~~
qnorm.c: In function ‘R_qnorm_using_target_via_subset’:
qnorm.c:3242:3: warning: ‘target_rows’ may be used uninitialized [-Wmaybe-uninitialized]
3242 | qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:3209:10: note: ‘target_rows’ was declared here
3209 | size_t target_rows, target_cols;
| ^~~~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c rlm.c -o rlm.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=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 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c rlm_se.c -o rlm_se.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=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:355:10: warning: unused variable ‘param’ [-Wunused-variable]
355 | double param[3];
| ^~~~~
rma_background4.c:354:10: warning: unused variable ‘j’ [-Wunused-variable]
354 | size_t j;
| ^
rma_background4.c: In function ‘R_rma_bg_correct’:
rma_background4.c:509:12: warning: ‘PMcopy’ may be used uninitialized [-Wmaybe-uninitialized]
509 | return PMcopy;
| ^~~~~~
rma_background4.c:482:13: note: ‘PMcopy’ was declared here
482 | SEXP dim1,PMcopy;
| ^~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c rma_common.c -o rma_common.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/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=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic -g -O2 -Wall -Werror=format-security -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -shared -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/rapidbuild/bbs-3.21-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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) (2025-01-20 r87609) -- "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)
-0.01396 1.00553
>
>
>
> 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] 46.47938
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 45.5225
>
>
> 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
8.2537 9.2409
as.factor(cp)3 as.factor(cp)4
10.1882 11.2103
as.factor(cp)5 as.factor(cp)6
12.2558 10.1991
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
3.7565 2.8349
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
1.7606 0.7775
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.2496 -2.2051
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-3.2517 -4.1900
>
>
> 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] 8.3499130 9.2006868 10.3306037 11.3144561 12.3888103 10.3139959
[7] 3.7446589 2.7708992 1.6516449 0.7645676 -2.3682444 -2.3408957
[13] -3.2096077 -1.0130228
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.0000000 1.0000000 1.0000000 0.8650891 1.0000000 1.0000000
[2,] 1.0000000 0.9405774 1.0000000 1.0000000 1.0000000 1.0000000
[3,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[4,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[5,] 1.0000000 0.3429128 0.3855095 1.0000000 0.7744882 1.0000000
[6,] 1.0000000 0.9512034 1.0000000 1.0000000 1.0000000 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8,] 0.1241502 0.1276704 0.1211603 0.1330528 0.1170340 0.1237615
$Residuals
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.363222137 0.11811281 -0.3594975 0.46362403 -0.017699518 0.2212302
[2,] -0.024526255 0.42666577 -0.1162335 0.03995250 0.065213161 -0.3657181
[3,] 0.090842701 0.06958577 0.1836716 -0.13012958 -0.037071816 -0.1768987
[4,] 0.296951083 -0.16044741 -0.2148606 -0.21634296 -0.072292269 0.3669922
[5,] 0.204106299 1.17021761 1.0408552 -0.30484845 -0.518235139 -0.3004330
[6,] 0.198513408 -0.42171903 0.3362512 -0.02054944 0.070887024 -0.1839616
[7,] -0.001379311 -0.02741950 0.1707023 -0.17043573 -0.008964411 0.0374967
[8,] -3.232260131 -3.14313874 -3.3120848 3.01592782 3.428874229 3.2424641
$StdErrors
[1] 0.2194573 0.2316211 0.2294157 0.2209443 0.2229561 0.2194738 0.2277440
[8] 0.2265503 0.2257145 0.2257145 0.2541660 0.2263986 0.2257145 0.5675690
$Scale
[1] 0.2984579
> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
[1] 8.0808924 8.9852291 10.0723734 10.9708467 12.1119197 10.0121425
[7] 4.0409669 3.0489394 1.9291553 0.9774811 -1.1312218 -2.4352988
[13] -2.0268273 -2.9320974 -3.9946144 2.5235171
$Weights
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.5396658 1.0000000 0.5300657 0.4123656 1 0.9288995
[2,] 1.0000000 0.5787699 1.0000000 1.0000000 1 0.6163017
[3,] 1.0000000 1.0000000 1.0000000 1.0000000 1 1.0000000
[4,] 0.5967985 1.0000000 1.0000000 1.0000000 1 0.4621404
[5,] 0.2758436 1.0000000 1.0000000 1.0000000 1 1.0000000
[6,] 1.0000000 0.4049442 0.7514425 1.0000000 1 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1 1.0000000
[8,] 1.0000000 1.0000000 1.0000000 1.0000000 1 1.0000000
$Residuals
[,1] [,2] [,3] [,4] [,5]
[1,] -0.390509542 0.037262582 -0.39757519 0.510925477 -0.037116883
[2,] -0.033545860 0.364083350 -0.13604342 0.105521738 0.064063595
[3,] 0.082352928 0.007533176 0.16439158 -0.064030502 -0.037691550
[4,] 0.353058159 -0.157903157 -0.16954386 -0.085647034 -0.008315154
[5,] -0.763895697 0.148652794 0.06206291 0.105815355 -0.174290141
[6,] 0.153465655 -0.520329601 0.28041318 0.008991657 0.033709310
[7,] -0.009869084 -0.089472096 0.15142220 -0.104336655 -0.009584145
[8,] 0.018352126 0.053910700 -0.07226283 -0.177002631 0.169224967
[,6]
[1,] 0.226775683
[2,] -0.341904817
[3,] -0.152555635
[4,] 0.455932133
[5,] 0.068474785
[6,] -0.196176529
[7,] 0.061839785
[8,] 0.007777664
$StdErrors
[1] 0.09534755 0.08692216 0.08686558 0.07989693 0.07300696 0.09702107
[7] 0.13585627 0.09778086 0.08003652 0.09647558 0.13986672 0.11447153
[13] 0.09966929 0.08003652 0.11497419 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
7.959 8.942
as.factor(cp)3 as.factor(cp)4
10.013 10.799
as.factor(cp)5 as.factor(cp)6
11.902 9.819
C(as.factor(pr), "contr.sum")1 C(as.factor(pr), "contr.sum")2
4.166 3.186
C(as.factor(pr), "contr.sum")3 C(as.factor(pr), "contr.sum")4
2.036 1.175
C(as.factor(pr), "contr.sum")5 C(as.factor(pr), "contr.sum")6
-1.742 -1.933
C(as.factor(pr), "contr.sum")7 C(as.factor(pr), "contr.sum")8
-2.799 -3.920
C(as.factor(pr), "contr.sum")9
2.715
>
>
> proc.time()
user system elapsed
0.918 0.087 0.996
preprocessCore.Rcheck/tests/qnormtest.Rout
R Under development (unstable) (2025-01-20 r87609) -- "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
0.107 0.062 0.152
preprocessCore.Rcheck/preprocessCore-Ex.timings
| name | user | system | elapsed | |
| colSummarize | 0.000 | 0.002 | 0.002 | |
| normalize.quantiles.in.blocks | 0.020 | 0.001 | 0.021 | |
| rcModelPLMd | 0.009 | 0.001 | 0.010 | |
| rcModelPLMr | 0.020 | 0.001 | 0.021 | |
| rcModels | 0.002 | 0.002 | 0.004 | |
| subColSummarize | 0.002 | 0.000 | 0.004 | |
| subrcModels | 0.005 | 0.001 | 0.006 | |