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This page was generated on 2022-10-19 13:20:41 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for preprocessCore on nebbiolo1


To the developers/maintainers of the preprocessCore package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1491/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.58.0  (landing page)
Ben Bolstad
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/preprocessCore
git_branch: RELEASE_3_15
git_last_commit: 2995e3e
git_last_commit_date: 2022-04-26 10:54:40 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: preprocessCore
Version: 1.58.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings preprocessCore_1.58.0.tar.gz
StartedAt: 2022-10-18 21:12:24 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:12:41 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 17.7 seconds
RetCode: 0
Status:   OK  
CheckDir: preprocessCore.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings preprocessCore_1.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/preprocessCore.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.58.0’
* 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 ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘PLMdtest.R’
  Running ‘qnormtest.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.



Installation output

preprocessCore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘preprocessCore’ ...
** 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... -lpthread
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
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c R_colSummarize.c -o R_colSummarize.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -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;
      |                     ^~~~~~
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/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -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/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c avg.c -o avg.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c avg_log.c -o avg_log.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c biweight.c -o biweight.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c init_package.c -o init_package.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c lm.c -o lm.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c log_avg.c -o log_avg.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c log_median.c -o log_median.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c median.c -o median.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c median_log.c -o median_log.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c medianpolish.c -o medianpolish.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c plmd.c -o plmd.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -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/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c psi_fns.c -o psi_fns.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c qnorm.c -o qnorm.o
qnorm.c: In function ‘qnorm_c_determine_target_l’:
qnorm.c:1910:7: warning: unused variable ‘non_na’ [-Wunused-variable]
 1910 |   int non_na;
      |       ^~~~~~
qnorm.c:1905:12: warning: unused variable ‘j’ [-Wunused-variable]
 1905 |   size_t i,j,row_mean_ind;
      |            ^
qnorm.c: In function ‘qnorm_c_determine_target_via_subset_l’:
qnorm.c:2509:7: warning: unused variable ‘non_na’ [-Wunused-variable]
 2509 |   int non_na;
      |       ^~~~~~
qnorm.c:2504:12: warning: unused variable ‘j’ [-Wunused-variable]
 2504 |   size_t i,j,row_mean_ind;
      |            ^
qnorm.c: In function ‘using_target_via_subset_part1’:
qnorm.c:2725:14: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
 2725 |   size_t i,j,ind,target_ind;
      |              ^~~
qnorm.c: In function ‘using_target_via_subset_part2’:
qnorm.c:2824:11: warning: unused variable ‘datvec’ [-Wunused-variable]
 2824 |   double *datvec;
      |           ^~~~~~
qnorm.c:2823:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
 2823 |   double *sample_percentiles;
      |           ^~~~~~~~~~~~~~~~~~
qnorm.c: In function ‘using_target_via_subset’:
qnorm.c:2973:11: warning: unused variable ‘datvec’ [-Wunused-variable]
 2973 |   double *datvec;
      |           ^~~~~~
qnorm.c:2972:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
 2972 |   double *sample_percentiles;
      |           ^~~~~~~~~~~~~~~~~~
qnorm.c:2968:7: warning: unused variable ‘non_na’ [-Wunused-variable]
 2968 |   int non_na = 0;
      |       ^~~~~~
qnorm.c:2967:7: warning: unused variable ‘targetnon_na’ [-Wunused-variable]
 2967 |   int targetnon_na = targetrows;
      |       ^~~~~~~~~~~~
qnorm.c:2965:28: warning: unused variable ‘target_ind_double_floor’ [-Wunused-variable]
 2965 |   double target_ind_double,target_ind_double_floor;
      |                            ^~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2965:10: warning: unused variable ‘target_ind_double’ [-Wunused-variable]
 2965 |   double target_ind_double,target_ind_double_floor;
      |          ^~~~~~~~~~~~~~~~~
qnorm.c:2964:10: warning: unused variable ‘samplepercentile’ [-Wunused-variable]
 2964 |   double samplepercentile;
      |          ^~~~~~~~~~~~~~~~
qnorm.c:2963:11: warning: unused variable ‘ranks’ [-Wunused-variable]
 2963 |   double *ranks = (double *)Calloc((rows),double);
      |           ^~~~~
qnorm.c:2961:11: warning: unused variable ‘row_mean’ [-Wunused-variable]
 2961 |   double *row_mean = target;
      |           ^~~~~~~~
qnorm.c:2959:14: warning: unused variable ‘dimat’ [-Wunused-variable]
 2959 |   dataitem **dimat;
      |              ^~~~~
qnorm.c:2957:18: warning: unused variable ‘target_ind’ [-Wunused-variable]
 2957 |   size_t i,j,ind,target_ind;
      |                  ^~~~~~~~~~
qnorm.c:2957:14: warning: unused variable ‘ind’ [-Wunused-variable]
 2957 |   size_t i,j,ind,target_ind;
      |              ^~~
qnorm.c:2957:12: warning: unused variable ‘j’ [-Wunused-variable]
 2957 |   size_t i,j,ind,target_ind;
      |            ^
qnorm.c: In function ‘R_qnorm_using_target’:
qnorm.c:2115:3: warning: ‘target_rows’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2115 |   qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c: In function ‘R_qnorm_using_target_via_subset’:
qnorm.c:3242:3: warning: ‘target_rows’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3242 |   qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c rlm.c -o rlm.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -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/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c rlm_se.c -o rlm_se.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -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 in this function [-Wmaybe-uninitialized]
  509 |     return PMcopy;
      |            ^~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c rma_common.c -o rma_common.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -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 -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -shared -L/home/biocbuild/bbs-3.15-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 -lpthread -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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)

Tests output

preprocessCore.Rcheck/tests/PLMdtest.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 
> 
> 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)  
      0.02146        0.95297  

> 
> 
> 
> 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] 42.28799
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 40.81438
> 
> 
> 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  
                         8.198                           9.223  
                as.factor(cp)3                  as.factor(cp)4  
                        10.167                          11.172  
                as.factor(cp)5                  as.factor(cp)6  
                        12.187                          10.204  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                         3.821                           2.820  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                         1.708                           0.781  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                        -1.176                          -2.212  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                        -3.189                          -4.283  

> 
> 
> 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]  8.4035930  9.5311206 10.4112863 11.2312123 12.2963297 10.4791288
 [7]  3.6666282  2.7238468  1.8701628  0.6798219 -2.2498136 -2.2667618
[13] -3.2930789 -1.1308054

$Weights
          [,1]      [,2]       [,3]      [,4]      [,5]      [,6]
[1,] 1.0000000 0.5117924 1.00000000 1.0000000 1.0000000 1.0000000
[2,] 1.0000000 1.0000000 1.00000000 1.0000000 1.0000000 1.0000000
[3,] 1.0000000 1.0000000 0.34418794 1.0000000 1.0000000 1.0000000
[4,] 1.0000000 0.7054109 1.00000000 1.0000000 1.0000000 1.0000000
[5,] 0.4502060 0.4814897 0.52619464 0.4661818 0.3269713 0.7305919
[6,] 1.0000000 1.0000000 1.00000000 1.0000000 1.0000000 1.0000000
[7,] 1.0000000 0.9794170 1.00000000 1.0000000 1.0000000 1.0000000
[8,] 0.1142062 0.1138465 0.09738526 0.1023152 0.1111062 0.1110270

$Residuals
            [,1]         [,2]        [,3]        [,4]        [,5]         [,6]
[1,]  0.20555943 -0.663643135  0.21064476 -0.06300432 -0.09314861  0.079596221
[2,] -0.06967811 -0.008650741  0.02811006  0.03450664  0.13583124 -0.120119078
[3,] -0.09664276 -0.204519808 -0.98636033  0.25917466  0.13625735  0.245223892
[4,]  0.02961421  0.481064286 -0.13052877 -0.23778583  0.10280616 -0.103453789
[5,]  0.75424374  0.705028560  0.64540697 -0.72835783 -1.03847000 -0.464748816
[6,] -0.07231327 -0.125678540  0.21456201 -0.05292038  0.03139940  0.004950782
[7,]  0.00344887  0.346391822  0.01664147  0.06001757 -0.31315463 -0.106215333
[8,] -2.97316058 -2.982766814 -3.48662491  3.31875356  3.05616503  3.058346567

$StdErrors
 [1] 0.2143053 0.2264622 0.2244179 0.2145662 0.2167824 0.2098631 0.2207591
 [8] 0.2134811 0.2238719 0.2175867 0.2822532 0.2134811 0.2137425 0.5659904

$Scale
[1] 0.2526146

> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
 [1]  8.086441  9.189629 10.043288 10.920946 11.918003 10.160056  4.028486
 [8]  3.062898  2.226686  1.000070 -1.206040 -2.667796 -1.931779 -2.970977
[15] -3.891052  2.349505

$Weights
     [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
[1,]    1 0.3262755 1.0000000 1.0000000 1.0000000 1.0000000
[2,]    1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[3,]    1 1.0000000 0.2289363 1.0000000 1.0000000 1.0000000
[4,]    1 0.4443315 1.0000000 0.9007926 1.0000000 1.0000000
[5,]    1 1.0000000 1.0000000 1.0000000 0.9213926 0.8197914
[6,]    1 1.0000000 0.9013916 1.0000000 1.0000000 1.0000000
[7,]    1 0.6101943 1.0000000 1.0000000 0.8686135 1.0000000
[8,]    1 1.0000000 0.6228301 1.0000000 1.0000000 1.0000000

$Residuals
            [,1]         [,2]        [,3]          [,4]        [,5]        [,6]
[1,]  0.16085428 -0.684009221  0.21678517 -0.1145959995 -0.07667957  0.03681154
[2,] -0.09157690 -0.006210469  0.05705682  0.0057213129  0.17510664 -0.14009740
[3,] -0.13601352 -0.219551515 -0.97488555  0.2129173534  0.15806077  0.20777359
[4,]  0.02651875  0.502307891 -0.08277867 -0.2477678188  0.16088489 -0.10462878
[5,]  0.02762245  0.002746325 -0.03036877 -0.0001094096 -0.24216086  0.27230661
[6,] -0.09014319 -0.119169393  0.24757765 -0.0776368272  0.07474368 -0.01095867
[7,] -0.00150044  0.365781574  0.06253771  0.0481817274 -0.25692975 -0.10924418
[8,]  0.10423858  0.118971409 -0.35838020  0.1487092674 -0.04581854 -0.10289073

$StdErrors
 [1] 0.07661605 0.10010718 0.09941629 0.08164650 0.08997212 0.08279981
 [7] 0.09110676 0.08345153 0.09058124 0.10263594 0.11909789 0.19881963
[13] 0.09058124 0.10088077 0.14424366 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  
                         8.122                           9.264  
                as.factor(cp)3                  as.factor(cp)4  
                        10.095                          10.664  
                as.factor(cp)5                  as.factor(cp)6  
                        11.658                           9.913  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                         4.052                           3.163  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                         2.674                           1.143  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                        -1.831                          -1.827  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                        -2.852                          -3.990  
C(as.factor(pr), "contr.sum")9  
                         2.604  

> 
> 
> proc.time()
   user  system elapsed 
  1.730   0.064   1.778 

preprocessCore.Rcheck/tests/qnormtest.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

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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 
  0.177   0.032   0.193 

Example timings

preprocessCore.Rcheck/preprocessCore-Ex.timings

nameusersystemelapsed
colSummarize0.0000.0030.003
normalize.quantiles.in.blocks0.0310.0070.037
rcModelPLMd0.0210.0010.022
rcModelPLMr0.0320.0040.036
rcModels0.0070.0100.018
subColSummarize0.0000.0070.006
subrcModels0.0020.0210.023