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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1589/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.68.0  (landing page)
Ben Bolstad
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/preprocessCore
git_branch: RELEASE_3_20
git_last_commit: fa0e33e
git_last_commit_date: 2024-10-29 09:21:09 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for preprocessCore on kjohnson1

To the developers/maintainers of the preprocessCore package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preprocessCore.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: preprocessCore
Version: 1.68.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preprocessCore_1.68.0.tar.gz
StartedAt: 2024-12-21 05:12:13 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 05:12:37 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 24.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: preprocessCore.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preprocessCore_1.68.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/preprocessCore.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.68.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘preprocessCore’ can be installed ... WARNING
Found the following significant warnings:
  qnorm.c:596:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  qnorm.c:617:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  qnorm.c:2005:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  qnorm.c:2605:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/preprocessCore.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (-1) colSummarize.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colSummarize.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (7) normalize.quantiles.Rd:47: Invalid email address: bmbolstad.com
checkRd: (7) rma.background.correct.Rd:35: Invalid email address: bmbolstad.com
checkRd: (-1) subColSummarize.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subColSummarize.Rd:61-63: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘PLMdtest.R’
  Running ‘qnormtest.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.


Installation output

preprocessCore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘preprocessCore’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch arm64
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 clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c R_colSummarize.c -o R_colSummarize.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c R_plmd_interfaces.c -o R_plmd_interfaces.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c R_plmr_interfaces.c -o R_plmr_interfaces.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c R_rlm_interfaces.c -o R_rlm_interfaces.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c:109:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:111:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:115:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:117:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:282:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:284:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:288:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:290:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:458:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:460:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:464:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:466:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:635:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:637:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:641:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:643:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:811:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:813:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:817:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:819:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:988:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:990:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:994:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:996:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1163:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:1165:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1169:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1171:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1337:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:1339:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1343:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1345:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1516:21: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subColSummarize.c:1516:30: warning: variable 'buffer2' set but not used [-Wunused-but-set-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subColSummarize.c:1518:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1522:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1524:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1696:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subColSummarize.c:1696:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subColSummarize.c:1698:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1702:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1704:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1660:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function]
static void *subColSummarize_medianpolish_group(void *data){
             ^
43 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:75:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:75:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:90:11: warning: unused variable 'weights' [-Wunused-variable]
  double *weights;
          ^
R_subrcModel_interfaces.c:91:11: warning: unused variable 'se' [-Wunused-variable]
  double *se;
          ^
R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subrcModel_interfaces.c:167:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subrcModel_interfaces.c:171:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:173:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:377:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:377:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:398:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=-1.0;
         ^
R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subrcModel_interfaces.c:487:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subrcModel_interfaces.c:491:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:493:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
19 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c avg.c -o avg.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c avg_log.c -o avg_log.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c biweight.c -o biweight.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c init_package.c -o init_package.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c lm.c -o lm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c log_avg.c -o log_avg.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c log_median.c -o log_median.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c matrix_functions.c -o matrix_functions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c median.c -o median.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c median_log.c -o median_log.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c medianpolish.c -o medianpolish.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c plmd.c -o plmd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c plmr.c -o plmr.o
plmr.c:82:13: warning: unused function 'XTWY_R' [-Wunused-function]
static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){
            ^
plmr.c:152:13: warning: unused function 'XTWX_R' [-Wunused-function]
static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){
            ^
plmr.c:279:13: warning: unused function 'XTWX_R_inv' [-Wunused-function]
static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c psi_fns.c -o psi_fns.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c qnorm.c -o qnorm.o
qnorm.c:596:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
qnorm.c:617:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
qnorm.c:2005:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
qnorm.c:1905:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,row_mean_ind;
           ^
qnorm.c:1910:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na;
      ^
qnorm.c:2102:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (isMatrix(target)){
             ^~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:945:19: note: expanded from macro 'isMatrix'
#define isMatrix                Rf_isMatrix
                                ^
qnorm.c:2115:55: note: uninitialized use occurs here
  qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
                                                      ^~~~~~~~~~~
qnorm.c:2102:10: note: remove the 'if' if its condition is always true
  } else if (isMatrix(target)){
         ^~~~~~~~~~~~~~~~~~~~~
qnorm.c:2083:21: note: initialize the variable 'target_rows' to silence this warning
  size_t target_rows, target_cols;
                    ^
                     = 0
qnorm.c:2605:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
qnorm.c:2504:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,row_mean_ind;
           ^
qnorm.c:2509:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na;
      ^
qnorm.c:2725:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable]
  size_t i,j,ind,target_ind;
             ^
qnorm.c:2823:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
  double *sample_percentiles;
          ^
qnorm.c:2824:11: warning: unused variable 'datvec' [-Wunused-variable]
  double *datvec;
          ^
qnorm.c:2957:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,ind,target_ind;
           ^
qnorm.c:2957:14: warning: unused variable 'ind' [-Wunused-variable]
  size_t i,j,ind,target_ind;
             ^
qnorm.c:2957:18: warning: unused variable 'target_ind' [-Wunused-variable]
  size_t i,j,ind,target_ind;
                 ^
qnorm.c:2959:14: warning: unused variable 'dimat' [-Wunused-variable]
  dataitem **dimat;
             ^
qnorm.c:2961:11: warning: unused variable 'row_mean' [-Wunused-variable]
  double *row_mean = target;
          ^
qnorm.c:2963:11: warning: unused variable 'ranks' [-Wunused-variable]
  double *ranks = (double *)R_Calloc((rows),double);
          ^
qnorm.c:2964:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
  double samplepercentile;
         ^
qnorm.c:2965:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
  double target_ind_double,target_ind_double_floor;
         ^
qnorm.c:2965:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
  double target_ind_double,target_ind_double_floor;
                           ^
qnorm.c:2967:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
  int targetnon_na = targetrows;
      ^
qnorm.c:2968:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na = 0;
      ^
qnorm.c:2972:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
  double *sample_percentiles;
          ^
qnorm.c:2973:11: warning: unused variable 'datvec' [-Wunused-variable]
  double *datvec;
          ^
qnorm.c:3228:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (isMatrix(target)){
             ^~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:945:19: note: expanded from macro 'isMatrix'
#define isMatrix                Rf_isMatrix
                                ^
qnorm.c:3242:77: note: uninitialized use occurs here
  qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
                                                                            ^~~~~~~~~~~
qnorm.c:3228:10: note: remove the 'if' if its condition is always true
  } else if (isMatrix(target)){
         ^~~~~~~~~~~~~~~~~~~~~
qnorm.c:3209:21: note: initialize the variable 'target_rows' to silence this warning
  size_t target_rows, target_cols;
                    ^
                     = 0
26 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c rlm.c -o rlm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c rlm_anova.c -o rlm_anova.o
rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable]
  double endprobe;
         ^
rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable]
  double k1 = psi_k;   /*  was 1.345; */
         ^
rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable]
  double sumpsi2=0.0;  /* sum of psi(r_i)^2 */
         ^
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
  double sumderivpsi=0.0; /* sum of psi'(r_i) */
         ^
rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
  double Kappa=0.0;      /* A correction factor */
         ^
rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=0.0;
         ^
rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
         ^
rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
                ^
rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
                  ^
rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable]
  double endprobe;
         ^
10 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c rlm_se.c -o rlm_se.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c rma_background4.c -o rma_background4.o
rma_background4.c:354:10: warning: unused variable 'j' [-Wunused-variable]
  size_t j;
         ^
rma_background4.c:355:10: warning: unused variable 'param' [-Wunused-variable]
  double param[3];
         ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -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  -falign-functions=64 -Wall -g -O2  -c weightedkerneldensity.c -o weightedkerneldensity.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-preprocessCore/00new/preprocessCore/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (preprocessCore)

Tests output

preprocessCore.Rcheck/tests/PLMdtest.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> 
> library(preprocessCore)
> 
> 
> values <- rnorm(100)
> group.labels <- sample(0:4,replace=TRUE, 100)
> 
> results <- double(10000)
> ngroups <- 2
> 
> 
> for (i in 1:10000){
+        values <- rnorm(100,sd=1)
+        values <- values/sd(values)
+        group.labels <- sample(0:(ngroups-1),replace=TRUE, 100)
+        blah <- .C("R_split_test",as.double(values), as.integer(100), as.integer(ngroups), as.integer(group.labels),double(1))
+        results[i] <- blah[[5]]
+ }
> 
> plot(sort(results),qchisq(0:9999/10000,ngroups-1))
> lm(qchisq(0:9999/10000,ngroups-1) ~ sort(results))

Call:
lm(formula = qchisq(0:9999/10000, ngroups - 1) ~ sort(results))

Coefficients:
  (Intercept)  sort(results)  
      0.01273        0.94872  

> 
> 
> 
> 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] 64.82679
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 62.99219
> 
> 
> 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  
                        8.2719                          9.2154  
                as.factor(cp)3                  as.factor(cp)4  
                       10.2359                         11.1997  
                as.factor(cp)5                  as.factor(cp)6  
                       12.1804                         10.1889  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                        3.8520                          2.7966  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                        1.7829                          0.8126  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                       -1.2427                         -2.2857  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                       -3.2872                         -4.2734  

> 
> 
> 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]  8.1465421  9.1417394 10.2514444 11.3236454 12.3620341 10.3171302
 [7]  3.6574090  2.7139582  1.7144681  0.6953611 -2.1657090 -2.3300785
[13] -3.3193543 -0.9660546

$Weights
          [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
[1,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[2,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[3,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[4,] 0.9227775 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[5,] 0.5251687 0.7277584 0.5567466 0.8490288 0.5418417 0.4565556
[6,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8,] 0.1399623 0.1468931 0.1225845 0.1369768 0.1307803 0.1395947

$Residuals
            [,1]        [,2]        [,3]         [,4]       [,5]        [,6]
[1,]  0.15988354  0.24281301  0.02577627  0.065537888 -0.3144293 -0.17958145
[2,]  0.33644427 -0.25089613 -0.31945055 -0.001886999 -0.1853168  0.42110619
[3,] -0.11729824  0.02024319 -0.14488964 -0.165525113  0.3231028  0.08436705
[4,] -0.49637816  0.01327358  0.18407187  0.111008872  0.1993787 -0.04968641
[5,]  0.87135953  0.62895340  0.82214415 -0.539049509 -0.8447027 -1.00250475
[6,] -0.07932519 -0.05334974  0.15687131 -0.234130693  0.2471831 -0.03724882
[7,]  0.15847065  0.02789919  0.09760394  0.224943487 -0.2699416 -0.23897563
[8,] -3.27044635 -3.11593452 -3.73382685  3.341594882  3.4999024  3.27890810

$StdErrors
 [1] 0.2483163 0.2429977 0.2472353 0.2414233 0.2471488 0.2484624 0.2467505
 [8] 0.2467505 0.2467505 0.2479784 0.3015338 0.2467505 0.2467505 0.5960181

$Scale
[1] 0.340307

> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
 [1]  7.888172  8.843507  9.904229 11.034267 12.055190  9.931079  3.977633
 [8]  2.981276  2.024207  1.054006 -1.090284 -2.633703 -2.015730 -3.005006
[15] -4.027238  2.734838

$Weights
          [,1] [,2]      [,3] [,4]      [,5]      [,6]
[1,] 1.0000000    1 1.0000000    1 0.8924666 1.0000000
[2,] 0.8933902    1 1.0000000    1 1.0000000 0.5419548
[3,] 1.0000000    1 1.0000000    1 0.9136215 1.0000000
[4,] 0.4903089    1 1.0000000    1 1.0000000 1.0000000
[5,] 1.0000000    1 1.0000000    1 1.0000000 1.0000000
[6,] 1.0000000    1 1.0000000    1 1.0000000 1.0000000
[7,] 1.0000000    1 1.0000000    1 1.0000000 1.0000000
[8,] 1.0000000    1 0.8990874    1 1.0000000 1.0000000

$Residuals
            [,1]         [,2]        [,3]        [,4]        [,5]        [,6]
[1,]  0.09802981  0.220822096  0.05276806  0.03469269 -0.32780883 -0.11375422
[2,]  0.32749648 -0.219981118 -0.23955284  0.02017373 -0.14579043  0.53983935
[3,] -0.16866705  0.008737184 -0.10741293 -0.18588539  0.32020810  0.16067919
[4,] -0.59665300 -0.047138462  0.17264254  0.04174255  0.14757798 -0.02228031
[5,]  0.05430440 -0.148238926  0.09393453  0.21832345 -0.06986408 -0.14845937
[6,] -0.13530385 -0.069465592  0.18973817 -0.25910082  0.23967861  0.03445348
[7,]  0.10249200  0.011783338  0.13047080  0.19997336 -0.27744615 -0.16727334
[8,]  0.04910684  0.243481480 -0.32542814 -0.06991958  0.10585351 -0.03593393

$StdErrors
 [1] 0.09897781 0.08325680 0.09013912 0.08381997 0.09922008 0.09044882
 [7] 0.09921756 0.11089897 0.09921756 0.09955576 0.12935256 0.12996480
[13] 0.09072542 0.09072542 0.15809406 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  
                         7.913                           8.887  
                as.factor(cp)3                  as.factor(cp)4  
                         9.942                          10.800  
                as.factor(cp)5                  as.factor(cp)6  
                        11.820                           9.727  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                         4.066                           3.123  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                         2.347                           1.098  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                        -1.767                          -1.921  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                        -2.910                          -4.074  
C(as.factor(pr), "contr.sum")9  
                         2.960  

> 
> 
> proc.time()
   user  system elapsed 
  1.968   0.114   2.101 

preprocessCore.Rcheck/tests/qnormtest.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(preprocessCore)
> 
> err.tol <- 10^-8
> 
> x <- matrix(c(100,15,200,250,110,16.5,220,275,120,18,240,300),ncol=3)
> x
     [,1]  [,2] [,3]
[1,]  100 110.0  120
[2,]   15  16.5   18
[3,]  200 220.0  240
[4,]  250 275.0  300
> normalize.quantiles(x)
      [,1]  [,2]  [,3]
[1,] 110.0 110.0 110.0
[2,]  16.5  16.5  16.5
[3,] 220.0 220.0 220.0
[4,] 275.0 275.0 275.0
> 
> x.norm.truth <- matrix(rep(c(110.0,16.5,220,275.0),3),ncol=3)
> 
> if (all(abs(x.norm.truth - normalize.quantiles(x)) < err.tol) != TRUE){
+ 	stop("Disagreement in normalize.quantiles(x)")
+ }
> 
> normalize.quantiles.determine.target(x)
[1]  16.5 110.0 220.0 275.0
> 
> x.norm.target.truth <- c(16.5,110.0,220.0,275.0)
> 
> if (all(abs(x.norm.target.truth - normalize.quantiles.determine.target(x)) < err.tol) != TRUE){
+ 	stop("Disagreement in normalize.quantiles.determine.target(x)")
+ }
> 
> 
> y <- x
> y[2,2] <- NA
> y
     [,1] [,2] [,3]
[1,]  100  110  120
[2,]   15   NA   18
[3,]  200  220  240
[4,]  250  275  300
> normalize.quantiles(y)
          [,1]      [,2]      [,3]
[1,] 134.44444  47.66667 134.44444
[2,]  47.66667        NA  47.66667
[3,] 226.11111 180.27778 226.11111
[4,] 275.00000 275.00000 275.00000
> 
> y.norm.target.truth <- c(47.6666666666667,134.4444444444444,226.1111111111111,275.0000000000000)
> 
> y.norm.truth <- matrix(c(134.4444444444444,  47.6666666666667, 134.4444444444444,
+                          47.6666666666667,                NA,  47.6666666666667,
+                         226.1111111111111, 180.2777777777778, 226.1111111111111,
+                         275.0000000000000, 275.0000000000000, 275.0000000000000),byrow=TRUE,ncol=3)
> 
> 
> if (all(abs(y.norm.truth - normalize.quantiles(y)) < err.tol,na.rm=TRUE) != TRUE){
+ 	stop("Disagreement in normalize.quantiles(y)")
+ }
> 
> 
> 
> if (all(abs(y.norm.target.truth - normalize.quantiles.determine.target(y)) < err.tol) != TRUE){
+ 	stop("Disagreement in normalize.quantiles.determine.target(y)")
+ }
> 
> 
> 
> if (all(abs(normalize.quantiles.use.target(y,y.norm.target.truth) - y.norm.truth) < err.tol,na.rm=TRUE) != TRUE){
+ 		stop("Disagreement in normalize.quantiles.use.target(y)")
+ }
> 
> 
> x <- matrix(c(100,15,200,250,110,16.5,220,275,120,18,240,300),ncol=3)
> rownames(x) <- letters[1:4]
> colnames(x) <- LETTERS[1:3]
> y <- normalize.quantiles(x, keep.names = TRUE)
> if(!all(colnames(x)==colnames(y))){
+     stop("Disagreement between initial and final column names despite keep.names=TRUE")
+ }
> if(!all(rownames(x)==rownames(y))){
+     stop("Disagreement between initial and final row names despite keep.names=TRUE")
+ }
> 
> proc.time()
   user  system elapsed 
  0.226   0.064   0.275 

Example timings

preprocessCore.Rcheck/preprocessCore-Ex.timings

nameusersystemelapsed
colSummarize0.0020.0020.004
normalize.quantiles.in.blocks0.0330.0020.035
rcModelPLMd0.0160.0030.019
rcModelPLMr0.0320.0060.037
rcModels0.0040.0080.012
subColSummarize0.0030.0020.005
subrcModels0.0050.0110.016