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CHECK report for preprocessCore on celaya2

This page was generated on 2019-04-09 12:46:40 -0400 (Tue, 09 Apr 2019).

Package 1221/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.45.0
Ben Bolstad
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/preprocessCore
Branch: master
Last Commit: 59d073d
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: preprocessCore
Version: 1.45.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings preprocessCore_1.45.0.tar.gz
StartedAt: 2019-04-09 04:31:42 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:32:15 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 32.8 seconds
RetCode: 0
Status:  OK 
CheckDir: preprocessCore.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings preprocessCore_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/preprocessCore.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.45.0’
* 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 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.



Installation output

preprocessCore.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘preprocessCore’ ...
** using staged installation
checking for gcc... clang
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 accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -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
configure: Enabling threading for preprocessCore
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c R_colSummarize.c -o R_colSummarize.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c R_plmd_interfaces.c -o R_plmd_interfaces.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c R_plmr_interfaces.c -o R_plmr_interfaces.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c R_rlm_interfaces.c -o R_rlm_interfaces.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c:105:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:103:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:99:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:97:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:273:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:271:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:265:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:267:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:444:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:436:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:438:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:442:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:614:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:616:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:610:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:608:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:785:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:787:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:779:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:781:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:951:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:953:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:957:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:959:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1129:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1127:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1121:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:1123:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1298:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1290:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:1292:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1296:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1466:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1472:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1470:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1647:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1645:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1641:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1639:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subColSummarize.c:1639:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subColSummarize.c:1603:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function]
static void *subColSummarize_medianpolish_group(void *data){
             ^
41 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:64:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:79:11: warning: unused variable 'weights' [-Wunused-variable]
  double *weights;
          ^
R_subrcModel_interfaces.c:80:11: warning: unused variable 'se' [-Wunused-variable]
  double *se;
          ^
R_subrcModel_interfaces.c:64:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:156:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subrcModel_interfaces.c:154:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subrcModel_interfaces.c:154:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subrcModel_interfaces.c:154:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:162:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:160:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:382:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=-1.0;
         ^
R_subrcModel_interfaces.c:361:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:361:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:469:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subrcModel_interfaces.c:469:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subrcModel_interfaces.c:469:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:477:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:475:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:471:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
19 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c avg.c -o avg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c avg_log.c -o avg_log.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c biweight.c -o biweight.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c init_package.c -o init_package.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c lm.c -o lm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c log_avg.c -o log_avg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c log_median.c -o log_median.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c matrix_functions.c -o matrix_functions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c median.c -o median.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c median_log.c -o median_log.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c medianpolish.c -o medianpolish.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c plmd.c -o plmd.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c psi_fns.c -o psi_fns.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c qnorm.c -o qnorm.o
qnorm.c:1882:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,row_mean_ind;
           ^
qnorm.c:1887:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na;
      ^
qnorm.c:2074:14: 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:1448:19: note: expanded from macro 'isMatrix'
#define isMatrix                Rf_isMatrix
                                ^
qnorm.c:2087:55: note: uninitialized use occurs here
  qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
                                                      ^˜˜˜˜˜˜˜˜˜˜
qnorm.c:2074:10: note: remove the 'if' if its condition is always true
  } else if (isMatrix(target)){
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
qnorm.c:2055:21: note: initialize the variable 'target_rows' to silence this warning
  size_t target_rows, target_cols;
                    ^
                     = 0
qnorm.c:2476:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,row_mean_ind;
           ^
qnorm.c:2481:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na;
      ^
qnorm.c:2790:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
  double *sample_percentiles;
          ^
qnorm.c:2791:11: warning: unused variable 'datvec' [-Wunused-variable]
  double *datvec;
          ^
qnorm.c:2924:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,ind,target_ind;
           ^
qnorm.c:2924:14: warning: unused variable 'ind' [-Wunused-variable]
  size_t i,j,ind,target_ind;
             ^
qnorm.c:2924:18: warning: unused variable 'target_ind' [-Wunused-variable]
  size_t i,j,ind,target_ind;
                 ^
qnorm.c:2926:14: warning: unused variable 'dimat' [-Wunused-variable]
  dataitem **dimat;
             ^
qnorm.c:2928:11: warning: unused variable 'row_mean' [-Wunused-variable]
  double *row_mean = target;
          ^
qnorm.c:2930:11: warning: unused variable 'ranks' [-Wunused-variable]
  double *ranks = (double *)Calloc((rows),double);
          ^
qnorm.c:2931:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
  double samplepercentile;
         ^
qnorm.c:2932:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
  double target_ind_double,target_ind_double_floor;
         ^
qnorm.c:2932:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
  double target_ind_double,target_ind_double_floor;
                           ^
qnorm.c:2934:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
  int targetnon_na = targetrows;
      ^
qnorm.c:2935:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na = 0;
      ^
qnorm.c:2939:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
  double *sample_percentiles;
          ^
qnorm.c:2940:11: warning: unused variable 'datvec' [-Wunused-variable]
  double *datvec;
          ^
qnorm.c:3191:14: 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:1448:19: note: expanded from macro 'isMatrix'
#define isMatrix                Rf_isMatrix
                                ^
qnorm.c:3205:77: note: uninitialized use occurs here
  qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
                                                                            ^˜˜˜˜˜˜˜˜˜˜
qnorm.c:3191:10: note: remove the 'if' if its condition is always true
  } else if (isMatrix(target)){
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
qnorm.c:3172:21: note: initialize the variable 'target_rows' to silence this warning
  size_t target_rows, target_cols;
                    ^
                     = 0
21 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c rlm.c -o rlm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -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:1426:10: warning: unused variable 'vs' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
         ^
rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=0.0;
         ^
rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
  double Kappa=0.0;      /* A correction factor */
         ^
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
  double sumderivpsi=0.0; /* sum of psi'(r_i) */
         ^
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:1426:19: warning: unused variable 'varderivpsi' [-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:1505:10: warning: unused variable 'endprobe' [-Wunused-variable]
  double endprobe;
         ^
10 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c rlm_se.c -o rlm_se.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c rma_background4.c -o rma_background4.o
rma_background4.c:343:10: warning: unused variable 'param' [-Wunused-variable]
  double param[3];
         ^
rma_background4.c:342:10: warning: unused variable 'j' [-Wunused-variable]
  size_t j;
         ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -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  -Wall -g -O2  -c weightedkerneldensity.c -o weightedkerneldensity.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
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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)  
     0.007889       0.938996  

> 
> 
> 
> 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] 45.75841
> sum((resid(lm(values ˜ as.factor(group.labels)))/sc)^2)/2
[1] 45.65322
> 
> 
> 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  
                        8.2549                          9.1971  
                as.factor(cp)3                  as.factor(cp)4  
                       10.2590                         11.1794  
                as.factor(cp)5                  as.factor(cp)6  
                       12.1873                         10.2454  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                        3.7824                          2.8139  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                        1.7637                          0.7443  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                       -1.2414                         -2.2535  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                       -3.2162                         -4.2505  

> 
> 
> 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]  8.1943866  9.4109684 10.2810779 11.3441021 12.2993311 10.3404033
 [7]  3.7282507  2.7166761  1.6191034  0.7680941 -2.1052546 -2.3813877
[13] -3.2031176 -1.1423645

$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 0.8201588 1.0000000 1.0000000
[3,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[4,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[5,] 0.3664093 0.5497321 0.4253477 0.3680185 0.3764994 0.6356233
[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,] 0.1215289 0.1070833 0.1216735 0.1103593 0.1198504 0.1195546

$Residuals
            [,1]        [,2]        [,3]        [,4]        [,5]        [,6]
[1,] -0.26511359  0.15699874 -0.09231242  0.18207991  0.04602878 -0.02768143
[2,]  0.08568506 -0.20517410  0.03238754 -0.47034456  0.16027404  0.31258467
[3,] -0.32478690  0.11195752  0.07146182 -0.08591074  0.21701677  0.01026153
[4,]  0.22513242 -0.09557231 -0.04093793  0.25163195 -0.24098856 -0.09926557
[5,]  1.05361266  0.70224357  0.90761421 -1.04884287 -1.02543527 -0.60740629
[6,] -0.08116024  0.07550836  0.15194653  0.06858001 -0.28370812  0.06883346
[7,]  0.36025925 -0.04369479 -0.12252772 -0.03071625  0.10139182 -0.26471232
[8,] -3.17676961 -3.60531664 -3.17299451  3.49844448  3.22119127  3.22916412

$StdErrors
 [1] 0.2327173 0.2297511 0.2314833 0.2360655 0.2325831 0.2276258 0.2299724
 [8] 0.2326192 0.2299724 0.2299724 0.3168035 0.2299724 0.2299724 0.5911156

$Scale
[1] 0.2870675

> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
 [1]  7.9231801  9.0242840  9.9741044 11.0423966 11.9444383 10.0384219
 [7]  4.0596260  3.0648901  1.9624130  1.0886681 -0.8958096 -2.6838541
[13] -2.0608137 -2.8894452 -4.1391033  2.4934286

$Weights
          [,1] [,2] [,3]      [,4] [,5]      [,6]
[1,] 0.8007651    1    1 1.0000000    1 1.0000000
[2,] 1.0000000    1    1 0.5040227    1 0.9777734
[3,] 0.6562938    1    1 1.0000000    1 1.0000000
[4,] 1.0000000    1    1 1.0000000    1 1.0000000
[5,] 1.0000000    1    1 1.0000000    1 0.9535330
[6,] 1.0000000    1    1 1.0000000    1 1.0000000
[7,] 0.8196712    1    1 1.0000000    1 0.9424840
[8,] 1.0000000    1    1 1.0000000    1 1.0000000

$Residuals
             [,1]        [,2]         [,3]        [,4]        [,5]        [,6]
[1,] -0.325282283  0.21230786 -0.116714196  0.15241009  0.06954629 -0.05707535
[2,]  0.008677641 -0.16670371 -0.008852967 -0.51685312  0.16695282  0.26635203
[3,] -0.396889918  0.15533231  0.035125715 -0.12751488  0.22859995 -0.03106671
[4,]  0.175764985 -0.02946193 -0.054538442  0.23276339 -0.20666979 -0.11785822
[5,]  0.115374269 -0.12051701  0.005142739 -0.16853794 -0.09194301  0.27317454
[6,] -0.130527673  0.14161875  0.138346019  0.04971145 -0.24938935  0.05024081
[7,]  0.317793436  0.02931721 -0.129226616 -0.04268319  0.14261220 -0.27640336
[8,]  0.091175732 -0.22189348  0.130717749  0.16435678 -0.05970911 -0.10464767

$StdErrors
 [1] 0.10352681 0.07851555 0.07851555 0.08500991 0.07808090 0.10223565
 [7] 0.09333856 0.10450655 0.09333856 0.08547107 0.12239537 0.14698058
[13] 0.08547107 0.10291365 0.12239537 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  
                         8.016                           9.033  
                as.factor(cp)3                  as.factor(cp)4  
                        10.012                          10.748  
                as.factor(cp)5                  as.factor(cp)6  
                        11.682                           9.776  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                         4.162                           3.136  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                         2.259                           1.202  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                        -1.674                          -1.947  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                        -2.769                          -4.186  
C(as.factor(pr), "contr.sum")9  
                         2.766  

> 
> 
> proc.time()
   user  system elapsed 
  2.680   0.243   2.871 

preprocessCore.Rcheck/tests/qnormtest.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)")
+ }
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.300   0.128   0.372 

Example timings

preprocessCore.Rcheck/preprocessCore-Ex.timings

nameusersystemelapsed
colSummarize0.0040.0020.006
normalize.quantiles.in.blocks0.0610.0040.065
rcModelPLMd0.0220.0060.028
rcModelPLMr0.0380.0070.047
rcModels0.0170.0190.036
subColSummarize0.0080.0040.013
subrcModels0.0230.0240.046