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CHECK report for preprocessCore on malbec2

This page was generated on 2020-10-17 11:55:25 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE preprocessCore PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1347/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.50.0
Ben Bolstad
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/preprocessCore
Branch: RELEASE_3_11
Last Commit: 9230366
Last Changed Date: 2020-04-27 14:08:06 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: preprocessCore
Version: 1.50.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings preprocessCore_1.50.0.tar.gz
StartedAt: 2020-10-17 04:14:53 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:15:16 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 22.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: preprocessCore.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:preprocessCore.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings preprocessCore_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/preprocessCore.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.50.0’
* 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:
  'config' variable 'CPP' is deprecated
See ‘/home/biocbuild/bbs-3.11-bioc/meat/preprocessCore.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘PLMdtest.R’
  Running ‘qnormtest.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.

Installation output

preprocessCore.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘preprocessCore’ ...
** using staged installation
'config' variable 'CPP' is deprecated
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for library containing pthread_create... -lpthread
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c R_colSummarize.c -o R_colSummarize.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c:61:23: warning: extra tokens at end of #ifdef directive
 #ifdef __GLIBC_PREREQ && __GLIBC_PREREQ(2, 15)
                       ^~
R_subColSummarize.c: In function ‘R_subColSummarize_avg_log’:
R_subColSummarize.c:128:22: warning: implicit declaration of function ‘__pthread_get_minstack’; did you mean ‘pthread_attr_setstack’? [-Wimplicit-function-declaration]
   size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
                      ^~~~~~~~~~~~~~~~~~~~~~
                      pthread_attr_setstack
R_subColSummarize.c:115:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:113:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:109:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:107:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_log_avg’:
R_subColSummarize.c:288:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:286:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:282:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:280:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_avg’:
R_subColSummarize.c:464:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:462:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:458:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:456:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_biweight_log’:
R_subColSummarize.c:641:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:639:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:635:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:633:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_biweight’:
R_subColSummarize.c:817:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:815:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:811:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:809:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_median_log’:
R_subColSummarize.c:994:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:992:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:988:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:986:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_log_median’:
R_subColSummarize.c:1169:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:1167:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:1163:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:1161:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_median’:
R_subColSummarize.c:1343:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:1341:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:1337:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:1335:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish_log’:
R_subColSummarize.c:1522:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:1520:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:1516:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:1514:30: warning: variable ‘buffer2’ set but not used [-Wunused-but-set-variable]
   double *results, *buffer, *buffer2;
                              ^~~~~~~
R_subColSummarize.c:1514:21: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable]
   double *results, *buffer, *buffer2;
                     ^~~~~~
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish’:
R_subColSummarize.c:1702:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subColSummarize.c:1700:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subColSummarize.c:1696:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subColSummarize.c:1694:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
                              ^~~~~~~
R_subColSummarize.c:1694:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
                     ^~~~~~
At top level:
R_subColSummarize.c:1658:14: warning: ‘subColSummarize_medianpolish_group’ defined but not used [-Wunused-function]
 static void *subColSummarize_medianpolish_group(void *data){
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:57:23: warning: extra tokens at end of #ifdef directive
 #ifdef __GLIBC_PREREQ && __GLIBC_PREREQ(2, 15)
                       ^~
R_subrcModel_interfaces.c: In function ‘sub_rcModelSummarize_medianpolish_group’:
R_subrcModel_interfaces.c:89:11: warning: unused variable ‘se’ [-Wunused-variable]
   double *se;
           ^~
R_subrcModel_interfaces.c:88:11: warning: unused variable ‘weights’ [-Wunused-variable]
   double *weights;
           ^~~~~~~
R_subrcModel_interfaces.c:73:20: warning: unused variable ‘buffer2’ [-Wunused-variable]
   double *buffer, *buffer2;
                    ^~~~~~~
R_subrcModel_interfaces.c:73:11: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *buffer, *buffer2;
           ^~~~~~
R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_medianpolish’:
R_subrcModel_interfaces.c:184:22: warning: implicit declaration of function ‘__pthread_get_minstack’; did you mean ‘pthread_attr_setstack’? [-Wimplicit-function-declaration]
   size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
                      ^~~~~~~~~~~~~~~~~~~~~~
                      pthread_attr_setstack
R_subrcModel_interfaces.c:171:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subrcModel_interfaces.c:169:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subrcModel_interfaces.c:165:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subrcModel_interfaces.c:163:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
                              ^~~~~~~
R_subrcModel_interfaces.c:163:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
                     ^~~~~~
R_subrcModel_interfaces.c:163:11: warning: unused variable ‘results’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
           ^~~~~~~
R_subrcModel_interfaces.c: In function ‘sub_rcModelSummarize_plm_group’:
R_subrcModel_interfaces.c:396:10: warning: unused variable ‘scale’ [-Wunused-variable]
   double scale=-1.0;
          ^~~~~
R_subrcModel_interfaces.c:375:20: warning: unused variable ‘buffer2’ [-Wunused-variable]
   double *buffer, *buffer2;
                    ^~~~~~~
R_subrcModel_interfaces.c:375:11: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *buffer, *buffer2;
           ^~~~~~
R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_plm’:
R_subrcModel_interfaces.c:491:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j;
         ^
R_subrcModel_interfaces.c:489:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable]
   int ncur_rows;
       ^~~~~~~~~
R_subrcModel_interfaces.c:485:8: warning: unused variable ‘cur_rows’ [-Wunused-variable]
   int *cur_rows;
        ^~~~~~~~
R_subrcModel_interfaces.c:483:30: warning: unused variable ‘buffer2’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
                              ^~~~~~~
R_subrcModel_interfaces.c:483:21: warning: unused variable ‘buffer’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
                     ^~~~~~
R_subrcModel_interfaces.c:483:11: warning: unused variable ‘results’ [-Wunused-variable]
   double *results, *buffer, *buffer2;
           ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c avg.c -o avg.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c avg_log.c -o avg_log.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c biweight.c -o biweight.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c init_package.c -o init_package.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c lm.c -o lm.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c log_avg.c -o log_avg.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c log_median.c -o log_median.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c median.c -o median.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c median_log.c -o median_log.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c medianpolish.c -o medianpolish.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c plmd.c -o plmd.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c plmr.c -o plmr.o
plmr.c:279:13: warning: ‘XTWX_R_inv’ defined but not used [-Wunused-function]
 static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
             ^~~~~~~~~~
plmr.c:152:13: warning: ‘XTWX_R’ defined but not used [-Wunused-function]
 static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){
             ^~~~~~
plmr.c:82:13: warning: ‘XTWY_R’ defined but not used [-Wunused-function]
 static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){
             ^~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c psi_fns.c -o psi_fns.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c qnorm.c -o qnorm.o
qnorm.c:117:23: warning: extra tokens at end of #ifdef directive
 #ifdef __GLIBC_PREREQ && __GLIBC_PREREQ(2, 15)
                       ^~
qnorm.c: In function ‘qnorm_c_l’:
qnorm.c:506:22: warning: implicit declaration of function ‘__pthread_get_minstack’; did you mean ‘pthread_attr_setstack’? [-Wimplicit-function-declaration]
   size_t stacksize = __pthread_get_minstack(&attr);
                      ^~~~~~~~~~~~~~~~~~~~~~
                      pthread_attr_setstack
qnorm.c: In function ‘qnorm_c_determine_target_l’:
qnorm.c:1906:7: warning: unused variable ‘non_na’ [-Wunused-variable]
   int non_na;
       ^~~~~~
qnorm.c:1901:12: warning: unused variable ‘j’ [-Wunused-variable]
   size_t i,j,row_mean_ind;
            ^
qnorm.c: In function ‘qnorm_c_determine_target_via_subset_l’:
qnorm.c:2505:7: warning: unused variable ‘non_na’ [-Wunused-variable]
   int non_na;
       ^~~~~~
qnorm.c:2500:12: warning: unused variable ‘j’ [-Wunused-variable]
   size_t i,j,row_mean_ind;
            ^
qnorm.c: In function ‘using_target_via_subset_part1’:
qnorm.c:2721:14: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable]
   size_t i,j,ind,target_ind;
              ^~~
qnorm.c: In function ‘using_target_via_subset_part2’:
qnorm.c:2820:11: warning: unused variable ‘datvec’ [-Wunused-variable]
   double *datvec;
           ^~~~~~
qnorm.c:2819:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
   double *sample_percentiles;
           ^~~~~~~~~~~~~~~~~~
qnorm.c: In function ‘using_target_via_subset’:
qnorm.c:2969:11: warning: unused variable ‘datvec’ [-Wunused-variable]
   double *datvec;
           ^~~~~~
qnorm.c:2968:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable]
   double *sample_percentiles;
           ^~~~~~~~~~~~~~~~~~
qnorm.c:2964:7: warning: unused variable ‘non_na’ [-Wunused-variable]
   int non_na = 0;
       ^~~~~~
qnorm.c:2963:7: warning: unused variable ‘targetnon_na’ [-Wunused-variable]
   int targetnon_na = targetrows;
       ^~~~~~~~~~~~
qnorm.c:2961:28: warning: unused variable ‘target_ind_double_floor’ [-Wunused-variable]
   double target_ind_double,target_ind_double_floor;
                            ^~~~~~~~~~~~~~~~~~~~~~~
qnorm.c:2961:10: warning: unused variable ‘target_ind_double’ [-Wunused-variable]
   double target_ind_double,target_ind_double_floor;
          ^~~~~~~~~~~~~~~~~
qnorm.c:2960:10: warning: unused variable ‘samplepercentile’ [-Wunused-variable]
   double samplepercentile;
          ^~~~~~~~~~~~~~~~
qnorm.c:2959:11: warning: unused variable ‘ranks’ [-Wunused-variable]
   double *ranks = (double *)Calloc((rows),double);
           ^~~~~
qnorm.c:2957:11: warning: unused variable ‘row_mean’ [-Wunused-variable]
   double *row_mean = target;
           ^~~~~~~~
qnorm.c:2955:14: warning: unused variable ‘dimat’ [-Wunused-variable]
   dataitem **dimat;
              ^~~~~
qnorm.c:2953:18: warning: unused variable ‘target_ind’ [-Wunused-variable]
   size_t i,j,ind,target_ind;
                  ^~~~~~~~~~
qnorm.c:2953:14: warning: unused variable ‘ind’ [-Wunused-variable]
   size_t i,j,ind,target_ind;
              ^~~
qnorm.c:2953:12: warning: unused variable ‘j’ [-Wunused-variable]
   size_t i,j,ind,target_ind;
            ^
qnorm.c: In function ‘R_qnorm_using_target’:
qnorm.c:2111:3: warning: ‘target_rows’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qnorm.c: In function ‘R_qnorm_using_target_via_subset’:
qnorm.c:3238:3: warning: ‘target_rows’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c rlm.c -o rlm.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c rlm_anova.c -o rlm_anova.o
rlm_anova.c: In function ‘rlm_fit_anova_given_probe_effects_engine’:
rlm_anova.c:1235:10: warning: unused variable ‘endprobe’ [-Wunused-variable]
   double endprobe;
          ^~~~~~~~
rlm_anova.c: In function ‘rlm_compute_se_anova_given_probe_effects’:
rlm_anova.c:1426:19: warning: unused variable ‘varderivpsi’ [-Wunused-variable]
   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:1426:10: 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:1415:10: warning: unused variable ‘sumpsi2’ [-Wunused-variable]
   double sumpsi2=0.0;  /* sum of psi(r_i)^2 */
          ^~~~~~~
rlm_anova.c:1414:10: warning: unused variable ‘k1’ [-Wunused-variable]
   double k1 = psi_k;   /*  was 1.345; */
          ^~
rlm_anova.c: In function ‘rlm_wfit_anova_given_probe_effects_engine’:
rlm_anova.c:1505:10: warning: unused variable ‘endprobe’ [-Wunused-variable]
   double endprobe;
          ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c rlm_se.c -o rlm_se.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c rma_background4.c -o rma_background4.o
rma_background4.c:65:23: warning: extra tokens at end of #ifdef directive
 #ifdef __GLIBC_PREREQ &&  __GLIBC_PREREQ(2, 15)
                       ^~
rma_background4.c: In function ‘rma_bg_correct’:
rma_background4.c:367:22: warning: implicit declaration of function ‘__pthread_get_minstack’; did you mean ‘pthread_attr_setstack’? [-Wimplicit-function-declaration]
   size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
                      ^~~~~~~~~~~~~~~~~~~~~~
                      pthread_attr_setstack
rma_background4.c:353:10: warning: unused variable ‘param’ [-Wunused-variable]
   double param[3];
          ^~~~~
rma_background4.c:352:10: warning: unused variable ‘j’ [-Wunused-variable]
   size_t j;
          ^
rma_background4.c: In function ‘R_rma_bg_correct’:
rma_background4.c:507:12: warning: ‘PMcopy’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     return PMcopy;
            ^~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2  -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -lpthread -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-preprocessCore/00new/preprocessCore/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (preprocessCore)

Tests output

preprocessCore.Rcheck/tests/PLMdtest.Rout


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

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

Coefficients:
  (Intercept)  sort(results)  
     0.002847       0.986784  

> 
> 
> 
> 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] 44.82796
> sum((resid(lm(values ~ as.factor(group.labels)))/sc)^2)/2
[1] 44.25978
> 
> 
> 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  
                        8.1929                          9.1774  
                as.factor(cp)3                  as.factor(cp)4  
                       10.2297                         11.1979  
                as.factor(cp)5                  as.factor(cp)6  
                       12.1960                         10.1960  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                        3.8681                          2.7850  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                        1.7590                          0.7927  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                       -1.1960                         -2.2661  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                       -3.1633                         -4.2515  

> 
> 
> 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]  8.2715480  9.3334205 10.3082814 11.2479051 12.3204417 10.4145523
 [7]  3.7174633  2.7959883  1.6105772  0.6902048 -2.0678384 -2.3301898
[13] -3.3653919 -1.0508134

$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 0.7089624
[4,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[5,] 0.3552129 0.7504587 1.0000000 0.7201710 0.9638612 0.5617632
[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,] 0.1341910 0.1334099 0.1368871 0.1223371 0.1517109 0.1334891

$Residuals
           [,1]         [,2]       [,3]       [,4]        [,5]        [,6]
[1,] -0.2363867  0.114522513  0.3902243  0.1169983 -0.40898472  0.02362622
[2,] -0.1573455  0.008742457  0.1040014 -0.0726358 -0.04348454  0.16072197
[3,] -0.1368251 -0.104534672 -0.3084906  0.2724860 -0.16548709  0.62464736
[4,]  0.2846421  0.190238118 -0.1623885 -0.3752644  0.13658531 -0.07381264
[5,]  1.2469880  0.590386688  0.4418887 -0.6146327 -0.45916185 -0.78803076
[6,]  0.3811881 -0.416965435  0.1312599 -0.1000124  0.35068900 -0.34615912
[7,] -0.1353733  0.207781308 -0.1536436  0.1582217  0.13040235 -0.20738847
[8,] -3.3001141 -3.319433010 -3.2351602  3.6198943  2.91902486  3.31747767

$StdErrors
 [1] 0.2470703 0.2396546 0.2356471 0.2406589 0.2355346 0.2479247 0.2427672
 [8] 0.2427672 0.2475762 0.2427672 0.2767280 0.2427672 0.2427672 0.5886862

$Scale
[1] 0.3292572

> rcModelPLMd(y,c(1,1,1,2,2,2))
$Estimates
 [1]  8.013633  9.025314  9.965738 11.002763 11.997684 10.069713  4.011148
 [8]  3.099539  1.882265  1.015527 -1.063957 -2.384200 -2.016052 -3.061841
[15] -4.032861  2.550434

$Weights
          [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
[1,] 1.0000000 1.0000000 0.7397404 1.0000000 0.8550280 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 0.4654964
[4,] 1.0000000 1.0000000 1.0000000 0.7131876 1.0000000 1.0000000
[5,] 0.6483492 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[6,] 0.9995643 0.7679044 1.0000000 1.0000000 0.9039465 1.0000000
[7,] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8,] 1.0000000 1.0000000 1.0000000 1.0000000 0.9037295 1.0000000

$Residuals
            [,1]        [,2]        [,3]        [,4]        [,5]        [,6]
[1,] -0.27215593  0.12894497  0.43908402  0.06845611 -0.37991077  0.07478097
[2,] -0.20298134  0.01329835  0.14299458 -0.13104459 -0.02427716  0.20201016
[3,] -0.15059758 -0.06811541 -0.23763409  0.24594055 -0.11441634  0.69779891
[4,]  0.21723511  0.17302283 -0.14516654 -0.45544438  0.13402152 -0.05429563
[5,]  0.50102152 -0.10538806 -0.21944882 -0.05312866  0.17995838 -0.12682972
[6,]  0.32496543 -0.42299638  0.15966617 -0.16900804  0.35930955 -0.31545777
[7,] -0.18100909  0.21233720 -0.11465048  0.09981291  0.14960973 -0.16610028
[8,] -0.06015189 -0.02927909  0.08943098  0.26378901 -0.35946421  0.06106940

$StdErrors
 [1] 0.1225187 0.1126210 0.1119779 0.1119228 0.1347422 0.1119228 0.1373386
 [8] 0.1132290 0.1245561 0.1245561 0.1948286 0.1613315 0.1574737 0.1132290
[15] 0.1609544 0.0000000

$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  
                         8.068                           9.037  
                as.factor(cp)3                  as.factor(cp)4  
                        10.021                          10.729  
                as.factor(cp)5                  as.factor(cp)6  
                        11.734                           9.859  
C(as.factor(pr), "contr.sum")1  C(as.factor(pr), "contr.sum")2  
                         4.125                           3.204  
C(as.factor(pr), "contr.sum")3  C(as.factor(pr), "contr.sum")4  
                         2.408                           1.098  
C(as.factor(pr), "contr.sum")5  C(as.factor(pr), "contr.sum")6  
                        -1.590                          -1.922  
C(as.factor(pr), "contr.sum")7  C(as.factor(pr), "contr.sum")8  
                        -2.958                          -4.073  
C(as.factor(pr), "contr.sum")9  
                         2.788  

> 
> 
> proc.time()
   user  system elapsed 
  2.857   0.037   2.880

preprocessCore.Rcheck/tests/qnormtest.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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)")
+ }
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.262   0.044   0.293

Example timings

preprocessCore.Rcheck/preprocessCore-Ex.timings

nameusersystemelapsed
colSummarize0.0030.0000.003
normalize.quantiles.in.blocks0.0580.0000.059
rcModelPLMd0.0190.0040.023
rcModelPLMr0.0570.0000.057
rcModels0.0100.0000.011
subColSummarize0.0080.0000.008
subrcModels0.0120.0000.012