BioC 3.2: CHECK report for preprocessCore on oaxaca

Package: preprocessCore

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings preprocessCore_1.32.0.tar.gz

StartedAt: 2016-04-23 03:11:08 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:11:34 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 25.1 seconds

RetCode: 0

Status:  OK

CheckDir: preprocessCore.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings preprocessCore_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/preprocessCore.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘preprocessCore/DESCRIPTION’ ... OK
* this is package ‘preprocessCore’ version ‘1.32.0’
* 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 ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘PLMdtest.R’ [2s/2s]
  Running ‘qnormtest.R’ [0s/0s]
 [3s/3s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/preprocessCore.Rcheck/00check.log’
for details.

* installing *source* package ‘preprocessCore’ ...
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: 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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -g -O2  -c R_subColSummarize.c -o R_subColSummarize.o
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:103:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:105:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:265:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:271:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:273:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
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:442:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:438:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:436:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
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:608:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:610:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_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:785:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_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: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: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:1127:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1129:9: 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:1298:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
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:1466:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
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:1647:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -g -O2  -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:80:11: warning: unused variable 'se' [-Wunused-variable]
  double *se;
          ^
R_subrcModel_interfaces.c:79:11: warning: unused variable 'weights' [-Wunused-variable]
  double *weights;
          ^
R_subrcModel_interfaces.c:64:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:64:20: warning: unused variable 'buffer2' [-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:160:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
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: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:382:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=-1.0;
         ^
R_subrcModel_interfaces.c:475:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:477:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:471:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subrcModel_interfaces.c:469:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *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;
                    ^
19 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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:1175:19: 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:1175:19: 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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
  double Kappa=0.0;      /* A correction factor */
         ^
rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=0.0;
         ^
rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable]
  double sumpsi2=0.0;  /* sum of psi(r_i)^2 */
         ^
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
  double sumderivpsi=0.0; /* sum of psi'(r_i) */
         ^
rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
                  ^
rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable]
  double k1 = psi_k;   /*  was 1.345; */
         ^
rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
         ^
rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
                ^
rlm_anova.c: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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -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 -mtune=core2 -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/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/preprocessCore.Rcheck/preprocessCore/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (preprocessCore)

name	user	system	elapsed
colSummarize	0.001	0.001	0.002
normalize.quantiles.in.blocks	0.034	0.001	0.035
rcModelPLMd	0.017	0.002	0.020
rcModelPLMr	0.039	0.004	0.043
rcModels	0.009	0.006	0.014
subColSummarize	0.006	0.002	0.007
subrcModels	0.011	0.007	0.018