Package: preprocessCore

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/2.10/Resources/bin/R CMD check --no-vignettes preprocessCore_1.8.0.tar.gz

StartedAt: 2009-12-14 06:33:49 -0800 (Mon, 14 Dec 2009)

EndedAt: 2009-12-14 06:34:24 -0800 (Mon, 14 Dec 2009)

EllapsedTime: 34.9 seconds

RetCode: 0

Status: OK

CheckDir: preprocessCore.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/preprocessCore.Rcheck'
* using R version 2.10.0 Patched (2009-10-27 r50222)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'preprocessCore' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated 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 ... NOTE
prepare_Rd: rcModelPLMd.Rd:35-36: Dropping empty section \seealso
prepare_Rd: rcModelPLMr.Rd:53-54: Dropping empty section \seealso
prepare_Rd: rcModels.Rd:46-47: Dropping empty section \seealso
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running ‘PLMdtest.R’
 OK
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘preprocessCore’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c R_colSummarize.c -o R_colSummarize.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o
R_rlm_interfaces.c: In function ‘R_rlm_rma_default_model’:
R_rlm_interfaces.c:80: warning: unused variable ‘scale’
R_rlm_interfaces.c: In function ‘R_wrlm_rma_default_model’:
R_rlm_interfaces.c:190: warning: unused variable ‘scale’
R_rlm_interfaces.c: In function ‘R_medianpolish_rma_default_model’:
R_rlm_interfaces.c:307: warning: unused variable ‘se’
R_rlm_interfaces.c:306: warning: unused variable ‘weights’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c: In function ‘R_subColSummarize_avg_log’:
R_subColSummarize.c:104: warning: unused variable ‘j’
R_subColSummarize.c:102: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:98: warning: unused variable ‘cur_rows’
R_subColSummarize.c:96: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_log_avg’:
R_subColSummarize.c:268: warning: unused variable ‘j’
R_subColSummarize.c:266: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:262: warning: unused variable ‘cur_rows’
R_subColSummarize.c:260: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_avg’:
R_subColSummarize.c:435: warning: unused variable ‘j’
R_subColSummarize.c:433: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:429: warning: unused variable ‘cur_rows’
R_subColSummarize.c:427: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_biweight_log’:
R_subColSummarize.c:603: warning: unused variable ‘j’
R_subColSummarize.c:601: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:597: warning: unused variable ‘cur_rows’
R_subColSummarize.c:595: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_biweight’:
R_subColSummarize.c:770: warning: unused variable ‘j’
R_subColSummarize.c:768: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:764: warning: unused variable ‘cur_rows’
R_subColSummarize.c:762: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_median_log’:
R_subColSummarize.c:938: warning: unused variable ‘j’
R_subColSummarize.c:936: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:932: warning: unused variable ‘cur_rows’
R_subColSummarize.c:930: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_log_median’:
R_subColSummarize.c:1104: warning: unused variable ‘j’
R_subColSummarize.c:1102: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:1098: warning: unused variable ‘cur_rows’
R_subColSummarize.c:1096: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_median’:
R_subColSummarize.c:1269: warning: unused variable ‘j’
R_subColSummarize.c:1267: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:1263: warning: unused variable ‘cur_rows’
R_subColSummarize.c:1261: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish_log’:
R_subColSummarize.c:1438: warning: unused variable ‘j’
R_subColSummarize.c:1436: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:1432: warning: unused variable ‘cur_rows’
R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish’:
R_subColSummarize.c:1608: warning: unused variable ‘j’
R_subColSummarize.c:1606: warning: unused variable ‘ncur_rows’
R_subColSummarize.c:1602: warning: unused variable ‘cur_rows’
R_subColSummarize.c:1600: warning: unused variable ‘buffer2’
R_subColSummarize.c:1600: warning: unused variable ‘buffer’
R_subColSummarize.c: In function ‘subColSummarize_median_group’:
R_subColSummarize.c:1251: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_medianpolish_log_group’:
R_subColSummarize.c:1419: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_log_median_group’:
R_subColSummarize.c:1085: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_median_log_group’:
R_subColSummarize.c:918: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_biweight_group’:
R_subColSummarize.c:751: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_biweight_log_group’:
R_subColSummarize.c:583: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_avg_group’:
R_subColSummarize.c:417: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_log_avg_group’:
R_subColSummarize.c:250: warning: control reaches end of non-void function
R_subColSummarize.c: In function ‘subColSummarize_avg_log_group’:
R_subColSummarize.c:83: warning: control reaches end of non-void function
R_subColSummarize.c: At top level:
R_subColSummarize.c:1565: warning: ‘subColSummarize_medianpolish_group’ defined but not used
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c avg.c -o avg.o
avg.c: In function ‘colaverage_no_copy’:
avg.c:90: warning: unused variable ‘i’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c avg_log.c -o avg_log.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c biweight.c -o biweight.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c init_package.c -o init_package.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c lm.c -o lm.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c log_avg.c -o log_avg.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c log_median.c -o log_median.o
log_median.c: In function ‘logmedian_no_copy’:
log_median.c:138: warning: unused variable ‘i’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c median.c -o median.o
median.c: In function ‘colmedian_no_copy’:
median.c:146: warning: unused variable ‘i’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c median_log.c -o median_log.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c medianpolish.c -o medianpolish.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c plmd.c -o plmd.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c plmr.c -o plmr.o
plmr.c:82: warning: ‘XTWY_R’ defined but not used
plmr.c:152: warning: ‘XTWX_R’ defined but not used
plmr.c:279: warning: ‘XTWX_R_inv’ defined but not used
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c qnorm.c -o qnorm.o
qnorm.c: In function ‘qnorm_c_determine_target’:
qnorm.c:1815: warning: unused variable ‘non_na’
qnorm.c:1810: warning: unused variable ‘j’
qnorm.c: In function ‘qnorm_c_determine_target_via_subset’:
qnorm.c:2398: warning: unused variable ‘non_na’
qnorm.c:2393: warning: unused variable ‘j’
qnorm.c: In function ‘using_target_group_via_subset’:
qnorm.c:2839: warning: control reaches end of non-void function
qnorm.c: In function ‘determine_target_group_via_subset’:
qnorm.c:2383: warning: control reaches end of non-void function
qnorm.c: In function ‘determine_target_group’:
qnorm.c:1801: warning: control reaches end of non-void function
qnorm.c: In function ‘using_target_group’:
qnorm.c:1521: warning: control reaches end of non-void function
qnorm.c: In function ‘distribute_group’:
qnorm.c:459: warning: control reaches end of non-void function
qnorm.c: In function ‘normalize_group’:
qnorm.c:454: warning: control reaches end of non-void function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c rlm.c -o rlm.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=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: warning: unused variable ‘endprobe’
rlm_anova.c: In function ‘rlm_compute_se_anova_given_probe_effects’:
rlm_anova.c:1426: warning: unused variable ‘varderivpsi’
rlm_anova.c:1426: warning: unused variable ‘m’
rlm_anova.c:1426: warning: unused variable ‘vs’
rlm_anova.c:1419: warning: unused variable ‘scale’
rlm_anova.c:1418: warning: unused variable ‘Kappa’
rlm_anova.c:1417: warning: unused variable ‘sumderivpsi’
rlm_anova.c:1415: warning: unused variable ‘sumpsi2’
rlm_anova.c:1414: warning: unused variable ‘k1’
rlm_anova.c: In function ‘rlm_wfit_anova_given_probe_effects_engine’:
rlm_anova.c:1505: warning: unused variable ‘endprobe’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c rlm_se.c -o rlm_se.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c rma_background4.c -o rma_background4.o
rma_background4.c: In function ‘rma_bg_correct’:
rma_background4.c:340: warning: unused variable ‘param’
rma_background4.c:339: warning: unused variable ‘j’
rma_background4.c: In function ‘R_rma_bg_correct’:
rma_background4.c:459: warning: unused variable ‘j’
rma_background4.c: In function ‘rma_bg_correct_group’:
rma_background4.c:321: warning: control reaches end of non-void function
rma_background4.c: In function ‘R_rma_bg_correct’:
rma_background4.c:458: warning: ‘PMcopy’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC  -g -O2 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 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 -lpthread -lgfortran -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (preprocessCore)