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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1
Package 179/247HostnameOSArchBUILDCHECKBUILD BIN

preprocessCore

0.99.12

Benjamin Milo Bolstad
Last Changed Date: 2007-08-12 11:55:18 -0700
Last Changed Rev: 26352
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) x64  OK  OK  OK 
pitt Mac OS X (10.4.10) i386  OK [ OK ] OK 
Package: preprocessCore
Version: 0.99.12
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check preprocessCore_0.99.12.tar.gz
RetCode: 0
Time: 31.0 seconds
Status: OK
CheckDir: preprocessCore.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/preprocessCore.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-10 r42465)
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '0.99.12'
* 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 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 ... 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
* creating preprocessCore-Ex.R ... OK
* checking examples ... OK
* creating preprocessCore-manual.tex ... OK
* checking preprocessCore-manual.tex ... OK

preprocessCore.Rcheck/00install.out:

* Installing *source* package 'preprocessCore' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c avg_log.c -o avg_log.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c biweight.c -o biweight.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c init_package.c -o init_package.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c lm.c -o lm.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c log_avg.c -o log_avg.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c matrix_functions.c -o matrix_functions.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c medianpolish.c -o medianpolish.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c psi_fns.c -o psi_fns.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c qnorm.c -o qnorm.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c rlm.c -o rlm.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c rlm_anova.c -o rlm_anova.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c rlm_se.c -o rlm_se.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c rma_common.c -o rma_common.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o preprocessCore.so R_rlm_interfaces.o avg_log.o biweight.o init_package.o lm.o log_avg.o matrix_functions.o medianpolish.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_common.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.1 -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
** arch - ppc
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c avg_log.c -o avg_log.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c biweight.c -o biweight.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c init_package.c -o init_package.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c lm.c -o lm.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c log_avg.c -o log_avg.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c medianpolish.c -o medianpolish.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c qnorm.c -o qnorm.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm.c -o rlm.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm_anova.c -o rlm_anova.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm_se.c -o rlm_se.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o preprocessCore.so R_rlm_interfaces.o avg_log.o biweight.o init_package.o lm.o log_avg.o matrix_functions.o medianpolish.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_common.o -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.1 -lgfortran -lSystemStubs -L/Library/Frameworks/R.framework/Resources/lib/ppc -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/ppc -lRblas  -F/Library/Frameworks/R.framework/.. -framework R
** R
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'preprocessCore'
     Formats: text html latex example 
  normalize.quantiles               text    html    latex
  normalize.quantiles.in.blocks     text    html    latex   example
  normalize.quantiles.robust        text    html    latex
  normalize.quantiles.target        text    html    latex
** building package indices ...
* DONE (preprocessCore)