* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/flowCore.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ASCII
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowCore' 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating flowCore-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating flowCore-manual.tex ... OK
* checking flowCore-manual.tex using pdflatex ... OK
* Installing *source* package 'flowCore' ...
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -march=nocona -c biexponential.c -o biexponential.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -march=nocona -c inPolygon.c -o inPolygon.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c biexponential.c -o biexponential.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c inPolygon.c -o inPolygon.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Loading required package: rrcov
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 0.4-07)
Loading required package: feature
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
>>> Building/Updating help pages for package 'flowCore'
Formats: text html latex example
GvHD text html latex
KmeansFilter text html latex example
Subset-methods text html latex example
arcsinhTransform text html latex example
biexponentialTransform text html latex example
coerce text html latex example
compensate text html latex example
concreteFilter-class text html latex
curv1Filter-class text html latex example
curv2Filter-class text html latex example
each_col-methods text html latex example
ellipsoidGate text html latex example
expressionFilter-class text html latex
filter-and-methods text html latex
filter-class text html latex
filter-in-methods text html latex
filter-methods text html latex example
filter-on-methods text html latex example
filterDetails-methods text html latex
filterReference-class text html latex
filterResult-class text html latex example
filterSet-class text html latex example
flowFrame-class text html latex example
flowSet-class text html latex example
fsApply text html latex example
identifier-methods text html latex example
keyword-methods text html latex example
linearTransform text html latex example
lnTransform text html latex example
logTransform text html latex example
logicalFilterResult-class text html latex example
logicleTransform text html latex example
manyFilterResult-class text html latex example
multipleFilterResult-class text html latex example
norm2Filter-class text html latex example
parameterFilter-class text html latex
parameters-methods text html latex example
print.filterSummary text html latex example
quadraticTransform text html latex example
randomFilterResult-class text html latex
read.FCS text html latex example
read.FCSheader text html latex example
read.flowSet text html latex example
rectangleGate text html latex example
sampleFilter-class text html latex example
sampleFilter text html latex example
scaleTransform text html latex example
setOperationFilter-class text html latex
spillover-flowSet text html latex
split-methods text html latex example
splitScaleTransform text html latex example
transform-class text html latex example
transformFilter-class text html latex example
transformList-class text html latex example
transformMap-class text html latex example
truncateTransform text html latex example
** building package indices ...
* DONE (flowCore)