Package: flowCore

Version: 1.17.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.17.2.tar.gz

StartedAt: 2011-02-24 15:36:04 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:38:56 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 171.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/flowCore.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.17.2'
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 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 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c FastLogicle.cpp -o FastLogicle.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Logicle.cpp -o Logicle.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c biexponential.c -o biexponential.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolygon.c -o inPolygon.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolytope.c -o inPolytope.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c logicleTransform.cpp -o logicleTransform.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.166	0.006	0.173
Subset-methods	1.047	0.018	1.064
actionItem-class	0.001	0.000	0.002
arcsinhTransform	0.139	0.003	0.142
asinht-class	0.052	0.001	0.054
biexponentialTransform	8.878	1.275	10.154
boundaryFilter-class	0.262	0.033	0.295
characterOrTransformation-class	0.001	0.000	0.002
coerce	0.113	0.018	0.131
compensateActionItem-class	0.001	0.000	0.001
compensateView-class	0.001	0.000	0.001
compensatedParameter-class	0.303	0.058	0.360
compensation-class	0.679	0.133	0.811
curv1Filter-class	0.950	0.123	1.073
curv2Filter-class	4.146	0.266	4.413
dg1polynomial-class	0.053	0.006	0.060
each_col-methods	0.069	0.013	0.081
ellipsoidGate	0.125	0.016	0.141
exponential-class	0.057	0.014	0.070
expressionFilter-class	0.128	0.018	0.146
fcReference-class	0.001	0.000	0.002
filter-methods	1.608	0.055	1.663
filter-on-methods	0.235	0.013	0.248
filterList-class	0.016	0.000	0.016
filterResult-class	0.001	0.001	0.002
filterResultList-class	2.235	0.274	2.509
filterSet-class	0.080	0.001	0.083
filterSummary-class	0.648	0.066	0.713
filterSummaryList-class	2.094	0.212	2.306
flowFrame-class	4.673	0.215	4.888
flowSet-class	4.921	0.278	5.229
fsApply	0.294	0.049	0.343
gateActionItem-class	0.001	0.001	0.001
gateView-class	0.001	0.000	0.001
hyperlog-class	2.031	0.016	2.046
identifier-methods	0.042	0.002	0.045
inverseLogicleTransform	1.148	0.036	1.184
invsplitscale-class	0.057	0.009	0.066
keyword-methods	1.371	0.129	1.500
kmeansFilter	0.320	0.030	0.351
linearTransform	0.076	0.009	0.086
lnTransform	3.304	0.657	3.961
logTransform	0.147	0.028	0.176
logarithm-class	0.051	0.006	0.057
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	1.191	0.040	1.231
manyFilterResult-class	0.001	0.001	0.001
multipleFilterResult-class	0.001	0.000	0.001
norm2Filter-class	0.270	0.026	0.295
normalizeActionItem-class	0.001	0.000	0.001
normalizeView-class	0.001	0.001	0.001
parameters-methods	0.051	0.006	0.056
polygonGate	0.128	0.020	0.147
quadGate	0.371	0.032	0.404
quadratic-class	0.054	0.008	0.063
quadraticTransform	0.074	0.009	0.083
ratio-class	0.054	0.006	0.060
read.FCS	0.096	0.019	0.116
read.FCSheader	0.007	0.002	0.010
read.flowSet	0.21	0.04	0.25
rectangleGate	0.231	0.018	0.248
sampleFilter-class	0.103	0.015	0.118
scaleTransform	0.077	0.010	0.087
singleParameterTransform-class	0.002	0.000	0.001
sinht-class	0.055	0.015	0.070
split-methods	2.021	0.163	2.184
splitScaleTransform	3.273	0.722	3.995
splitscale-class	0.054	0.006	0.060
squareroot-class	0.054	0.005	0.060
subsettingActionItem-class	0.001	0.000	0.001
subsettingView-class	0.001	0.000	0.001
timeFilter-class	3.037	0.129	3.167
transform-class	0.002	0.000	0.003
transformActionItem-class	0.001	0.000	0.001
transformFilter-class	0.209	0.020	0.229
transformList-class	1.129	0.037	1.165
transformMap-class	0.001	0.000	0.001
transformView-class	0.001	0.000	0.001
truncateTransform	0.086	0.022	0.107
unitytransform-class	0.045	0.006	0.051
view-class	0.001	0.000	0.001
workFlow-class	0.001	0.000	0.001
write.FCS	0.080	0.014	0.095
write.flowSet	1.426	0.094	1.522