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 19:08:14 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:12:18 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 244.3 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: UTF-8
* 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	0.223	0.021	0.244
Subset-methods	1.515	0.156	1.680
actionItem-class	0.002	0.000	0.003
arcsinhTransform	0.199	0.040	0.249
asinht-class	0.073	0.022	0.096
biexponentialTransform	12.422	3.128	15.696
boundaryFilter-class	0.363	0.065	0.429
characterOrTransformation-class	0.001	0.000	0.002
coerce	0.144	0.045	0.189
compensateActionItem-class	0.002	0.000	0.002
compensateView-class	0.002	0.000	0.002
compensatedParameter-class	0.394	0.143	0.541
compensation-class	0.932	0.329	1.274
curv1Filter-class	1.335	0.279	1.630
curv2Filter-class	5.636	0.687	6.363
dg1polynomial-class	0.068	0.018	0.086
each_col-methods	0.087	0.031	0.119
ellipsoidGate	0.164	0.036	0.201
exponential-class	0.070	0.024	0.095
expressionFilter-class	0.173	0.049	0.231
fcReference-class	0.002	0.000	0.003
filter-methods	2.252	0.117	2.405
filter-on-methods	0.338	0.050	0.399
filterList-class	0.022	0.001	0.023
filterResult-class	0.002	0.001	0.002
filterResultList-class	3.265	0.615	3.922
filterSet-class	0.110	0.002	0.112
filterSummary-class	0.905	0.130	1.049
filterSummaryList-class	2.929	0.463	3.429
flowFrame-class	6.465	0.701	7.231
flowSet-class	6.877	0.693	7.640
fsApply	0.415	0.153	0.580
gateActionItem-class	0.002	0.000	0.003
gateView-class	0.002	0.000	0.002
hyperlog-class	2.871	0.034	2.916
identifier-methods	0.058	0.018	0.083
inverseLogicleTransform	1.644	0.091	1.746
invsplitscale-class	0.072	0.027	0.099
keyword-methods	1.903	0.247	2.162
kmeansFilter	0.431	0.080	0.518
linearTransform	0.102	0.042	0.145
lnTransform	4.847	1.673	6.590
logTransform	0.211	0.068	0.287
logarithm-class	0.069	0.020	0.089
logicalFilterResult-class	0.001	0.000	0.002
logicleTransform	1.730	0.108	1.851
manyFilterResult-class	0.001	0.001	0.002
multipleFilterResult-class	0.002	0.000	0.002
norm2Filter-class	0.365	0.062	0.430
normalizeActionItem-class	0.002	0.000	0.002
normalizeView-class	0.002	0.000	0.002
parameters-methods	0.061	0.016	0.077
polygonGate	0.166	0.044	0.211
quadGate	0.497	0.086	0.590
quadratic-class	0.069	0.025	0.094
quadraticTransform	0.104	0.042	0.147
ratio-class	0.068	0.021	0.092
read.FCS	0.125	0.036	0.164
read.FCSheader	0.014	0.004	0.019
read.flowSet	0.289	0.114	0.412
rectangleGate	0.336	0.053	0.395
sampleFilter-class	0.133	0.035	0.168
scaleTransform	0.100	0.036	0.137
singleParameterTransform-class	0.003	0.000	0.003
sinht-class	0.073	0.035	0.112
split-methods	2.945	0.396	3.426
splitScaleTransform	4.583	1.700	6.395
splitscale-class	0.176	0.052	0.231
squareroot-class	0.066	0.018	0.091
subsettingActionItem-class	0.002	0.000	0.002
subsettingView-class	0.003	0.000	0.003
timeFilter-class	4.113	0.327	4.478
transform-class	0.005	0.001	0.005
transformActionItem-class	0.002	0.000	0.002
transformFilter-class	0.283	0.060	0.344
transformList-class	1.621	0.084	1.722
transformMap-class	0.001	0.000	0.001
transformView-class	0.002	0.001	0.003
truncateTransform	0.123	0.062	0.185
unitytransform-class	0.058	0.016	0.074
view-class	0.002	0.000	0.002
workFlow-class	0.002	0.001	0.003
write.FCS	0.101	0.034	0.137
write.flowSet	2.083	0.209	2.309