Package: flowCore

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.16.0.tar.gz

StartedAt: 2011-03-31 05:37:26 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 05:41:45 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 259.2 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/flowCore.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘1.16.0’
* 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 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) and $(LAPACK_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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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-2.7-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
  'openVignette()'. 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	0.224	0.022	0.248
Subset-methods	1.662	0.165	1.890
actionItem-class	0.002	0.000	0.003
arcsinhTransform	0.190	0.041	0.238
asinht-class	0.074	0.020	0.095
biexponentialTransform	12.607	3.224	16.052
boundaryFilter-class	0.285	0.033	0.320
characterOrTransformation-class	0.002	0.000	0.002
coerce	0.241	0.096	0.346
compensateActionItem-class	0.002	0.001	0.003
compensateView-class	0.002	0.001	0.002
compensatedParameter-class	0.398	0.155	0.561
compensation-class	0.923	0.326	1.267
curv1Filter-class	1.297	0.252	1.569
curv2Filter-class	5.661	0.737	6.463
dg1polynomial-class	0.068	0.020	0.100
each_col-methods	0.085	0.028	0.115
ellipsoidGate	0.169	0.052	0.225
exponential-class	0.072	0.023	0.095
expressionFilter-class	0.178	0.058	0.238
fcReference-class	0.002	0.001	0.003
filter-methods	2.167	0.120	2.354
filter-on-methods	0.336	0.049	0.388
filterList-class	0.017	0.001	0.017
filterResult-class	0.002	0.000	0.002
filterResultList-class	3.274	0.632	4.042
filterSet-class	0.107	0.004	0.111
filterSummary-class	0.845	0.133	1.045
filterSummaryList-class	2.969	0.492	3.529
flowFrame-class	6.718	0.755	8.188
flowSet-class	6.824	0.726	8.061
fsApply	0.414	0.153	0.580
gateActionItem-class	0.002	0.001	0.002
gateView-class	0.002	0.000	0.002
hyperlog-class	2.688	0.037	2.757
identifier-methods	0.058	0.020	0.081
inverseLogicleTransform	1.644	0.095	1.789
invsplitscale-class	0.072	0.019	0.091
keyword-methods	1.920	0.265	2.208
kmeansFilter	0.440	0.092	0.541
linearTransform	0.102	0.040	0.144
lnTransform	5.079	1.704	6.891
logTransform	0.108	0.045	0.155
logarithm-class	0.070	0.022	0.093
logicalFilterResult-class	0.001	0.001	0.002
logicleTransform	1.847	0.125	1.996
manyFilterResult-class	0.001	0.000	0.002
multipleFilterResult-class	0.002	0.000	0.002
norm2Filter-class	0.366	0.063	0.441
normalizeActionItem-class	0.002	0.000	0.002
normalizeView-class	0.003	0.000	0.002
parameters-methods	0.063	0.019	0.083
polygonGate	0.177	0.051	0.230
quadGate	0.500	0.101	0.617
quadratic-class	0.070	0.022	0.096
quadraticTransform	0.105	0.043	0.150
ratio-class	0.069	0.030	0.101
read.FCS	0.118	0.020	0.138
read.FCSheader	0.014	0.004	0.017
read.flowSet	0.269	0.105	0.389
rectangleGate	0.320	0.049	0.372
sampleFilter-class	0.137	0.043	0.189
scaleTransform	0.098	0.035	0.133
singleParameterTransform-class	0.002	0.000	0.002
sinht-class	0.066	0.019	0.086
split-methods	2.928	0.356	3.316
splitScaleTransform	4.432	1.677	6.198
splitscale-class	0.071	0.023	0.098
squareroot-class	0.069	0.024	0.095
subsettingActionItem-class	0.002	0.001	0.002
subsettingView-class	0.002	0.000	0.002
timeFilter-class	4.160	0.339	4.549
transform-class	0.004	0.000	0.005
transformActionItem-class	0.002	0.000	0.002
transformFilter-class	0.270	0.049	0.330
transformList-class	1.625	0.080	1.724
transformMap-class	0.001	0.000	0.002
transformView-class	0.002	0.001	0.002
truncateTransform	0.099	0.035	0.134
unitytransform-class	0.067	0.030	0.095
view-class	0.002	0.001	0.003
workFlow-class	0.002	0.000	0.002
write.FCS	0.100	0.036	0.145
write.flowSet	2.086	0.214	2.322