Package: flowCore

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.20.0.tar.gz

StartedAt: 2012-03-24 00:55:58 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:00:13 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 255.4 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/flowCore.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'flowCore' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.2Mb
    extdata   1.1Mb
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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-2.9-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import '.__C__character' when loading 'methods'
Creating a new generic function for 'filter' in package 'flowCore'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'HowTo-flowCore.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning message:
replacing previous import '.__C__character' when loading 'methods' 

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.237	0.023	0.260
Subset-methods	1.520	0.167	1.751
actionItem-class	0.002	0.001	0.002
arcsinhTransform	0.114	0.041	0.156
asinht-class	0.161	0.021	0.183
biexponentialTransform	13.801	3.380	17.715
boundaryFilter-class	0.305	0.068	0.385
characterOrTransformation-class	0.002	0.000	0.002
coerce	0.130	0.041	0.181
compensateActionItem-class	0.001	0.000	0.002
compensateView-class	0.001	0.001	0.002
compensatedParameter-class	0.375	0.157	0.533
compensation-class	0.827	0.347	1.185
curv1Filter-class	0.631	0.243	0.882
curv2Filter-class	3.920	0.718	4.713
dg1polynomial-class	0.060	0.019	0.080
each_col-methods	0.078	0.027	0.105
ellipsoidGate	0.153	0.057	0.212
exponential-class	0.060	0.017	0.078
expressionFilter-class	0.157	0.060	0.217
fcReference-class	0.001	0.000	0.002
filter-methods	3.078	0.237	3.360
filter-on-methods	0.250	0.046	0.303
filterList-class	0.013	0.001	0.013
filterResult-class	0.002	0.000	0.001
filterResultList-class	3.779	0.905	4.801
filterSet-class	0.089	0.007	0.096
filterSummary-class	0.231	0.111	0.343
filterSummaryList-class	3.418	0.653	4.108
flowFrame-class	7.407	0.893	8.376
flowSet-class	6.570	0.812	7.465
fsApply	0.375	0.153	0.671
gateActionItem-class	0.001	0.000	0.001
gateView-class	0.001	0.000	0.001
hyperlog-class	2.581	0.030	3.333
identifier-methods	0.055	0.017	0.186
inverseLogicleTransform	2.858	0.247	3.384
invsplitscale-class	0.062	0.017	0.079
keyword-methods	2.901	0.390	3.549
kmeansFilter	0.375	0.097	0.553
linearTransform	0.098	0.044	0.148
lnTransform	5.646	1.792	7.680
logTransform	0.094	0.040	0.150
logarithm-class	0.185	0.056	0.337
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	2.810	0.206	3.187
manyFilterResult-class	0.001	0.000	0.001
multipleFilterResult-class	0.001	0.000	0.001
norm2Filter-class	0.333	0.069	0.404
normalizeActionItem-class	0.002	0.000	0.001
normalizeView-class	0.001	0.001	0.002
parameters-methods	0.059	0.018	0.077
polygonGate	0.151	0.051	0.204
quadGate	0.438	0.096	0.535
quadratic-class	0.062	0.017	0.088
quadraticTransform	0.091	0.036	0.127
ratio-class	0.063	0.018	0.081
read.FCS	0.111	0.037	0.148
read.FCSheader	0.009	0.004	0.013
read.flowSet	0.248	0.094	0.346
rectangleGate	0.231	0.063	0.295
sampleFilter-class	0.117	0.034	0.152
scaleTransform	0.092	0.035	0.128
singleParameterTransform-class	0.002	0.000	0.002
sinht-class	0.063	0.019	0.082
split-methods	3.801	0.515	4.354
splitScaleTransform	5.510	1.855	7.463
splitscale-class	0.062	0.017	0.079
squareroot-class	0.063	0.020	0.085
subsettingActionItem-class	0.001	0.000	0.001
subsettingView-class	0.001	0.001	0.001
timeFilter-class	4.692	0.466	5.202
transform-class	0.003	0.000	0.003
transformActionItem-class	0.001	0.000	0.001
transformFilter-class	0.272	0.060	0.341
transformList-class	2.723	0.232	2.982
transformMap-class	0.001	0.000	0.001
transformView-class	0.000	0.000	0.002
truncateTransform	0.117	0.058	0.177
unitytransform-class	0.057	0.018	0.075
view-class	0.001	0.000	0.001
workFlow-class	0.001	0.001	0.002
write.FCS	0.096	0.035	0.134
write.flowSet	3.114	0.373	3.545