Package: flowCore

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.18.0.tar.gz

StartedAt: 2011-10-20 14:43:29 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:47:35 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 246.4 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 2.13.2 (2011-09-30)
* 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 '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowCore' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      8.1Mb
    doc       7.2Mb
    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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'HowTo-flowCore.pdf' from 7.0Mb to 1.0Mb
  consider running tools::compactPDF() on these files
* 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++-4.2 -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++-4.2 -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-4.2 -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-4.2 -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-4.2 -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-4.2 -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++-4.2 -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++-4.2 -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
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.202	0.021	0.224
Subset-methods	1.438	0.146	1.607
actionItem-class	0.001	0.000	0.002
arcsinhTransform	0.184	0.039	0.223
asinht-class	0.073	0.020	0.093
biexponentialTransform	12.023	3.091	16.237
boundaryFilter-class	0.353	0.066	0.426
characterOrTransformation-class	0.001	0.000	0.002
coerce	0.138	0.040	0.182
compensateActionItem-class	0.002	0.001	0.001
compensateView-class	0.005	0.009	0.013
compensatedParameter-class	0.380	0.135	0.524
compensation-class	0.889	0.309	1.203
curv1Filter-class	0.706	0.241	0.957
curv2Filter-class	4.703	0.727	5.495
dg1polynomial-class	0.067	0.020	0.088
each_col-methods	0.082	0.025	0.107
ellipsoidGate	0.167	0.049	0.217
exponential-class	0.064	0.017	0.085
expressionFilter-class	0.170	0.054	0.227
fcReference-class	0.002	0.000	0.002
filter-methods	2.171	0.104	2.291
filter-on-methods	0.338	0.047	0.388
filterList-class	0.017	0.001	0.017
filterResult-class	0.001	0.000	0.002
filterResultList-class	2.624	0.598	3.245
filterSet-class	0.101	0.001	0.103
filterSummary-class	0.246	0.105	0.353
filterSummaryList-class	2.303	0.475	2.811
flowFrame-class	6.470	0.701	7.277
flowSet-class	6.602	0.661	7.373
fsApply	0.497	0.164	0.677
gateActionItem-class	0.001	0.000	0.001
gateView-class	0.001	0.000	0.001
hyperlog-class	2.637	0.036	2.687
identifier-methods	0.055	0.017	0.073
inverseLogicleTransform	1.640	0.091	1.749
invsplitscale-class	0.066	0.018	0.085
keyword-methods	1.803	0.264	2.094
kmeansFilter	0.415	0.079	0.495
linearTransform	0.104	0.040	0.144
lnTransform	4.941	1.629	6.725
logTransform	0.100	0.039	0.139
logarithm-class	0.169	0.056	0.227
logicalFilterResult-class	0.001	0.001	0.002
logicleTransform	1.738	0.092	1.851
manyFilterResult-class	0.001	0.000	0.001
multipleFilterResult-class	0.001	0.001	0.001
norm2Filter-class	0.349	0.055	0.410
normalizeActionItem-class	0.001	0.000	0.002
normalizeView-class	0.001	0.000	0.001
parameters-methods	0.066	0.028	0.095
polygonGate	0.168	0.039	0.207
quadGate	0.507	0.101	0.614
quadratic-class	0.071	0.020	0.097
quadraticTransform	0.098	0.038	0.137
ratio-class	0.066	0.018	0.084
read.FCS	0.129	0.046	0.176
read.FCSheader	0.010	0.004	0.014
read.flowSet	0.275	0.112	0.388
rectangleGate	0.308	0.043	0.359
sampleFilter-class	0.133	0.042	0.177
scaleTransform	0.104	0.042	0.148
singleParameterTransform-class	0.002	0.000	0.002
sinht-class	0.067	0.018	0.094
split-methods	2.842	0.368	3.257
splitScaleTransform	4.413	1.657	6.238
splitscale-class	0.169	0.047	0.222
squareroot-class	0.069	0.020	0.098
subsettingActionItem-class	0.002	0.000	0.001
subsettingView-class	0.001	0.000	0.002
timeFilter-class	4.209	0.345	4.729
transform-class	0.004	0.001	0.005
transformActionItem-class	0.002	0.000	0.001
transformFilter-class	0.281	0.057	0.342
transformList-class	1.656	0.096	1.763
transformMap-class	0.001	0.000	0.002
transformView-class	0.001	0.001	0.001
truncateTransform	0.101	0.037	0.138
unitytransform-class	0.058	0.019	0.077
view-class	0.001	0.000	0.002
workFlow-class	0.002	0.000	0.002
write.FCS	0.107	0.053	0.165
write.flowSet	2.069	0.207	2.339