Package: flowCore

Version: 1.19.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.19.2.tar.gz

StartedAt: 2011-06-22 02:50:38 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 02:54:45 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 247.1 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 2.14.0 Under development (unstable) (2011-06-03 r56037)
* 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 ‘1.19.2’
* 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 installed package size ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data      8.1Mb
    doc       1.1Mb
    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 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 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’ ... 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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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-2.9-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 1.3-00)
** 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 1.3-00)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.218	0.021	0.241
Subset-methods	1.515	0.146	1.690
actionItem-class	0.003	0.001	0.004
arcsinhTransform	0.196	0.041	0.238
asinht-class	0.071	0.018	0.090
biexponentialTransform	12.317	3.043	15.650
boundaryFilter-class	0.275	0.032	0.308
characterOrTransformation-class	0.001	0.001	0.002
coerce	0.144	0.042	0.192
compensateActionItem-class	0.002	0.001	0.002
compensateView-class	0.002	0.000	0.002
compensatedParameter-class	0.382	0.135	0.520
compensation-class	0.887	0.305	1.201
curv1Filter-class	1.257	0.270	1.558
curv2Filter-class	5.385	0.658	6.131
dg1polynomial-class	0.068	0.021	0.092
each_col-methods	0.087	0.035	0.127
ellipsoidGate	0.162	0.039	0.205
exponential-class	0.069	0.028	0.098
expressionFilter-class	0.173	0.050	0.225
fcReference-class	0.002	0.001	0.003
filter-methods	2.242	0.137	2.411
filter-on-methods	0.340	0.047	0.390
filterList-class	0.018	0.000	0.019
filterResult-class	0.002	0.001	0.002
filterResultList-class	3.364	0.767	4.190
filterSet-class	0.101	0.008	0.111
filterSummary-class	0.758	0.111	0.893
filterSummaryList-class	2.760	0.465	3.260
flowFrame-class	6.552	0.733	7.399
flowSet-class	6.671	0.678	7.515
fsApply	0.391	0.148	0.570
gateActionItem-class	0.002	0.001	0.003
gateView-class	0.002	0.000	0.002
hyperlog-class	2.709	0.052	2.825
identifier-methods	0.058	0.017	0.074
inverseLogicleTransform	1.625	0.081	1.711
invsplitscale-class	0.076	0.034	0.109
keyword-methods	1.810	0.252	2.363
kmeansFilter	0.536	0.098	0.720
linearTransform	0.099	0.033	0.146
lnTransform	4.753	1.540	6.548
logTransform	0.205	0.067	0.287
logarithm-class	0.067	0.017	0.087
logicalFilterResult-class	0.001	0.001	0.002
logicleTransform	1.740	0.113	1.933
manyFilterResult-class	0.001	0.000	0.002
multipleFilterResult-class	0.001	0.000	0.002
norm2Filter-class	0.351	0.059	0.414
normalizeActionItem-class	0.002	0.000	0.002
normalizeView-class	0.002	0.001	0.003
parameters-methods	0.061	0.015	0.077
polygonGate	0.165	0.034	0.201
quadGate	0.484	0.086	0.572
quadratic-class	0.069	0.024	0.095
quadraticTransform	0.098	0.035	0.134
ratio-class	0.067	0.018	0.085
read.FCS	0.124	0.022	0.148
read.FCSheader	0.019	0.017	0.039
read.flowSet	0.264	0.085	0.394
rectangleGate	0.313	0.058	0.379
sampleFilter-class	0.133	0.033	0.204
scaleTransform	0.108	0.046	0.201
singleParameterTransform-class	0.003	0.001	0.002
sinht-class	0.066	0.017	0.093
split-methods	2.830	0.375	3.565
splitScaleTransform	4.536	1.637	6.280
splitscale-class	0.172	0.048	0.223
squareroot-class	0.065	0.017	0.083
subsettingActionItem-class	0.002	0.000	0.003
subsettingView-class	0.001	0.001	0.002
timeFilter-class	4.079	0.294	4.452
transform-class	0.004	0.001	0.005
transformActionItem-class	0.002	0.000	0.002
transformFilter-class	0.268	0.043	0.321
transformList-class	1.617	0.087	1.734
transformMap-class	0.001	0.000	0.001
transformView-class	0.002	0.000	0.002
truncateTransform	0.229	0.062	0.300
unitytransform-class	0.057	0.017	0.075
view-class	0.002	0.000	0.003
workFlow-class	0.002	0.000	0.002
write.FCS	0.099	0.036	0.140
write.flowSet	2.026	0.200	2.275