Package: flowCore

Version: 1.19.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.19.1.tar.gz

StartedAt: 2011-05-09 14:25:04 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:29:13 -0700 (Mon, 09 May 2011)

EllapsedTime: 249.7 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) (2011-04-24 r55634)
* 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 ‘1.19.1’
* 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 17.6Mb
  sub-directories of 1Mb or more:
    data      8.1Mb
    doc       7.1Mb
    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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘HowTo-flowCore.pdf’ from 7154Kb to 971Kb
  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/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -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 -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 -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 -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 -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 -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 -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	0.226	0.021	0.250
Subset-methods	1.561	0.154	1.731
actionItem-class	0.002	0.001	0.003
arcsinhTransform	0.195	0.040	0.242
asinht-class	0.073	0.019	0.093
biexponentialTransform	12.246	3.059	15.507
boundaryFilter-class	0.352	0.062	0.417
characterOrTransformation-class	0.002	0.000	0.002
coerce	0.144	0.046	0.192
compensateActionItem-class	0.002	0.000	0.002
compensateView-class	0.002	0.001	0.003
compensatedParameter-class	0.392	0.135	0.529
compensation-class	0.911	0.322	1.243
curv1Filter-class	1.325	0.272	1.617
curv2Filter-class	5.583	0.688	6.334
dg1polynomial-class	0.072	0.027	0.099
each_col-methods	0.083	0.023	0.107
ellipsoidGate	0.165	0.045	0.212
exponential-class	0.070	0.018	0.090
expressionFilter-class	0.180	0.062	0.250
fcReference-class	0.002	0.000	0.002
filter-methods	2.167	0.105	2.303
filter-on-methods	0.339	0.049	0.389
filterList-class	0.019	0.000	0.019
filterResult-class	0.002	0.000	0.003
filterResultList-class	3.464	0.796	4.314
filterSet-class	0.106	0.002	0.114
filterSummary-class	0.815	0.112	0.936
filterSummaryList-class	2.927	0.468	3.444
flowFrame-class	6.495	0.699	7.331
flowSet-class	6.780	0.698	7.542
fsApply	0.393	0.147	0.547
gateActionItem-class	0.002	0.000	0.002
gateView-class	0.002	0.001	0.002
hyperlog-class	2.698	0.035	2.769
identifier-methods	0.055	0.016	0.071
inverseLogicleTransform	1.655	0.087	1.762
invsplitscale-class	0.070	0.018	0.088
keyword-methods	1.932	0.265	2.211
kmeansFilter	0.437	0.087	0.528
linearTransform	0.099	0.039	0.138
lnTransform	4.543	1.737	6.388
logTransform	0.210	0.065	0.276
logarithm-class	0.070	0.021	0.092
logicalFilterResult-class	0.002	0.000	0.002
logicleTransform	1.745	0.100	1.863
manyFilterResult-class	0.002	0.000	0.002
multipleFilterResult-class	0.001	0.000	0.002
norm2Filter-class	0.351	0.067	0.419
normalizeActionItem-class	0.002	0.000	0.002
normalizeView-class	0.002	0.000	0.003
parameters-methods	0.064	0.018	0.082
polygonGate	0.164	0.041	0.206
quadGate	0.491	0.100	0.595
quadratic-class	0.070	0.027	0.097
quadraticTransform	0.099	0.037	0.135
ratio-class	0.067	0.019	0.086
read.FCS	0.126	0.026	0.154
read.FCSheader	0.014	0.005	0.020
read.flowSet	0.266	0.106	0.379
rectangleGate	0.326	0.073	0.409
sampleFilter-class	0.132	0.032	0.164
scaleTransform	0.106	0.050	0.170
singleParameterTransform-class	0.002	0.000	0.002
sinht-class	0.065	0.017	0.083
split-methods	2.842	0.362	3.349
splitScaleTransform	4.587	1.770	6.777
splitscale-class	0.069	0.019	0.091
squareroot-class	0.069	0.020	0.089
subsettingActionItem-class	0.002	0.000	0.002
subsettingView-class	0.002	0.000	0.002
timeFilter-class	4.269	0.362	4.798
transform-class	0.004	0.000	0.005
transformActionItem-class	0.002	0.001	0.002
transformFilter-class	0.275	0.048	0.334
transformList-class	1.643	0.094	1.740
transformMap-class	0.002	0.000	0.001
transformView-class	0.002	0.000	0.002
truncateTransform	0.096	0.033	0.130
unitytransform-class	0.059	0.017	0.076
view-class	0.002	0.001	0.003
workFlow-class	0.002	0.000	0.002
write.FCS	0.107	0.038	0.147
write.flowSet	2.078	0.233	2.703