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: 2011-07-07 02:51:24 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:57:06 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 342.3 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) (2011-06-22 r56208)
* 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 '1.19.2'
* 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       1.2Mb
    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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
           old_size new_size compress
  GvHD.rda    8.0Mb    5.0Mb       xz
* 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/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++-4.2 -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-4.2 -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-4.2 -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-4.2 -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-4.2 -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++-4.2 -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++-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 1.3-01)
** 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)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.231	0.025	0.277
Subset-methods	1.676	0.162	1.919
actionItem-class	0.002	0.000	0.003
arcsinhTransform	0.219	0.051	0.332
asinht-class	0.076	0.024	0.119
biexponentialTransform	12.268	3.149	16.314
boundaryFilter-class	0.366	0.067	0.442
characterOrTransformation-class	0.002	0.001	0.002
coerce	0.142	0.041	0.190
compensateActionItem-class	0.005	0.008	0.013
compensateView-class	0.002	0.000	0.002
compensatedParameter-class	0.396	0.141	0.562
compensation-class	0.895	0.306	1.243
curv1Filter-class	1.293	0.271	1.584
curv2Filter-class	5.583	0.715	6.465
dg1polynomial-class	0.071	0.018	0.094
each_col-methods	0.086	0.024	0.112
ellipsoidGate	0.171	0.048	0.236
exponential-class	0.067	0.017	0.085
expressionFilter-class	0.178	0.056	0.237
fcReference-class	0.002	0.001	0.002
filter-methods	2.256	0.112	2.393
filter-on-methods	0.368	0.050	0.430
filterList-class	0.019	0.001	0.021
filterResult-class	0.001	0.000	0.001
filterResultList-class	3.486	0.773	4.324
filterSet-class	0.109	0.006	0.115
filterSummary-class	0.790	0.105	0.907
filterSummaryList-class	2.871	0.479	3.393
flowFrame-class	6.791	0.731	7.911
flowSet-class	6.974	0.667	7.781
fsApply	0.405	0.135	0.551
gateActionItem-class	0.001	0.001	0.002
gateView-class	0.001	0.000	0.002
hyperlog-class	2.866	0.045	2.936
identifier-methods	0.056	0.016	0.072
inverseLogicleTransform	1.701	0.090	1.824
invsplitscale-class	0.075	0.032	0.108
keyword-methods	1.882	0.257	2.206
kmeansFilter	0.560	0.105	0.697
linearTransform	0.105	0.035	0.144
lnTransform	5.050	1.588	6.922
logTransform	0.202	0.069	0.303
logarithm-class	0.069	0.019	0.111
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	1.791	0.106	2.118
manyFilterResult-class	0.001	0.001	0.002
multipleFilterResult-class	0.001	0.000	0.002
norm2Filter-class	0.385	0.064	0.459
normalizeActionItem-class	0.002	0.000	0.031
normalizeView-class	0.001	0.001	0.002
parameters-methods	0.065	0.017	0.093
polygonGate	0.177	0.047	0.227
quadGate	0.618	0.096	0.730
quadratic-class	0.068	0.017	0.087
quadraticTransform	0.110	0.040	0.152
ratio-class	0.072	0.032	0.107
read.FCS	0.124	0.021	0.146
read.FCSheader	0.010	0.004	0.015
read.flowSet	0.273	0.098	0.374
rectangleGate	0.321	0.046	0.370
sampleFilter-class	0.141	0.040	0.189
scaleTransform	0.101	0.034	0.138
singleParameterTransform-class	0.002	0.001	0.002
sinht-class	0.068	0.018	0.086
split-methods	2.970	0.384	3.493
splitScaleTransform	5.067	1.665	7.175
splitscale-class	0.069	0.019	0.093
squareroot-class	0.073	0.021	0.107
subsettingActionItem-class	0.001	0.000	0.003
subsettingView-class	0.001	0.001	0.002
timeFilter-class	4.388	0.343	4.886
transform-class	0.004	0.000	0.004
transformActionItem-class	0.001	0.001	0.001
transformFilter-class	0.274	0.044	0.328
transformList-class	1.674	0.087	1.815
transformMap-class	0.001	0.000	0.002
transformView-class	0.002	0.001	0.002
truncateTransform	0.130	0.061	0.204
unitytransform-class	0.060	0.016	0.076
view-class	0.001	0.000	0.001
workFlow-class	0.001	0.001	0.002
write.FCS	0.106	0.035	0.163
write.flowSet	2.134	0.222	2.421