Package: flowCore

Version: 1.22.3

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.22.3.tar.gz

StartedAt: 2012-09-24 00:03:57 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:07:31 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 214.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/flowCore.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.22.3'
* 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 installed files from '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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/flowCore.Rcheck/00check.log'
for details.

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c FastLogicle.cpp -o FastLogicle.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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-2.10-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'filter' in package 'flowCore'
** help
*** installing help indices
** building package indices
** installing vignettes
   'HowTo-flowCore.Rnw' 
** testing if installed package can be loaded

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.191	0.021	0.225
Subset-methods	1.149	0.119	1.273
actionItem-class	0.002	0.000	0.002
arcsinhTransform	0.183	0.029	0.212
asinht-class	0.060	0.019	0.080
biexponentialTransform	10.203	2.082	12.372
boundaryFilter-class	0.332	0.061	0.394
characterOrTransformation-class	0.001	0.000	0.002
coerce	0.127	0.037	0.166
compensateActionItem-class	0.001	0.001	0.001
compensateView-class	0.001	0.000	0.001
compensatedParameter-class	0.350	0.121	0.473
compensation-class	0.756	0.260	1.019
curv1Filter-class	0.557	0.191	0.751
curv2Filter-class	3.625	0.580	4.212
dg1polynomial-class	0.072	0.017	0.090
each_col-methods	0.087	0.032	0.120
ellipsoidGate	0.148	0.032	0.181
exponential-class	0.049	0.013	0.063
expressionFilter-class	0.140	0.053	0.193
fcReference-class	0.001	0.001	0.001
filter-methods	1.267	0.124	1.399
filter-on-methods	0.246	0.038	0.286
filterList-class	0.01	0.00	0.01
filterResult-class	0.001	0.001	0.001
filterResultList-class	1.960	0.660	2.651
filterSet-class	0.070	0.004	0.074
filterSummary-class	0.179	0.072	0.254
filterSummaryList-class	1.608	0.392	2.007
flowFrame-class	5.647	0.696	6.381
flowSet-class	4.872	0.602	5.887
fsApply	0.338	0.124	0.468
gateActionItem-class	0.001	0.001	0.001
gateView-class	0.001	0.000	0.001
hyperlog-class	1.990	0.022	2.014
identifier-methods	0.041	0.012	0.054
inverseLogicleTransform	0.962	0.106	1.071
invsplitscale-class	0.052	0.014	0.065
keyword-methods	1.282	0.258	1.546
kmeansFilter	0.430	0.075	0.506
linearTransform	0.102	0.037	0.139
lnTransform	3.515	1.124	4.669
logTransform	0.102	0.033	0.136
logarithm-class	0.071	0.021	0.094
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	1.470	0.170	1.647
manyFilterResult-class	0.001	0.001	0.001
multipleFilterResult-class	0.000	0.000	0.001
norm2Filter-class	0.281	0.044	0.326
normalizeActionItem-class	0.001	0.000	0.001
normalizeView-class	0.001	0.001	0.001
parameters-methods	0.051	0.014	0.065
polygonGate	0.126	0.037	0.165
quadGate	0.353	0.067	0.421
quadratic-class	0.050	0.015	0.065
quadraticTransform	0.068	0.024	0.095
ratio-class	0.058	0.024	0.091
read.FCS	0.095	0.016	0.112
read.FCSheader	0.010	0.007	0.016
read.flowSet	0.204	0.081	0.285
rectangleGate	0.190	0.035	0.226
sampleFilter-class	0.097	0.031	0.128
scaleTransform	0.073	0.027	0.102
singleParameterTransform-class	0.001	0.000	0.001
sinht-class	0.065	0.019	0.084
split-methods	2.242	0.375	2.646
splitScaleTransform	3.414	1.198	4.654
splitscale-class	0.066	0.016	0.082
squareroot-class	0.068	0.020	0.088
subsettingActionItem-class	0.001	0.000	0.001
subsettingView-class	0.001	0.001	0.001
timeFilter-class	2.619	0.329	2.965
transform-class	0.002	0.000	0.003
transformActionItem-class	0.001	0.001	0.001
transformFilter-class	0.203	0.039	0.242
transformList-class	0.945	0.102	1.049
transformMap-class	0.001	0.001	0.001
transformView-class	0.001	0.000	0.001
truncateTransform	0.084	0.035	0.118
unitytransform-class	0.043	0.013	0.056
view-class	0.001	0.000	0.001
workFlow-class	0.001	0.001	0.002
write.FCS	0.158	0.025	0.184
write.flowSet	1.711	0.202	1.932