Package: flowCore

Version: 1.22.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.22.0.tar.gz

StartedAt: 2012-04-01 00:52:12 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 00:54:19 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 126.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/flowCore.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.22.0'
* 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  8.8Mb
  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 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
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/flowCore.Rcheck/00check.log'
for details.

* installing *source* package 'flowCore' ...
** libs
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Logicle.cpp -o Logicle.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c biexponential.c -o biexponential.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c logicleTransform.cpp -o logicleTransform.o
g++ -shared -L/usr/local/lib -o flowCore.so FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
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
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.148	0.000	0.149
Subset-methods	0.672	0.012	0.689
actionItem-class	0.000	0.000	0.001
arcsinhTransform	0.128	0.000	0.131
asinht-class	0.108	0.000	0.114
biexponentialTransform	6.944	0.140	7.098
boundaryFilter-class	0.180	0.008	0.199
characterOrTransformation-class	0.000	0.000	0.001
coerce	0.076	0.000	0.082
compensateActionItem-class	0	0	0
compensateView-class	0.000	0.000	0.001
compensatedParameter-class	0.196	0.000	0.203
compensation-class	0.476	0.008	0.487
curv1Filter-class	0.356	0.000	0.360
curv2Filter-class	2.532	0.000	2.539
dg1polynomial-class	0.032	0.000	0.035
each_col-methods	0.044	0.000	0.047
ellipsoidGate	0.072	0.000	0.077
exponential-class	0.032	0.000	0.036
expressionFilter-class	0.088	0.004	0.095
fcReference-class	0.000	0.000	0.001
filter-methods	0.776	0.040	0.828
filter-on-methods	0.140	0.004	0.149
filterList-class	0.008	0.000	0.008
filterResult-class	0.004	0.000	0.000
filterResultList-class	1.097	0.020	1.124
filterSet-class	0.056	0.000	0.056
filterSummary-class	0.124	0.000	0.127
filterSummaryList-class	1.024	0.012	1.045
flowFrame-class	3.140	0.060	3.261
flowSet-class	2.788	0.044	2.849
fsApply	0.208	0.004	0.217
gateActionItem-class	0	0	0
gateView-class	0.004	0.000	0.001
hyperlog-class	1.476	0.000	1.482
identifier-methods	0.028	0.000	0.033
inverseLogicleTransform	0.604	0.016	0.631
invsplitscale-class	0.032	0.004	0.042
keyword-methods	0.760	0.036	0.812
kmeansFilter	0.212	0.004	0.220
linearTransform	0.048	0.000	0.055
lnTransform	2.240	0.020	2.272
logTransform	0.048	0.000	0.053
logarithm-class	0.124	0.004	0.132
logicalFilterResult-class	0.004	0.000	0.000
logicleTransform	0.648	0.024	0.683
manyFilterResult-class	0.000	0.000	0.001
multipleFilterResult-class	0	0	0
norm2Filter-class	0.172	0.004	0.182
normalizeActionItem-class	0.000	0.000	0.001
normalizeView-class	0	0	0
parameters-methods	0.036	0.000	0.037
polygonGate	0.080	0.004	0.091
quadGate	0.240	0.000	0.246
quadratic-class	0.036	0.000	0.039
quadraticTransform	0.048	0.000	0.057
ratio-class	0.036	0.000	0.042
read.FCS	0.064	0.004	0.075
read.FCSheader	0.008	0.000	0.015
read.flowSet	0.136	0.004	0.141
rectangleGate	0.124	0.000	0.131
sampleFilter-class	0.072	0.000	0.078
scaleTransform	0.048	0.000	0.052
singleParameterTransform-class	0.000	0.000	0.001
sinht-class	0.036	0.000	0.044
split-methods	1.177	0.036	1.221
splitScaleTransform	2.248	0.036	2.292
splitscale-class	0.036	0.000	0.039
squareroot-class	0.032	0.004	0.041
subsettingActionItem-class	0	0	0
subsettingView-class	0.000	0.000	0.001
timeFilter-class	1.768	0.032	1.806
transform-class	0.004	0.000	0.002
transformActionItem-class	0	0	0
transformFilter-class	0.136	0.004	0.141
transformList-class	0.588	0.028	0.628
transformMap-class	0.000	0.000	0.001
transformView-class	0.000	0.000	0.001
truncateTransform	0.048	0.000	0.055
unitytransform-class	0.036	0.000	0.041
view-class	0.000	0.000	0.001
workFlow-class	0.000	0.000	0.001
write.FCS	0.108	0.004	0.117
write.flowSet	1.132	0.020	1.171