Package: flowCore

Version: 1.25.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.25.13.tar.gz

StartedAt: 2013-03-24 04:59:50 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:04:02 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 251.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.25.13'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flowCore' can be installed ... [20s/24s] 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 DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
[[<-,filterSet-character-ANY-formula : harvest: warning in exists(f,
  env = x@env): partial argument match of 'env' to 'envir'
coerce,environment-flowSet: warning in ls(env = from): partial argument
  match of 'env' to 'envir'
coerce,environment-flowSet : <anonymous>: warning in get(f, env =
  from): partial argument match of 'env' to 'envir'
coerce,filterSet-list: warning in ls(env = from@env): partial argument
  match of 'env' to 'envir'
identifier,filterReference: warning in exists(object@name, env =
  object@env): partial argument match of 'env' to 'envir'
names,filterSet: warning in ls(env = x@env): partial argument match of
  'env' to 'envir'
plot,workFlow-missing : <anonymous>: warning in edgeData(..., at =
  "actionItem"): partial argument match of 'at' to 'attr'
show,filterReference: warning in exists(object@name, env = object@env):
  partial argument match of 'env' to 'envir'
summary,transform: warning in ls(env = e): partial argument match of
  'env' to 'envir'
* 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 ... [80s/82s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
biexponentialTransform 13.061  2.103  15.562
flowFrame-class         5.241  0.513   5.836
flowSet-class           5.002  0.620   5.666
lnTransform             4.044  1.250   5.323
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck/00check.log'
for details.

* installing *source* package 'flowCore' ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c FastLogicle.cpp -o FastLogicle.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Logicle.cpp -o Logicle.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c biexponential.c -o biexponential.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c inPolygon.c -o inPolygon.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c inPolytope.c -o inPolytope.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c init.c -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c logicleTransform.cpp -o logicleTransform.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c zeroin.c -o zeroin.o
llvm-g++-4.2 -arch x86_64 -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 zeroin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'filter' in package 'flowCore'
Creating a new generic function for 'ls' 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	0.140	0.014	0.180
Subset-methods	1.718	0.065	1.852
actionItem-class	0.008	0.007	0.015
arcsinhTransform	0.298	0.021	0.323
asinht-class	0.075	0.013	0.091
biexponentialTransform	13.061	2.103	15.562
boundaryFilter-class	0.217	0.036	0.254
characterOrTransformation-class	0.004	0.005	0.008
coerce	0.151	0.049	0.201
compensateActionItem-class	0.005	0.007	0.011
compensateView-class	0.003	0.005	0.009
compensatedParameter-class	0.406	0.138	0.550
compensation-class	0.801	0.221	1.029
curv1Filter-class	0.710	0.203	0.935
curv2Filter-class	3.116	0.490	3.907
dg1polynomial-class	0.073	0.024	0.120
each_col-methods	0.088	0.018	0.111
ellipsoidGate	0.155	0.044	0.230
exponential-class	0.079	0.046	0.133
expressionFilter-class	0.182	0.058	0.265
fcReference-class	0.006	0.011	0.018
filter-methods	1.253	0.208	1.468
filter-on-methods	0.258	0.039	0.302
filterList-class	0.019	0.009	0.036
filterResult-class	0.004	0.006	0.011
filterResultList-class	2.104	0.766	2.963
filterSet-class	0.103	0.018	0.123
filterSummary-class	0.287	0.107	0.398
filterSummaryList-class	1.753	0.464	2.393
flowFrame-class	5.241	0.513	5.836
flowSet-class	5.002	0.620	5.666
fsApply	0.399	0.100	0.501
gateActionItem-class	0.006	0.008	0.015
gateView-class	0.003	0.006	0.010
hyperlog-class	2.306	0.053	2.367
identifier-methods	0.064	0.017	0.082
inverseLogicleTransform	0.930	0.183	1.112
invsplitscale-class	0.083	0.020	0.103
keyword-methods	1.152	0.341	1.498
kmeansFilter	0.423	0.075	0.504
linearTransform	0.104	0.026	0.132
lnTransform	4.044	1.250	5.323
logTransform	0.105	0.023	0.132
logarithm-class	0.080	0.039	0.119
logicalFilterResult-class	0.004	0.006	0.010
logicleTransform	1.006	0.178	1.188
manyFilterResult-class	0.005	0.007	0.012
multipleFilterResult-class	0.012	0.012	0.025
norm2Filter-class	0.329	0.075	0.405
normalizeActionItem-class	0.004	0.005	0.010
normalizeView-class	0.003	0.005	0.008
parameters-methods	0.074	0.023	0.165
polygonGate	0.178	0.063	0.242
quadGate	0.491	0.098	0.592
quadratic-class	0.078	0.018	0.097
quadraticTransform	0.112	0.039	0.150
ratio-class	0.076	0.016	0.093
read.FCS	0.135	0.040	0.176
read.FCSheader	0.013	0.011	0.024
read.flowSet	0.299	0.084	0.385
rectangleGate	0.233	0.050	0.284
sampleFilter-class	0.138	0.042	0.180
scaleTransform	0.100	0.021	0.123
singleParameterTransform-class	0.004	0.005	0.008
sinht-class	0.076	0.016	0.094
split-methods	2.215	0.439	2.672
splitScaleTransform	3.360	1.314	4.692
splitscale-class	0.071	0.015	0.087
squareroot-class	0.071	0.014	0.086
subsettingActionItem-class	0.004	0.006	0.010
subsettingView-class	0.004	0.005	0.009
timeFilter-class	2.632	0.342	2.989
transform-class	0.008	0.009	0.017
transformActionItem-class	0.009	0.019	0.028
transformFilter-class	0.262	0.038	0.302
transformList-class	0.900	0.146	1.047
transformMap-class	0.010	0.034	0.045
transformView-class	0.004	0.005	0.009
truncateTransform	0.118	0.041	0.161
unitytransform-class	0.063	0.016	0.080
view-class	0.004	0.007	0.012
workFlow-class	0.006	0.010	0.017
write.FCS	0.227	0.034	0.263
write.flowSet	1.927	0.302	2.247