Package: flowCore

Version: 1.24.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.24.2.tar.gz

StartedAt: 2013-03-24 23:27:43 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:31:05 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 201.3 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/flowCore.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.24.2'
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
biexponentialTransform 9.963  2.818  13.972
flowFrame-class        4.397  0.856   5.552
lnTransform            3.536  1.526   5.438
splitScaleTransform    3.365  1.584   5.114
* 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-2.11-bioc/meat/flowCore.Rcheck/00check.log'
for details.

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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-2.11-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	0.327	0.026	0.363
Subset-methods	1.205	0.151	1.473
actionItem-class	0.002	0.000	0.002
arcsinhTransform	0.187	0.041	0.270
asinht-class	0.047	0.018	0.089
biexponentialTransform	9.963	2.818	13.972
boundaryFilter-class	0.269	0.090	0.412
characterOrTransformation-class	0.001	0.001	0.002
coerce	0.100	0.044	0.153
compensateActionItem-class	0.001	0.000	0.004
compensateView-class	0.001	0.000	0.002
compensatedParameter-class	0.274	0.145	0.457
compensation-class	0.603	0.297	0.909
curv1Filter-class	0.479	0.281	0.819
curv2Filter-class	2.780	0.713	3.585
dg1polynomial-class	0.048	0.018	0.069
each_col-methods	0.061	0.032	0.105
ellipsoidGate	0.113	0.053	0.169
exponential-class	0.045	0.017	0.067
expressionFilter-class	0.126	0.055	0.190
fcReference-class	0.001	0.000	0.002
filter-methods	1.107	0.197	1.364
filter-on-methods	0.206	0.058	0.303
filterList-class	0.010	0.000	0.011
filterResult-class	0.000	0.000	0.001
filterResultList-class	1.749	0.904	2.832
filterSet-class	0.065	0.001	0.066
filterSummary-class	0.143	0.099	0.253
filterSummaryList-class	1.213	0.537	2.055
flowFrame-class	4.397	0.856	5.552
flowSet-class	4.009	0.804	4.916
fsApply	0.264	0.143	0.432
gateActionItem-class	0.001	0.000	0.001
gateView-class	0.001	0.000	0.001
hyperlog-class	1.843	0.041	1.904
identifier-methods	0.040	0.020	0.076
inverseLogicleTransform	0.846	0.148	1.015
invsplitscale-class	0.048	0.030	0.079
keyword-methods	1.138	0.342	1.567
kmeansFilter	0.282	0.076	0.361
linearTransform	0.068	0.033	0.108
lnTransform	3.536	1.526	5.438
logTransform	0.076	0.041	0.122
logarithm-class	0.049	0.023	0.075
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	1.045	0.200	1.335
manyFilterResult-class	0.000	0.000	0.001
multipleFilterResult-class	0.001	0.000	0.001
norm2Filter-class	0.257	0.061	0.324
normalizeActionItem-class	0.001	0.000	0.001
normalizeView-class	0.001	0.000	0.001
parameters-methods	0.047	0.024	0.078
polygonGate	0.114	0.051	0.172
quadGate	0.330	0.095	0.455
quadratic-class	0.045	0.016	0.063
quadraticTransform	0.069	0.034	0.113
ratio-class	0.045	0.016	0.065
read.FCS	0.092	0.042	0.151
read.FCSheader	0.007	0.005	0.012
read.flowSet	0.191	0.091	0.323
rectangleGate	0.171	0.059	0.254
sampleFilter-class	0.096	0.034	0.136
scaleTransform	0.070	0.031	0.107
singleParameterTransform-class	0.001	0.000	0.002
sinht-class	0.054	0.044	0.102
split-methods	1.726	0.426	2.391
splitScaleTransform	3.365	1.584	5.114
splitscale-class	0.208	0.067	0.298
squareroot-class	0.046	0.016	0.067
subsettingActionItem-class	0.001	0.000	0.001
subsettingView-class	0.001	0.001	0.000
timeFilter-class	2.280	0.415	2.892
transform-class	0.003	0.000	0.002
transformActionItem-class	0.001	0.000	0.001
transformFilter-class	0.185	0.037	0.223
transformList-class	0.847	0.162	1.045
transformMap-class	0.001	0.000	0.001
transformView-class	0.000	0.000	0.001
truncateTransform	0.080	0.038	0.119
unitytransform-class	0.049	0.032	0.082
view-class	0.000	0.001	0.001
workFlow-class	0.001	0.000	0.002
write.FCS	0.149	0.031	0.185
write.flowSet	1.596	0.295	1.943