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: 2013-03-25 02:23:26 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:27:06 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 219.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowCore.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.25.13'
* 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 ... [18s/19s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [71s/72s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
biexponentialTransform 10.232  2.216  12.534
flowFrame-class         4.635  0.671   5.365
curv2Filter-class       4.207  0.788   5.025
* 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
*** 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
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 zeroin.c -o zeroin.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 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/i386
** 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	0.098	0.022	0.122
Subset-methods	1.275	0.131	1.410
actionItem-class	0.007	0.006	0.013
arcsinhTransform	0.122	0.044	0.168
asinht-class	0.058	0.023	0.082
biexponentialTransform	10.232	2.216	12.534
boundaryFilter-class	0.170	0.041	0.211
characterOrTransformation-class	0.003	0.004	0.007
coerce	0.117	0.048	0.167
compensateActionItem-class	0.004	0.005	0.009
compensateView-class	0.003	0.006	0.009
compensatedParameter-class	0.287	0.130	0.421
compensation-class	0.833	0.347	1.201
curv1Filter-class	0.657	0.232	0.899
curv2Filter-class	4.207	0.788	5.025
dg1polynomial-class	0.073	0.028	0.102
each_col-methods	0.087	0.033	0.124
ellipsoidGate	0.179	0.076	0.262
exponential-class	0.069	0.025	0.095
expressionFilter-class	0.190	0.076	0.269
fcReference-class	0.008	0.011	0.019
filter-methods	1.356	0.173	1.543
filter-on-methods	0.225	0.057	0.283
filterList-class	0.016	0.008	0.025
filterResult-class	0.003	0.005	0.008
filterResultList-class	1.715	0.645	2.389
filterSet-class	0.075	0.015	0.089
filterSummary-class	0.153	0.081	0.235
filterSummaryList-class	1.387	0.388	1.800
flowFrame-class	4.635	0.671	5.365
flowSet-class	4.107	0.603	4.732
fsApply	0.296	0.135	0.436
gateActionItem-class	0.004	0.005	0.008
gateView-class	0.003	0.005	0.008
hyperlog-class	2.145	0.037	2.184
identifier-methods	0.045	0.019	0.064
inverseLogicleTransform	0.972	0.134	1.113
invsplitscale-class	0.058	0.023	0.081
keyword-methods	1.281	0.268	1.563
kmeansFilter	0.292	0.080	0.374
linearTransform	0.077	0.032	0.112
lnTransform	2.901	1.136	4.074
logTransform	0.175	0.051	0.231
logarithm-class	0.050	0.023	0.077
logicalFilterResult-class	0.003	0.004	0.008
logicleTransform	0.974	0.142	1.142
manyFilterResult-class	0.004	0.007	0.010
multipleFilterResult-class	0.003	0.006	0.010
norm2Filter-class	0.253	0.064	0.323
normalizeActionItem-class	0.003	0.006	0.010
normalizeView-class	0.003	0.005	0.010
parameters-methods	0.053	0.034	0.088
polygonGate	0.123	0.043	0.169
quadGate	0.349	0.080	0.433
quadratic-class	0.070	0.036	0.110
quadraticTransform	0.085	0.033	0.118
ratio-class	0.056	0.031	0.087
read.FCS	0.098	0.029	0.127
read.FCSheader	0.011	0.012	0.025
read.flowSet	0.244	0.107	0.361
rectangleGate	0.234	0.067	0.304
sampleFilter-class	0.094	0.037	0.133
scaleTransform	0.069	0.031	0.100
singleParameterTransform-class	0.007	0.020	0.025
sinht-class	0.050	0.018	0.068
split-methods	1.714	0.336	2.075
splitScaleTransform	2.700	1.100	3.839
splitscale-class	0.155	0.042	0.201
squareroot-class	0.051	0.021	0.075
subsettingActionItem-class	0.003	0.005	0.009
subsettingView-class	0.003	0.005	0.009
timeFilter-class	2.413	0.319	2.753
transform-class	0.006	0.008	0.015
transformActionItem-class	0.004	0.005	0.009
transformFilter-class	0.191	0.045	0.240
transformList-class	0.994	0.121	1.125
transformMap-class	0.005	0.005	0.009
transformView-class	0.004	0.005	0.009
truncateTransform	0.099	0.039	0.140
unitytransform-class	0.062	0.026	0.088
view-class	0.005	0.008	0.012
workFlow-class	0.007	0.012	0.019
write.FCS	0.243	0.044	0.288
write.flowSet	1.749	0.216	1.974