BioC 2.12: CHECK report for flowCore on petty

Package: flowCore

Version: 1.26.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.26.3.tar.gz

StartedAt: 2013-10-08 22:19:39 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:24:20 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 280.9 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 3.0.1 (2013-05-16)
* 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 '1.26.3'
* 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 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 ... [23s/27s] 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 ... [84s/85s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
biexponentialTransform 12.893  1.692  14.791
flowFrame-class         6.307  0.470   6.935
flowSet-class           5.700  0.529   6.247
* 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 -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
** testing if installed package can be loaded
* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.145	0.011	0.157
Subset-methods	1.664	0.045	1.728
actionItem-class	0.010	0.002	0.012
arcsinhTransform	0.288	0.009	0.297
asinht-class	0.079	0.008	0.086
biexponentialTransform	12.893	1.692	14.791
boundaryFilter-class	0.243	0.035	0.280
characterOrTransformation-class	0.003	0.004	0.007
coerce	0.158	0.041	0.201
compensateActionItem-class	0.004	0.004	0.007
compensateView-class	0.003	0.004	0.008
compensatedParameter-class	0.413	0.104	0.521
compensation-class	0.839	0.194	1.038
curv1Filter-class	0.745	0.182	0.936
curv2Filter-class	3.949	0.391	4.374
dg1polynomial-class	0.075	0.015	0.089
each_col-methods	0.078	0.017	0.096
ellipsoidGate	0.183	0.055	0.239
exponential-class	0.074	0.013	0.087
expressionFilter-class	0.191	0.047	0.238
fcReference-class	0.011	0.034	0.045
filter-methods	1.455	0.182	1.651
filter-on-methods	0.284	0.027	0.322
filterList-class	0.018	0.006	0.026
filterResult-class	0.004	0.005	0.009
filterResultList-class	2.116	0.622	2.823
filterSet-class	0.117	0.022	0.140
filterSummary-class	0.262	0.073	0.338
filterSummaryList-class	1.811	0.383	2.210
flowFrame-class	6.307	0.470	6.935
flowSet-class	5.700	0.529	6.247
fsApply	0.391	0.070	0.463
gateActionItem-class	0.003	0.004	0.008
gateView-class	0.004	0.004	0.008
hyperlog-class	2.967	0.025	3.003
identifier-methods	0.063	0.013	0.078
inverseLogicleTransform	1.073	0.148	1.242
invsplitscale-class	0.080	0.024	0.105
keyword-methods	1.476	0.306	1.789
kmeansFilter	0.467	0.070	0.538
linearTransform	0.104	0.019	0.123
lnTransform	3.637	0.984	4.645
logTransform	0.099	0.017	0.116
logarithm-class	0.074	0.012	0.086
logicalFilterResult-class	0.003	0.004	0.007
logicleTransform	1.143	0.155	1.302
manyFilterResult-class	0.004	0.005	0.009
multipleFilterResult-class	0.008	0.008	0.017
norm2Filter-class	0.327	0.042	0.369
normalizeActionItem-class	0.003	0.004	0.008
normalizeView-class	0.003	0.004	0.007
parameters-methods	0.070	0.015	0.085
polygonGate	0.172	0.038	0.210
quadGate	0.445	0.063	0.508
quadratic-class	0.076	0.029	0.105
quadraticTransform	0.102	0.018	0.120
ratio-class	0.082	0.028	0.109
read.FCS	0.142	0.022	0.165
read.FCSheader	0.014	0.010	0.024
read.flowSet	0.474	0.113	0.589
rectangleGate	0.261	0.048	0.310
sampleFilter-class	0.139	0.031	0.170
scaleTransform	0.093	0.017	0.111
singleParameterTransform-class	0.004	0.004	0.007
sinht-class	0.072	0.013	0.084
split-methods	2.211	0.362	2.579
splitScaleTransform	3.851	0.936	4.869
splitscale-class	0.076	0.014	0.091
squareroot-class	0.073	0.012	0.090
subsettingActionItem-class	0.008	0.012	0.020
subsettingView-class	0.003	0.004	0.007
timeFilter-class	3.407	0.294	3.912
transform-class	0.008	0.007	0.015
transformActionItem-class	0.003	0.005	0.009
transformFilter-class	0.267	0.035	0.325
transformList-class	1.053	0.154	1.278
transformMap-class	0.004	0.005	0.008
transformView-class	0.010	0.031	0.042
truncateTransform	0.102	0.019	0.132
unitytransform-class	0.067	0.014	0.083
view-class	0.005	0.006	0.010
workFlow-class	0.007	0.009	0.020
write.FCS	0.254	0.030	0.303
write.flowSet	2.258	0.272	2.546