BioC 2.13: CHECK report for flowCore on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowCore.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.28.24’
* 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/22s] OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.1Mb
    extdata   1.1Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘:::’ calls which should be ‘::’:
  ‘Rgraphviz:::layoutGraph’ ‘Rgraphviz:::renderGraph’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘inpolygon’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [74s/82s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
biexponentialTransform 11.981  1.915  16.159
splitScaleTransform     5.144  1.019   6.431
lnTransform             4.174  1.043   5.413
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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 -Wall  -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 -Wall  -c Hyperlog.cpp -o Hyperlog.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 -Wall  -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 -Wall  -c biexponential.c -o biexponential.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 -Wall  -c hyperlogTransform.cpp -o hyperlogTransform.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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 Hyperlog.o Logicle.o biexponential.o hyperlogTransform.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-2.13-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.097	0.012	0.109
FCSTransTransform	2.770	0.153	4.424
Subset-methods	0.739	0.089	1.485
actionItem-class	0.008	0.004	0.012
arcsinhTransform	0.091	0.035	0.128
asinht-class	0.050	0.016	0.066
asinhtGml2-class	0.056	0.015	0.073
biexponentialTransform	11.981	1.915	16.159
boundaryFilter-class	0.166	0.030	0.222
characterOrTransformation-class	0.003	0.004	0.009
coerce	0.124	0.043	0.185
compensateActionItem-class	0.003	0.004	0.009
compensateView-class	0.003	0.004	0.007
compensatedParameter-class	0.313	0.136	0.494
compensation-class	0.672	0.225	0.916
curv1Filter-class	0.544	0.183	0.733
curv2Filter-class	2.405	0.417	2.939
dg1polynomial-class	0.051	0.015	0.067
each_col-methods	0.055	0.015	0.072
ellipsoidGate	0.139	0.071	0.212
exponential-class	0.048	0.014	0.064
expressionFilter-class	0.144	0.053	0.203
fcReference-class	0.010	0.026	0.035
filter-methods	0.908	0.163	1.074
filter-on-methods	0.200	0.039	0.240
filterList-class	0.014	0.007	0.021
filterResult-class	0.003	0.003	0.007
filterResultList-class	1.855	0.698	2.686
filterSet-class	0.089	0.030	0.120
filterSummary-class	0.198	0.098	0.299
filterSummaryList-class	1.191	0.386	1.607
flowFrame-class	4.329	0.486	4.940
flowSet-class	4.201	0.577	4.941
fsApply	0.289	0.079	0.371
gateActionItem-class	0.004	0.004	0.008
gateView-class	0.003	0.004	0.008
getIndexSort-methods	0.052	0.017	0.070
hyperlog-class	1.948	0.030	1.996
hyperlogtGml2-class	0.066	0.019	0.084
identifier-methods	0.065	0.019	0.086
inverseLogicleTransform	0.690	0.162	0.903
invsplitscale-class	0.064	0.027	0.092
keyword-methods	1.142	0.310	1.486
kmeansFilter	0.351	0.077	0.440
linearTransform	0.074	0.021	0.096
lintGml2-class	0.045	0.013	0.058
lnTransform	4.174	1.043	5.413
logTransform	0.327	0.076	0.433
logarithm-class	0.050	0.014	0.066
logicalFilterResult-class	0.004	0.005	0.009
logicleTransform	0.760	0.154	0.923
logicletGml2-class	0.055	0.016	0.070
logtGml2-class	0.059	0.032	0.092
manyFilterResult-class	0.003	0.005	0.009
multipleFilterResult-class	0.003	0.007	0.010
norm2Filter-class	0.249	0.061	0.314
normalizeActionItem-class	0.004	0.005	0.009
normalizeView-class	0.004	0.005	0.009
parameters-methods	0.059	0.033	0.101
polygonGate	0.138	0.047	0.184
quadGate	0.355	0.068	0.424
quadratic-class	0.052	0.013	0.067
quadraticTransform	0.077	0.021	0.101
ratio-class	0.055	0.016	0.072
ratiotGml2-class	0.054	0.026	0.082
read.FCS	0.108	0.027	0.136
read.FCSheader	0.015	0.010	0.026
read.flowSet	0.227	0.082	0.317
rectangleGate	0.193	0.057	0.253
sampleFilter-class	0.110	0.044	0.155
scaleTransform	0.075	0.022	0.099
singleParameterTransform-class	0.004	0.004	0.008
sinht-class	0.056	0.016	0.072
split-methods	1.536	0.366	1.928
splitScaleTransform	5.144	1.019	6.431
splitscale-class	0.046	0.013	0.059
squareroot-class	0.047	0.013	0.061
subsettingActionItem-class	0.008	0.014	0.022
subsettingView-class	0.004	0.006	0.009
timeFilter-class	2.278	0.315	2.628
transform-class	0.007	0.008	0.014
transformActionItem-class	0.003	0.005	0.009
transformFilter-class	0.180	0.028	0.208
transformList-class	0.660	0.134	0.850
transformMap-class	0.003	0.004	0.007
transformView-class	0.003	0.004	0.008
truncateTransform	0.066	0.017	0.087
unitytransform-class	0.046	0.015	0.064
view-class	0.003	0.005	0.008
workFlow-class	0.012	0.024	0.036
write.FCS	0.163	0.028	0.197
write.flowSet	1.517	0.263	1.907

BioC 2.13: CHECK report for flowCore on perceval

Summary

Command output