BioC 3.0: CHECK report for flowCore on zin1

Package: flowCore

Version: 1.32.2

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.32.2.tar.gz

StartedAt: 2015-04-09 23:51:37 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:53:42 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 125.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.32.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/flowCore.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.32.2’
* 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 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 ... [11s/11s] OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.3Mb
    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
'library' or 'require' calls in package code:
  ‘Rgraphviz’ ‘ncdf’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
ncdfExpressionMatrix: no visible global function definition for
  ‘dim.def.ncdf’
ncdfExpressionMatrix: no visible global function definition for
  ‘var.def.ncdf’
ncdfExpressionMatrix: no visible global function definition for
  ‘create.ncdf’
ncdfExpressionMatrix: no visible global function definition for
  ‘put.var.ncdf’
ncdfExpressionMatrix: no visible global function definition for
  ‘close.ncdf’
%in%,flowFrame-norm2Filter: no visible global function definition for
  ‘cov.rob’
exprs,flowFrame: no visible global function definition for ‘open.ncdf’
exprs,flowFrame: no visible global function definition for
  ‘get.var.ncdf’
exprs,flowFrame: no visible global function definition for ‘close.ncdf’
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
biexponentialTransform 5.78  0.088   6.053
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run-all.R’ [5s/6s]
 [6s/6s] OK
* 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
* DONE

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/flowCore.Rcheck/00check.log’
for details.

* installing *source* package ‘flowCore’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Hyperlog.cpp -o Hyperlog.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Logicle.cpp -o Logicle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c biexponential.c -o biexponential.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hyperlogTransform.cpp -o hyperlogTransform.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c logicleTransform.cpp -o logicleTransform.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c zeroin.c -o zeroin.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/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 -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.068	0.000	0.069
FCSTransTransform	1.360	0.024	1.388
Subset-methods	0.352	0.004	0.356
actionItem-class	0.000	0.000	0.002
arcsinhTransform	0.048	0.000	0.048
asinht-class	0.036	0.000	0.035
asinhtGml2-class	0.068	0.000	0.068
biexponentialTransform	5.780	0.088	6.053
boundaryFilter-class	0.092	0.004	0.098
characterOrTransformation-class	0.000	0.000	0.001
coerce	0.156	0.004	0.158
compensateActionItem-class	0.000	0.000	0.001
compensateView-class	0.000	0.000	0.001
compensatedParameter-class	0.164	0.000	0.162
compensation-class	0.400	0.004	0.404
dg1polynomial-class	0.032	0.000	0.032
each_col-methods	0.040	0.004	0.044
ellipsoidGate	0.072	0.000	0.071
exponential-class	0.032	0.000	0.033
expressionFilter-class	0.068	0.004	0.074
fcReference-class	0.004	0.000	0.001
filter-methods	0.740	0.028	0.773
filter-on-methods	0.120	0.004	0.124
filterList-class	0.008	0.000	0.008
filterResult-class	0.004	0.000	0.001
filterResultList-class	0.000	0.000	0.001
filterSummary-class	0.000	0.000	0.002
filterSummaryList-class	0.000	0.000	0.001
flowFrame-class	3.328	0.060	3.409
flowSet-class	2.513	0.008	2.647
fsApply	0.184	0.004	0.189
gateActionItem-class	0.000	0.000	0.001
gateView-class	0.004	0.000	0.001
getIndexSort-methods	0.024	0.004	0.030
hyperlog-class	1.928	0.000	2.027
hyperlogtGml2-class	0.068	0.000	0.067
identifier-methods	0.028	0.000	0.029
inverseLogicleTransform	0.564	0.028	0.620
invsplitscale-class	0.040	0.000	0.038
keyword-methods	0.608	0.020	0.664
kmeansFilter	0.212	0.000	0.209
linearTransform	0.044	0.004	0.047
lintGml2-class	0.072	0.000	0.074
lnTransform	1.340	0.016	1.357
logTransform	0.048	0.000	0.045
logarithm-class	0.036	0.000	0.035
logicalFilterResult-class	0.000	0.000	0.001
logicleTransform	0.732	0.008	0.746
logicletGml2-class	0.068	0.000	0.069
logtGml2-class	0.064	0.000	0.064
manyFilterResult-class	0.000	0.000	0.002
multipleFilterResult-class	0.000	0.000	0.001
norm2Filter-class	0.168	0.000	0.166
normalizeActionItem-class	0.000	0.000	0.001
normalizeView-class	0.000	0.000	0.001
parameters-methods	0.032	0.000	0.032
polygonGate	0.080	0.000	0.078
quadGate	0.208	0.004	0.214
quadratic-class	0.028	0.004	0.033
quadraticTransform	0.044	0.000	0.044
ratio-class	0.036	0.000	0.037
ratiotGml2-class	0.064	0.000	0.062
read.FCS	0.060	0.004	0.064
read.FCSheader	0.008	0.000	0.010
read.flowSet	0.112	0.000	0.114
rectangleGate	0.108	0.000	0.110
sampleFilter-class	0.06	0.00	0.06
scaleTransform	0.040	0.000	0.044
singleParameterTransform-class	0.000	0.000	0.001
sinht-class	0.036	0.000	0.033
split-methods	1.204	0.024	1.242
splitScaleTransform	1.984	0.012	2.002
splitscale-class	0.036	0.000	0.043
squareroot-class	0.036	0.000	0.063
subsettingActionItem-class	0.000	0.004	0.002
subsettingView-class	0.000	0.000	0.002
timeFilter-class	1.544	0.012	1.669
transform-class	0.004	0.000	0.002
transformActionItem-class	0.004	0.000	0.002
transformFilter-class	0.120	0.004	0.127
transformList-class	0.672	0.020	0.706
transformMap-class	0.000	0.000	0.001
transformView-class	0.000	0.000	0.001
truncateTransform	0.036	0.004	0.042
unitytransform-class	0.028	0.000	0.030
view-class	0.004	0.000	0.001
workFlow-class	0.000	0.000	0.001
write.FCS	0.104	0.004	0.108
write.flowSet	1.036	0.036	1.105