BioC 3.0: CHECK report for flowCore on oaxaca

Package: flowCore

Version: 1.32.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.32.2.tar.gz

StartedAt: 2015-04-09 23:26:28 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:28:57 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 149.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.32.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/flowCore.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [13s/14s] OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
biexponentialTransform 5.249    0.2   5.456
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run-all.R’ [6s/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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/flowCore.Rcheck/00check.log’
for details.

* installing *source* package ‘flowCore’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c FastLogicle.cpp -o FastLogicle.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Hyperlog.cpp -o Hyperlog.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Logicle.cpp -o Logicle.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c biexponential.c -o biexponential.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hyperlogTransform.cpp -o hyperlogTransform.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c inPolygon.c -o inPolygon.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c inPolytope.c -o inPolytope.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c logicleTransform.cpp -o logicleTransform.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c zeroin.c -o zeroin.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-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	0.077	0.006	0.083
FCSTransTransform	1.498	0.065	1.567
Subset-methods	0.396	0.023	0.420
actionItem-class	0.002	0.000	0.002
arcsinhTransform	0.057	0.003	0.060
asinht-class	0.041	0.002	0.044
asinhtGml2-class	0.087	0.002	0.089
biexponentialTransform	5.249	0.200	5.456
boundaryFilter-class	0.196	0.024	0.220
characterOrTransformation-class	0.001	0.000	0.001
coerce	0.085	0.009	0.095
compensateActionItem-class	0.001	0.001	0.002
compensateView-class	0.001	0.000	0.001
compensatedParameter-class	0.189	0.010	0.200
compensation-class	0.414	0.036	0.450
dg1polynomial-class	0.039	0.004	0.043
each_col-methods	0.048	0.005	0.053
ellipsoidGate	0.097	0.002	0.099
exponential-class	0.041	0.002	0.043
expressionFilter-class	0.089	0.005	0.094
fcReference-class	0.002	0.000	0.002
filter-methods	0.910	0.061	0.971
filter-on-methods	0.142	0.001	0.144
filterList-class	0.005	0.001	0.006
filterResult-class	0.001	0.000	0.001
filterResultList-class	0.002	0.000	0.002
filterSummary-class	0.002	0.001	0.002
filterSummaryList-class	0.002	0.000	0.002
flowFrame-class	3.254	0.139	3.431
flowSet-class	2.785	0.096	2.899
fsApply	0.201	0.013	0.217
gateActionItem-class	0.002	0.000	0.002
gateView-class	0.001	0.000	0.002
getIndexSort-methods	0.026	0.002	0.027
hyperlog-class	1.965	0.010	1.980
hyperlogtGml2-class	0.089	0.001	0.091
identifier-methods	0.038	0.002	0.039
inverseLogicleTransform	0.674	0.052	0.729
invsplitscale-class	0.044	0.012	0.056
keyword-methods	0.700	0.059	0.761
kmeansFilter	0.232	0.013	0.246
linearTransform	0.049	0.003	0.052
lintGml2-class	0.083	0.005	0.089
lnTransform	1.591	0.142	1.739
logTransform	0.061	0.009	0.071
logarithm-class	0.143	0.014	0.157
logicalFilterResult-class	0.001	0.000	0.002
logicleTransform	0.748	0.056	0.805
logicletGml2-class	0.083	0.014	0.098
logtGml2-class	0.080	0.001	0.081
manyFilterResult-class	0.001	0.000	0.001
multipleFilterResult-class	0.001	0.000	0.001
norm2Filter-class	0.196	0.004	0.220
normalizeActionItem-class	0.001	0.000	0.002
normalizeView-class	0.001	0.000	0.002
parameters-methods	0.037	0.002	0.038
polygonGate	0.095	0.007	0.101
quadGate	0.244	0.003	0.247
quadratic-class	0.041	0.004	0.044
quadraticTransform	0.053	0.004	0.058
ratio-class	0.041	0.003	0.045
ratiotGml2-class	0.078	0.007	0.085
read.FCS	0.079	0.002	0.081
read.FCSheader	0.009	0.002	0.012
read.flowSet	0.138	0.003	0.141
rectangleGate	0.132	0.004	0.135
sampleFilter-class	0.073	0.002	0.075
scaleTransform	0.049	0.003	0.052
singleParameterTransform-class	0.001	0.000	0.002
sinht-class	0.040	0.002	0.042
split-methods	1.354	0.080	1.436
splitScaleTransform	2.136	0.121	2.299
splitscale-class	0.039	0.003	0.040
squareroot-class	0.041	0.002	0.042
subsettingActionItem-class	0.001	0.000	0.001
subsettingView-class	0.001	0.000	0.002
timeFilter-class	1.875	0.077	1.955
transform-class	0.003	0.000	0.003
transformActionItem-class	0.002	0.000	0.002
transformFilter-class	0.138	0.009	0.147
transformList-class	0.673	0.059	0.731
transformMap-class	0.001	0.000	0.002
transformView-class	0.001	0.000	0.002
truncateTransform	0.053	0.012	0.065
unitytransform-class	0.036	0.002	0.038
view-class	0.001	0.000	0.001
workFlow-class	0.003	0.000	0.003
write.FCS	0.149	0.006	0.157
write.flowSet	1.518	0.084	1.604