BioC 3.0: CHECK report for flowCore on perceval

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: 2015-04-10 01:26:30 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:29:53 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 203.7 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-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 ‘1.32.2’
* 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 ... [16s/31s] OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  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:
  ‘ncdf’ ‘Rgraphviz’
  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 ... [46s/46s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
biexponentialTransform 7.678  0.365   8.062
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run-all.R’ [8s/8s]
 [9s/9s] 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
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/Library/Frameworks/R.framework/Resources/lib -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-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	0.225	0.007	0.232
FCSTransTransform	2.066	0.130	2.198
Subset-methods	0.539	0.053	0.593
actionItem-class	0.003	0.000	0.003
arcsinhTransform	0.068	0.002	0.069
asinht-class	0.038	0.001	0.039
asinhtGml2-class	0.092	0.002	0.093
biexponentialTransform	7.678	0.365	8.062
boundaryFilter-class	0.137	0.007	0.149
characterOrTransformation-class	0.002	0.001	0.002
coerce	0.094	0.007	0.103
compensateActionItem-class	0.002	0.000	0.002
compensateView-class	0.002	0.001	0.002
compensatedParameter-class	0.402	0.058	0.463
compensation-class	0.449	0.070	0.520
dg1polynomial-class	0.041	0.006	0.047
each_col-methods	0.046	0.006	0.051
ellipsoidGate	0.102	0.016	0.119
exponential-class	0.041	0.001	0.043
expressionFilter-class	0.096	0.009	0.106
fcReference-class	0.002	0.001	0.003
filter-methods	0.880	0.118	0.999
filter-on-methods	0.171	0.002	0.172
filterList-class	0.015	0.000	0.015
filterResult-class	0.002	0.000	0.001
filterResultList-class	0.002	0.001	0.002
filterSummary-class	0.001	0.000	0.002
filterSummaryList-class	0.001	0.000	0.002
flowFrame-class	3.901	0.265	4.317
flowSet-class	3.234	0.216	3.482
fsApply	0.221	0.027	0.248
gateActionItem-class	0.002	0.000	0.002
gateView-class	0.002	0.000	0.002
getIndexSort-methods	0.037	0.002	0.039
hyperlog-class	2.352	0.013	2.366
hyperlogtGml2-class	0.098	0.002	0.101
identifier-methods	0.033	0.002	0.036
inverseLogicleTransform	0.645	0.104	0.750
invsplitscale-class	0.045	0.026	0.071
keyword-methods	0.683	0.120	0.804
kmeansFilter	0.243	0.044	0.286
linearTransform	0.050	0.003	0.053
lintGml2-class	0.085	0.005	0.090
lnTransform	1.819	0.289	2.162
logTransform	0.065	0.008	0.073
logarithm-class	0.044	0.005	0.049
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	0.935	0.121	1.056
logicletGml2-class	0.090	0.003	0.094
logtGml2-class	0.082	0.003	0.084
manyFilterResult-class	0.001	0.000	0.002
multipleFilterResult-class	0.002	0.000	0.002
norm2Filter-class	0.201	0.019	0.220
normalizeActionItem-class	0.001	0.000	0.002
normalizeView-class	0.001	0.000	0.002
parameters-methods	0.042	0.002	0.045
polygonGate	0.104	0.010	0.114
quadGate	0.294	0.005	0.300
quadratic-class	0.040	0.003	0.042
quadraticTransform	0.050	0.006	0.056
ratio-class	0.048	0.007	0.055
ratiotGml2-class	0.086	0.002	0.087
read.FCS	0.082	0.003	0.085
read.FCSheader	0.012	0.004	0.015
read.flowSet	0.134	0.004	0.139
rectangleGate	0.146	0.007	0.154
sampleFilter-class	0.082	0.003	0.084
scaleTransform	0.059	0.001	0.060
singleParameterTransform-class	0.002	0.000	0.003
sinht-class	0.045	0.003	0.049
split-methods	1.642	0.174	1.818
splitScaleTransform	3.106	0.253	3.368
splitscale-class	0.045	0.006	0.051
squareroot-class	0.050	0.008	0.057
subsettingActionItem-class	0.001	0.000	0.002
subsettingView-class	0.002	0.000	0.002
timeFilter-class	2.017	0.150	2.174
transform-class	0.003	0.000	0.004
transformActionItem-class	0.001	0.001	0.002
transformFilter-class	0.174	0.017	0.191
transformList-class	0.670	0.118	0.792
transformMap-class	0.001	0.001	0.002
transformView-class	0.001	0.000	0.002
truncateTransform	0.062	0.009	0.071
unitytransform-class	0.035	0.005	0.040
view-class	0.002	0.001	0.002
workFlow-class	0.002	0.000	0.003
write.FCS	0.160	0.023	0.206
write.flowSet	1.557	0.141	1.719