BioC 2.14: CHECK report for flowCore on morelia

Package: flowCore

Version: 1.30.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.30.7.tar.gz

StartedAt: 2014-10-07 22:45:21 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:47:52 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 151.1 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_1.30.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/flowCore.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.30.7’
* 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 ... [12s/13s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
%in%,flowFrame-norm2Filter: no visible global function definition for
  ‘cov.rob’
* 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
biexponentialTransform 5.27  0.183   5.458
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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/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-2.14-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	0.078	0.004	0.082
FCSTransTransform	1.449	0.069	1.520
Subset-methods	0.515	0.024	0.540
actionItem-class	0.002	0.001	0.003
arcsinhTransform	0.051	0.002	0.055
asinht-class	0.038	0.001	0.039
asinhtGml2-class	0.044	0.004	0.048
biexponentialTransform	5.270	0.183	5.458
boundaryFilter-class	0.225	0.023	0.248
characterOrTransformation-class	0.001	0.000	0.002
coerce	0.087	0.005	0.093
compensateActionItem-class	0.001	0.001	0.002
compensateView-class	0.001	0.000	0.001
compensatedParameter-class	0.196	0.021	0.217
compensation-class	0.452	0.019	0.472
dg1polynomial-class	0.037	0.002	0.040
each_col-methods	0.039	0.005	0.044
ellipsoidGate	0.091	0.005	0.096
exponential-class	0.044	0.001	0.045
expressionFilter-class	0.103	0.006	0.108
fcReference-class	0.002	0.001	0.002
filter-methods	0.821	0.054	0.876
filter-on-methods	0.163	0.002	0.165
filterList-class	0.01	0.00	0.01
filterResult-class	0.001	0.000	0.002
filterResultList-class	0.001	0.001	0.002
filterSet-class	0.055	0.001	0.056
filterSummary-class	0.000	0.000	0.001
filterSummaryList-class	0.001	0.000	0.001
flowFrame-class	3.558	0.135	3.748
flowSet-class	3.164	0.105	3.276
fsApply	0.204	0.017	0.221
gateActionItem-class	0.001	0.000	0.002
gateView-class	0.001	0.000	0.001
getIndexSort-methods	0.035	0.003	0.038
hyperlog-class	2.036	0.013	2.052
hyperlogtGml2-class	0.048	0.001	0.050
identifier-methods	0.034	0.003	0.037
inverseLogicleTransform	0.718	0.063	0.782
invsplitscale-class	0.054	0.014	0.067
keyword-methods	0.733	0.063	0.798
kmeansFilter	0.357	0.024	0.381
linearTransform	0.047	0.003	0.050
lintGml2-class	0.038	0.002	0.041
lnTransform	1.766	0.139	1.912
logTransform	0.153	0.017	0.170
logarithm-class	0.046	0.003	0.049
logicalFilterResult-class	0.001	0.001	0.001
logicleTransform	0.767	0.060	0.828
logicletGml2-class	0.051	0.016	0.066
logtGml2-class	0.044	0.001	0.046
manyFilterResult-class	0.002	0.001	0.002
multipleFilterResult-class	0.002	0.000	0.001
norm2Filter-class	0.174	0.006	0.181
normalizeActionItem-class	0.002	0.000	0.001
normalizeView-class	0.002	0.000	0.002
parameters-methods	0.037	0.003	0.040
polygonGate	0.101	0.005	0.106
quadGate	0.312	0.005	0.318
quadratic-class	0.044	0.003	0.047
quadraticTransform	0.060	0.004	0.065
ratio-class	0.046	0.002	0.049
ratiotGml2-class	0.043	0.003	0.047
read.FCS	0.092	0.007	0.098
read.FCSheader	0.011	0.003	0.014
read.flowSet	0.145	0.002	0.148
rectangleGate	0.149	0.006	0.155
sampleFilter-class	0.078	0.002	0.081
scaleTransform	0.055	0.002	0.058
singleParameterTransform-class	0.001	0.000	0.002
sinht-class	0.041	0.001	0.043
split-methods	1.508	0.081	1.590
splitScaleTransform	2.312	0.150	2.767
splitscale-class	0.170	0.018	0.188
squareroot-class	0.040	0.003	0.042
subsettingActionItem-class	0.002	0.000	0.002
subsettingView-class	0.001	0.001	0.001
timeFilter-class	1.761	0.080	1.843
transform-class	0.003	0.000	0.004
transformActionItem-class	0.002	0.001	0.002
transformFilter-class	0.132	0.007	0.139
transformList-class	0.666	0.057	0.723
transformMap-class	0.002	0.000	0.002
transformView-class	0.002	0.000	0.001
truncateTransform	0.048	0.003	0.051
unitytransform-class	0.037	0.003	0.039
view-class	0.002	0.000	0.002
workFlow-class	0.003	0.001	0.003
write.FCS	0.166	0.011	0.177
write.flowSet	1.513	0.094	1.608