BioC 2.14: CHECK report for flowCore on petty

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 21:56:54 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:01:10 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 256.3 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-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 ‘1.30.7’
* 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 ... [21s/25s] 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 ... [63s/64s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
biexponentialTransform 9.165  0.338   9.531
flowFrame-class        6.098  0.265   6.636
flowSet-class          5.186  0.206   5.421
* 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
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-2.14-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	0.116	0.007	0.122
FCSTransTransform	2.318	0.133	2.454
Subset-methods	0.847	0.037	0.892
actionItem-class	0.002	0.000	0.002
arcsinhTransform	0.085	0.001	0.086
asinht-class	0.061	0.002	0.064
asinhtGml2-class	0.067	0.005	0.072
biexponentialTransform	9.165	0.338	9.531
boundaryFilter-class	0.349	0.037	0.388
characterOrTransformation-class	0.002	0.000	0.002
coerce	0.119	0.005	0.124
compensateActionItem-class	0.002	0.001	0.003
compensateView-class	0.002	0.000	0.002
compensatedParameter-class	0.335	0.039	0.375
compensation-class	0.713	0.030	0.744
dg1polynomial-class	0.060	0.004	0.064
each_col-methods	0.068	0.005	0.073
ellipsoidGate	0.140	0.006	0.146
exponential-class	0.064	0.004	0.068
expressionFilter-class	0.153	0.008	0.161
fcReference-class	0.003	0.000	0.004
filter-methods	1.380	0.121	1.502
filter-on-methods	0.238	0.002	0.240
filterList-class	0.02	0.00	0.02
filterResult-class	0.003	0.001	0.003
filterResultList-class	0.003	0.001	0.003
filterSet-class	0.100	0.001	0.102
filterSummary-class	0.003	0.001	0.003
filterSummaryList-class	0.002	0.000	0.002
flowFrame-class	6.098	0.265	6.636
flowSet-class	5.186	0.206	5.421
fsApply	0.306	0.015	0.323
gateActionItem-class	0.003	0.000	0.003
gateView-class	0.003	0.000	0.003
getIndexSort-methods	0.055	0.006	0.060
hyperlog-class	3.879	0.018	3.910
hyperlogtGml2-class	0.069	0.003	0.071
identifier-methods	0.053	0.002	0.055
inverseLogicleTransform	1.099	0.121	1.228
invsplitscale-class	0.069	0.020	0.094
keyword-methods	1.124	0.129	1.257
kmeansFilter	0.613	0.034	0.648
linearTransform	0.082	0.002	0.084
lintGml2-class	0.063	0.005	0.067
lnTransform	2.906	0.263	3.183
logTransform	0.267	0.030	0.296
logarithm-class	0.067	0.005	0.073
logicalFilterResult-class	0.002	0.000	0.003
logicleTransform	1.143	0.121	1.270
logicletGml2-class	0.074	0.025	0.098
logtGml2-class	0.062	0.002	0.064
manyFilterResult-class	0.002	0.000	0.003
multipleFilterResult-class	0.002	0.000	0.003
norm2Filter-class	0.323	0.010	0.346
normalizeActionItem-class	0.002	0.000	0.002
normalizeView-class	0.003	0.000	0.003
parameters-methods	0.059	0.006	0.065
polygonGate	0.154	0.009	0.163
quadGate	0.480	0.005	0.485
quadratic-class	0.063	0.004	0.066
quadraticTransform	0.086	0.007	0.094
ratio-class	0.064	0.005	0.069
ratiotGml2-class	0.060	0.005	0.064
read.FCS	0.128	0.010	0.138
read.FCSheader	0.015	0.004	0.019
read.flowSet	0.216	0.004	0.220
rectangleGate	0.239	0.009	0.248
sampleFilter-class	0.120	0.003	0.122
scaleTransform	0.090	0.003	0.094
singleParameterTransform-class	0.002	0.001	0.003
sinht-class	0.064	0.002	0.069
split-methods	2.527	0.161	2.704
splitScaleTransform	3.695	0.273	3.974
splitscale-class	0.250	0.026	0.277
squareroot-class	0.053	0.003	0.056
subsettingActionItem-class	0.001	0.000	0.002
subsettingView-class	0.002	0.000	0.003
timeFilter-class	2.863	0.152	3.040
transform-class	0.005	0.000	0.005
transformActionItem-class	0.002	0.001	0.003
transformFilter-class	0.242	0.012	0.257
transformList-class	1.059	0.119	1.186
transformMap-class	0.002	0.001	0.002
transformView-class	0.002	0.000	0.003
truncateTransform	0.090	0.006	0.096
unitytransform-class	0.053	0.005	0.058
view-class	0.002	0.001	0.003
workFlow-class	0.004	0.001	0.004
write.FCS	0.250	0.015	0.267
write.flowSet	2.420	0.147	2.586