BioC 3.2: CHECK report for flowCore on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.35.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.35.10’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/boost_regex/c_regex_traits.o src/boost_regex/cpp_regex_traits.o
  src/boost_regex/cregex.o src/boost_regex/fileiter.o
  src/boost_regex/icu.o src/boost_regex/instances.o
  src/boost_regex/posix_api.o src/boost_regex/regex.o
  src/boost_regex/regex_debug.o src/boost_regex/regex_raw_buffer.o
  src/boost_regex/regex_traits_defaults.o
  src/boost_regex/static_mutex.o src/boost_regex/usinstances.o
  src/boost_regex/w32_regex_traits.o src/boost_regex/wc_regex_traits.o
  src/boost_regex/wide_posix_api.o src/boost_regex/winstances.o
Object files/libraries should not be included in a source package.
* 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 ... [69s/70s] OK
* checking installed package size ... NOTE
  installed size is 32.0Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.3Mb
    extdata   1.1Mb
    lib      19.6Mb
    libs      3.5Mb
* 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' call to ‘Rgraphviz’ in package code.
  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
rbind2,flowSet-flowSet : .local: warning in assign(i, x[[i]], env =
  env): partial argument match of 'env' to 'envir'
rbind2,flowSet-flowSet : .local: warning in assign(i, y[[i]], env =
  env): partial argument match of 'env' to 'envir'
%in%,flowFrame-norm2Filter: no visible global function definition for
  ‘cov.rob’
spillover,flowSet : .local : <anonymous>: no visible global function
  definition for ‘rangeGate’
split,flowFrame-factor : .local: no visible binding for global variable
  ‘i’
summary,workFlow : .local: no visible binding for global variable ‘wf’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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 ... [27s/27s] OK
* 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

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/00check.log’
for details.

* installing *source* package ‘flowCore’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c Hyperlog.cpp -o Hyperlog.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c Logicle.cpp -o Logicle.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c biexponential.c -o biexponential.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c fcsTextParse.cpp -o fcsTextParse.o
fcsTextParse.cpp:44:80: warning: multi-line comment [-Wcomment]
    txt = boost::regex_replace(txt, boost::regex(doubleDelimiter), magicString);//somehow boost::replace_all won't do the job for \\\\
                                                                                ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c hyperlogTransform.cpp -o hyperlogTransform.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c logicleTransform.cpp -o logicleTransform.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c zeroin.c -o zeroin.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/cregex.cpp -o boost_regex/cregex.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/icu.cpp -o boost_regex/icu.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/instances.cpp -o boost_regex/instances.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib"
ar rs "/home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating /home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o init.o logicleTransform.o pairVectorRcppWrap.o zeroin.o /home/biocbuild/bbs-3.2-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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	0.049	0.004	0.052
FCSTransTransform	0.990	0.016	1.007
Subset-methods	0.299	0.004	0.304
actionItem-class	0.001	0.003	0.001
arcsinhTransform	0.035	0.001	0.037
asinht-class	0.032	0.000	0.032
asinhtGml2-class	0.054	0.000	0.055
biexponentialTransform	4.495	0.035	4.540
boundaryFilter-class	0.076	0.004	0.081
characterOrTransformation-class	0.001	0.000	0.001
coerce	0.146	0.000	0.147
compensateActionItem-class	0.001	0.000	0.001
compensateView-class	0.001	0.000	0.001
compensatedParameter-class	0.129	0.000	0.132
compensation-class	0.329	0.008	0.337
dg1polynomial-class	0.03	0.00	0.03
each_col-methods	0.040	0.000	0.041
ellipsoidGate	0.061	0.000	0.061
exponential-class	0.031	0.000	0.032
expressionFilter-class	0.066	0.000	0.067
fcReference-class	0.002	0.000	0.002
filter-methods	0.680	0.008	0.688
filter-on-methods	0.091	0.000	0.091
filterList-class	0.006	0.000	0.006
filterResult-class	0.000	0.000	0.001
filterResultList-class	0.001	0.000	0.001
filterSummary-class	0.001	0.000	0.001
filterSummaryList-class	0.001	0.000	0.001
flowFrame-class	2.817	0.028	2.864
flowSet-class	2.167	0.016	2.185
fsApply	0.152	0.000	0.152
gateActionItem-class	0.001	0.000	0.001
gateView-class	0.001	0.000	0.001
getIndexSort-methods	0.023	0.000	0.023
hyperlog-class	1.811	0.000	1.812
hyperlogtGml2-class	0.053	0.000	0.054
identifier-methods	0.025	0.000	0.025
inverseLogicleTransform	0.619	0.004	0.623
invsplitscale-class	0.034	0.000	0.034
keyword-methods	0.684	0.008	0.692
kmeansFilter	0.165	0.000	0.165
linearTransform	0.033	0.004	0.037
lintGml2-class	0.053	0.000	0.053
lnTransform	1.093	0.008	1.102
logTransform	0.04	0.00	0.04
logarithm-class	0.03	0.00	0.03
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	0.771	0.012	0.783
logicletGml2-class	0.058	0.000	0.058
logtGml2-class	0.055	0.000	0.055
manyFilterResult-class	0.001	0.000	0.001
multipleFilterResult-class	0.000	0.004	0.001
norm2Filter-class	0.146	0.000	0.148
normalizeActionItem-class	0.001	0.000	0.001
normalizeView-class	0.001	0.000	0.000
parameters-methods	0.024	0.004	0.028
polygonGate	0.064	0.000	0.063
quadGate	0.171	0.000	0.171
quadratic-class	0.026	0.000	0.027
quadraticTransform	0.034	0.000	0.033
ratio-class	0.030	0.000	0.031
ratiotGml2-class	0.052	0.000	0.052
read.FCS	0.059	0.000	0.058
read.FCSheader	0.001	0.004	0.006
read.flowSet	0.103	0.000	0.103
rectangleGate	0.093	0.000	0.093
sampleFilter-class	0.054	0.000	0.055
scaleTransform	0.036	0.000	0.036
singleParameterTransform-class	0.001	0.000	0.001
sinht-class	0.03	0.00	0.03
split-methods	1.217	0.024	1.259
splitScaleTransform	1.184	0.004	1.193
splitscale-class	0.136	0.004	0.143
squareroot-class	0.031	0.000	0.032
subsettingActionItem-class	0.001	0.000	0.002
subsettingView-class	0.001	0.000	0.001
timeFilter-class	1.371	0.000	1.385
transform-class	0.002	0.000	0.002
transformActionItem-class	0.002	0.000	0.001
transformFilter-class	0.12	0.00	0.12
transformList-class	0.719	0.016	0.739
transformMap-class	0.000	0.000	0.001
transformView-class	0.001	0.000	0.001
truncateTransform	0.037	0.000	0.036
unitytransform-class	0.027	0.000	0.027
view-class	0.001	0.000	0.002
workFlow-class	0.001	0.000	0.001
write.FCS	0.065	0.000	0.064
write.flowSet	0.98	0.00	0.98

BioC 3.2: CHECK report for flowCore on zin1

Summary

Command output