BioC 3.4: CHECK report for flowCore on morelia

Package: flowCore

Version: 1.39.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowCore_1.39.11.tar.gz

StartedAt: 2016-09-20 06:31:56 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:34:38 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 161.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowCore_1.39.11.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.39.11’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 18.9Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    extdata   1.1Mb
    lib      10.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
* 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: warning in assign(i, x[[i]], env = env):
  partial argument match of 'env' to 'envir'
rbind2,flowSet-flowSet: 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: no visible global function definition for
  ‘devAskNewPage’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘rangeGate’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘density’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘abline’
spillover,flowSet : <anonymous> : <anonymous>: no visible global
  function definition for ‘density’
split,flowFrame-factor: no visible binding for global variable ‘i’
summary,workFlow: no visible binding for global variable ‘wf’
Undefined global functions or variables:
  abline cov.rob density devAskNewPage i rangeGate wf
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline")
  importFrom("stats", "density")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/00check.log’
for details.

* installing *source* package ‘flowCore’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c FastLogicle.cpp -o FastLogicle.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c Hyperlog.cpp -o Hyperlog.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c Logicle.cpp -o Logicle.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c biexponential.cpp -o biexponential.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c convertRawBytes.cpp -o convertRawBytes.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c fcsTextParse.cpp -o fcsTextParse.o
In file included from fcsTextParse.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from fcsTextParse.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
fcsTextParse.cpp:45:133: warning: multi-line // comment [-Wcomment]
                        txt = boost::regex_replace(txt, boost::regex(doubleDelimiter), magicString);//somehow boost::replace_all won't do the job for \\\\
                                                                                                                                                         ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c hyperlogTransform.cpp -o hyperlogTransform.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c inPolygon.cpp -o inPolygon.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c inPolytope.cpp -o inPolytope.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c logicleTransform.cpp -o logicleTransform.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c sortBytes.cpp -o sortBytes.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c uint2double.cpp -o uint2double.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c zeroin.cpp -o zeroin.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
In file included from boost_regex/cregex.cpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/cregex.cpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/icu.cpp -o boost_regex/icu.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/instances.cpp -o boost_regex/instances.o
In file included from boost_regex/instances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/instances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
In file included from boost_regex/posix_api.cpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/posix_api.cpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o
In file included from boost_regex/regex.cpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/regex.cpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
In file included from boost_regex/wide_posix_api.cpp:25:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/wide_posix_api.cpp:25:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
In file included from boost_regex/winstances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/winstances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
mkdir -p "/Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/flowCore/lib"
ar rs "/Users/biocbuild/bbs-3.4-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 archive /Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a(icu.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a(regex_debug.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a(usinstances.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a(w32_regex_traits.o) has no symbols
clang++ -std=c++11 -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 RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o sortBytes.o uint2double.o zeroin.o /Users/biocbuild/bbs-3.4-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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	0.035	0.002	0.037
FCSTransTransform	0.864	0.046	0.911
Subset-methods	0.226	0.010	0.238
actionItem-class	0.001	0.000	0.001
arcsinhTransform	0.026	0.000	0.026
asinht-class	0.022	0.001	0.024
asinhtGml2-class	0.027	0.004	0.030
biexponentialTransform	2.853	0.087	2.941
boundaryFilter-class	0.094	0.002	0.097
characterOrTransformation-class	0.001	0.001	0.001
coerce	0.068	0.004	0.073
compensateActionItem-class	0.001	0.001	0.001
compensateView-class	0.002	0.000	0.001
compensatedParameter-class	0.215	0.021	0.236
compensation-class	0.404	0.040	0.444
dg1polynomial-class	0.022	0.002	0.024
each_col-methods	0.025	0.002	0.027
ellipsoidGate	0.077	0.006	0.083
exponential-class	0.036	0.002	0.037
expressionFilter-class	0.081	0.006	0.087
fcReference-class	0.002	0.000	0.003
filter-methods	0.822	0.060	0.883
filter-on-methods	0.112	0.010	0.123
filterList-class	0.005	0.000	0.005
filterResult-class	0.001	0.000	0.001
filterResultList-class	0.001	0.000	0.001
filterSummary-class	0.001	0.000	0.002
filterSummaryList-class	0.001	0.001	0.001
flowFrame-class	2.166	0.107	2.300
flowSet-class	1.724	0.069	1.797
fsApply	0.100	0.012	0.112
gateActionItem-class	0.001	0.001	0.002
gateView-class	0.001	0.000	0.002
getIndexSort-methods	0.033	0.005	0.038
hyperlog-class	1.278	0.002	1.281
hyperlogtGml2-class	0.024	0.001	0.025
identifier-methods	0.018	0.000	0.018
inverseLogicleTransform	0.516	0.041	0.557
invsplitscale-class	0.024	0.009	0.033
keyword-methods	0.625	0.051	0.676
kmeansFilter	0.168	0.016	0.183
linearTransform	0.037	0.001	0.038
lintGml2-class	0.036	0.002	0.038
lnTransform	0.972	0.078	1.055
logTransform	0.033	0.002	0.035
logarithm-class	0.021	0.001	0.022
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	0.646	0.044	0.690
logicletGml2-class	0.035	0.001	0.036
logtGml2-class	0.023	0.001	0.024
manyFilterResult-class	0.000	0.000	0.001
markernames	0.484	0.027	0.511
multipleFilterResult-class	0.001	0.000	0.001
norm2Filter-class	0.114	0.010	0.125
normalizeActionItem-class	0.002	0.001	0.001
normalizeView-class	0.002	0.000	0.001
parameters-methods	0.034	0.001	0.035
polygonGate	0.072	0.005	0.077
quadGate	0.209	0.008	0.217
quadratic-class	0.029	0.002	0.031
quadraticTransform	0.047	0.005	0.052
ratio-class	0.037	0.001	0.038
ratiotGml2-class	0.033	0.002	0.035
read.FCS	0.057	0.001	0.058
read.FCSheader	0.005	0.001	0.006
read.flowSet	0.069	0.003	0.072
rectangleGate	0.069	0.006	0.075
sampleFilter-class	0.037	0.001	0.038
scaleTransform	0.026	0.001	0.027
singleParameterTransform-class	0.001	0.000	0.001
sinht-class	0.021	0.002	0.023
split-methods	1.053	0.071	1.125
splitScaleTransform	0.911	0.068	0.979
splitscale-class	0.024	0.002	0.025
squareroot-class	0.020	0.000	0.021
subsettingActionItem-class	0.001	0.001	0.001
subsettingView-class	0.000	0.000	0.001
timeFilter-class	1.219	0.061	1.281
transform-class	0.002	0.000	0.002
transformActionItem-class	0.001	0.000	0.000
transformFilter-class	0.080	0.003	0.082
transformList-class	0.602	0.034	0.635
transformMap-class	0.001	0.000	0.001
transformView-class	0.002	0.000	0.002
truncateTransform	0.042	0.002	0.045
unitytransform-class	0.031	0.002	0.034
view-class	0.001	0.000	0.002
workFlow-class	0.002	0.000	0.003
write.FCS	0.088	0.006	0.094
write.flowSet	0.838	0.047	0.884