BioC 3.4: CHECK report for flowCore on morelia
This page was generated on 2016-09-21 03:49:40 -0700 (Wed, 21 Sep 2016).
flowCore 1.39.11 M.Jiang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore | Last Changed Rev: 120258 / Revision: 121152 | Last Changed Date: 2016-08-18 14:21:48 -0700 (Thu, 18 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | | |
moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
Summary
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 |
Command output
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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.
flowCore.Rcheck/00install.out:
* 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)
flowCore.Rcheck/flowCore-Ex.timings:
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 |
|