Multiple platform build/check report for BioC 3.11 - CHECK report for flowCore on malbec2

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings flowCore_2.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/flowCore.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.0.1’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    data      5.0Mb
    extdata   1.1Mb
    libs      5.0Mb
* 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
eval,compensatedParameter-missing : <anonymous>: no visible binding for
  global variable ‘mat’
eval,compensatedParameter-missing : <anonymous>: no visible binding for
  global variable ‘msv’
Undefined global functions or variables:
  mat msv
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/flowCore/libs/flowCore.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/flowCore.Rcheck/00check.log’
for details.

Installation output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL flowCore
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘flowCore’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Hyperlog.cpp -o Hyperlog.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Logicle.cpp -o Logicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c biexponential.cpp -o biexponential.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c convertRawBytes.cpp -o convertRawBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fcsTextParse.cpp -o fcsTextParse.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from fcsTextParse.cpp:8:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from fcsTextParse.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hyperlogTransform.cpp -o hyperlogTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c inPolygon.cpp -o inPolygon.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c inPolytope.cpp -o inPolytope.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c logicleTransform.cpp -o logicleTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
/home/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from /home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c poly_centroid.cpp -o poly_centroid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sortBytes.cpp -o sortBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c uint2double.cpp -o uint2double.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c zeroin.cpp -o zeroin.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/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 poly_centroid.o sortBytes.o uint2double.o zeroin.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-flowCore/00new/flowCore/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘HowTo-flowCore.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowCore)

Tests output


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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> library(testthat)
> library(flowCore)
> library(flowStats)
> 
> 
> test_check("flowCore")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:flowStats':

    normalize

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 334 | SKIPPED: 3 | WARNINGS: 2 | FAILED: 0 ]
> 
> #devtools::test("~/rglab/workspace/flowCore")
> 
> proc.time()
   user  system elapsed 
 19.542   0.669  20.270

Example timings

name	user	system	elapsed
EHtrans-class	0.075	0.000	0.086
FCSTransTransform	1.084	0.028	1.112
Subset-methods	0.316	0.020	0.355
arcsinhTransform	0.087	0.000	0.086
asinht-class	0.032	0.000	0.032
asinhtGml2-class	0.039	0.000	0.039
biexponentialTransform	3.989	0.060	4.049
boundaryFilter-class	0.092	0.004	0.096
characterOrNumeric-class	0.001	0.000	0.001
characterOrParameters-class	0	0	0
characterOrTransformation-class	0.001	0.000	0.001
coerce	0.125	0.004	0.129
collapse_desc	0.485	0.012	0.497
compensatedParameter-class	0.106	0.000	0.111
compensation-class	0.248	0.000	0.247
decompensate	0.042	0.000	0.041
dg1polynomial-class	0.016	0.004	0.019
each_col	0.023	0.000	0.022
ellipsoidGate-class	0.053	0.000	0.053
exponential-class	0.019	0.000	0.020
expressionFilter-class	0.071	0.000	0.072
filter-methods	0.604	0.036	0.641
filter-on-methods	0.069	0.000	0.068
filterList-class	0.004	0.000	0.004
filterResult-class	0.001	0.000	0.000
filterResultList-class	4.137	0.182	4.319
filterSummary-class	0.107	0.000	0.107
filterSummaryList-class	1.094	0.028	1.122
flowFrame-class	3.836	0.076	3.913
flowSet-class	2.345	0.040	2.385
fr_append_cols	0.536	0.016	0.552
fsApply	0.168	0.012	0.180
getIndexSort	0.010	0.008	0.018
hyperlog-class	1.213	0.000	1.213
hyperlogtGml2-class	0.041	0.000	0.041
identifier-methods	0.026	0.000	0.026
inverseLogicleTransform	0.830	0.008	0.838
invsplitscale-class	0.033	0.000	0.033
keyword-methods	0.81	0.04	0.85
kmeansFilter-class	0.178	0.000	0.178
linearTransform	0.039	0.000	0.039
lintGml2-class	0.032	0.000	0.032
lnTransform	1.284	0.028	1.312
logTransform	0.046	0.000	0.046
logarithm-class	0.031	0.000	0.031
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	1.232	0.024	1.256
logicletGml2-class	0.059	0.000	0.059
logtGml2-class	0.038	0.000	0.038
manyFilterResult-class	0.001	0.000	0.001
markernames	0.789	0.024	0.813
multipleFilterResult-class	0.001	0.000	0.001
parameters-methods	0.030	0.000	0.031
polygonGate-class	0.07	0.00	0.07
quadGate-class	0.19	0.00	0.19
quadratic-class	0.03	0.00	0.03
quadraticTransform	0.037	0.000	0.037
ratio-class	0.037	0.000	0.037
ratiotGml2-class	0.032	0.004	0.036
read.FCS	0.091	0.000	0.091
read.FCSheader	0.003	0.005	0.007
read.flowSet	0.114	0.002	0.117
rectangleGate-class	0.106	0.000	0.106
rotate_gate	0.000	0.000	0.001
sampleFilter-class	0.054	0.000	0.054
scaleTransform	0.036	0.000	0.036
scale_gate	0	0	0
shift_gate	0	0	0
singleParameterTransform-class	0.001	0.000	0.001
sinht-class	0.032	0.000	0.032
split-methods	0.973	0.012	0.984
splitScaleTransform	0.891	0.012	0.903
splitscale-class	0.019	0.000	0.019
squareroot-class	0.020	0.000	0.019
timeFilter-class	1.497	0.036	1.533
transform-class	0.001	0.000	0.001
transform	1.067	0.028	1.095
transformFilter-class	0.114	0.000	0.113
transformList-class	0.793	0.008	0.801
transformMap-class	0	0	0
transform_gate	0	0	0
truncateTransform	0.024	0.000	0.024
unitytransform-class	0.017	0.000	0.017
write.FCS	0.033	0.000	0.033
write.flowSet	0.627	0.012	0.638

CHECK report for flowCore on malbec2

Summary

Command output

Installation output

Tests output

Example timings