Multiple platform build/check report for BioC 3.12 - CHECK report for flowCore on malbec1

Package: flowCore

Version: 2.2.0

Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowCore_2.2.0.tar.gz

StartedAt: 2021-05-06 01:36:09 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 01:38:41 -0400 (Thu, 06 May 2021)

EllapsedTime: 152.5 seconds

RetCode: 0

Status: OK

CheckDir: flowCore.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowCore_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/flowCore.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.2.0’
* 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 13.4Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    data      5.0Mb
    extdata   1.1Mb
    libs      5.3Mb
* 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’
show,flowFrame: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output mat msv
Consider adding
  importFrom("utils", "capture.output")
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 ... 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
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
filterResultList-class 5.588  0.084   5.750
flowFrame-class        4.992  0.068   5.104
* 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-3.12-bioc/meat/flowCore.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL flowCore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘flowCore’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from /home/biocbuild/bbs-3.12-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;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10:0,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from fcsTextParse.cpp:8:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
                 from /home/biocbuild/bbs-3.12-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;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10:0,
                 from fcsTextParse.cpp:10:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
/home/biocbuild/bbs-3.12-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-3.12-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from /home/biocbuild/bbs-3.12-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;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10:0,
                 from pairVectorRcppWrap.cpp:7:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-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-3.12-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-3.12-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-3.12-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)


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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.max, which.min

Welcome to Bioconductor

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

══ Skipped tests ═══════════════════════════════════════════════════════════════
• dir.exists(dataPath) is not TRUE (1)
• file.exists(filename) is not TRUE (2)

[ FAIL 0 | WARN 2 | SKIP 3 | PASS 334 ]
> 
> #devtools::test("~/rglab/workspace/flowCore")
> 
> proc.time()
   user  system elapsed 
 23.508   0.648  24.274

name	user	system	elapsed
EHtrans-class	0.064	0.008	0.161
FCSTransTransform	0.572	0.044	0.617
Subset-methods	0.212	0.000	0.213
arcsinhTransform	0.064	0.000	0.065
asinht-class	0.02	0.00	0.02
asinhtGml2-class	0.024	0.000	0.025
biexponentialTransform	3.248	0.060	3.308
boundaryFilter-class	0.068	0.000	0.069
characterOrNumeric-class	0.000	0.000	0.001
characterOrParameters-class	0.000	0.000	0.001
characterOrTransformation-class	0.000	0.000	0.001
coerce	0.04	0.00	0.04
collapse_desc	0.744	0.036	0.780
compensatedParameter-class	0.172	0.000	0.187
compensation-class	0.392	0.000	0.392
decompensate	0.060	0.004	0.063
dg1polynomial-class	0.028	0.000	0.031
each_col	0.036	0.000	0.036
ellipsoidGate-class	0.080	0.008	0.089
exponential-class	0.032	0.000	0.031
expressionFilter-class	0.128	0.004	0.132
filter-methods	0.984	0.012	0.996
filter-on-methods	0.124	0.000	0.122
filterList-class	0.004	0.004	0.007
filterResult-class	0.004	0.000	0.001
filterResultList-class	5.588	0.084	5.750
filterSummary-class	0.068	0.000	0.067
filterSummaryList-class	0.808	0.024	0.831
flowFrame-class	4.992	0.068	5.104
flowSet-class	2.636	0.080	2.721
fr_append_cols	0.584	0.036	0.620
fsApply	0.176	0.004	0.181
getIndexSort	0.028	0.000	0.028
hyperlog-class	1.452	0.000	1.451
hyperlogtGml2-class	0.024	0.000	0.022
identifier-methods	0.016	0.000	0.017
inverseLogicleTransform	0.536	0.032	0.571
invsplitscale-class	0.024	0.008	0.033
keyword-methods	0.808	0.020	0.830
kmeansFilter-class	0.116	0.000	0.115
linearTransform	0.028	0.000	0.026
lintGml2-class	0.02	0.00	0.02
lnTransform	1.336	0.020	1.366
logTransform	0.020	0.004	0.026
logarithm-class	0.020	0.000	0.021
logicalFilterResult-class	0.000	0.000	0.001
logicleTransform	0.640	0.016	0.656
logicletGml2-class	0.044	0.000	0.045
logtGml2-class	0.040	0.000	0.037
manyFilterResult-class	0.000	0.000	0.001
markernames	0.784	0.012	0.795
multipleFilterResult-class	0.000	0.000	0.001
parameters-methods	0.02	0.00	0.02
polygonGate-class	0.052	0.000	0.053
quadGate-class	0.18	0.00	0.18
quadratic-class	0.032	0.000	0.032
quadraticTransform	0.032	0.000	0.031
ratio-class	0.028	0.000	0.029
ratiotGml2-class	0.016	0.000	0.018
read.FCS	0.060	0.000	0.063
read.FCSheader	0.004	0.000	0.005
read.flowSet	0.080	0.000	0.078
rectangleGate-class	0.076	0.000	0.075
rotate_gate	0	0	0
sampleFilter-class	0.044	0.004	0.047
scaleTransform	0.024	0.000	0.026
scale_gate	0	0	0
shift_gate	0	0	0
singleParameterTransform-class	0.000	0.000	0.001
sinht-class	0.02	0.00	0.02
split-methods	1.524	0.016	1.540
splitScaleTransform	1.712	0.012	1.731
splitscale-class	0.036	0.000	0.033
squareroot-class	0.032	0.000	0.031
timeFilter-class	1.980	0.028	2.012
transform-class	0.000	0.004	0.001
transform	1.236	0.016	1.251
transformFilter-class	0.588	0.000	0.588
transformList-class	0.708	0.016	0.727
transformMap-class	0.000	0.000	0.001
transform_gate	0	0	0
truncateTransform	0.040	0.000	0.037
unitytransform-class	0.028	0.000	0.028
write.FCS	0.064	0.000	0.064
write.flowSet	0.788	0.044	0.832

CHECK report for flowCore on malbec1

Summary

Command output

Installation output

Tests output

Example timings