##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings flowCore_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/flowCore.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘2.14.0’
* 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 ... WARNING
Found the following significant warnings:
  Hyperlog.cpp:47:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=]
  Hyperlog.cpp:53:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=]
See ‘/home/biocbuild/bbs-3.18-bioc/meat/flowCore.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 18.1Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    data      5.4Mb
    extdata   1.1Mb
    libs      9.6Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
* 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 ... NOTE
checkRd: (-1) identifier-methods.Rd:36: Escaped LaTeX specials: \^
checkRd: (-1) quadraticTransform.Rd:26: Escaped LaTeX specials: \^
checkRd: (-1) read.FCS.Rd:26: Escaped LaTeX specials: \$
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘multiRangeGate’
Undocumented S4 classes:
  ‘multiRangeGate’
Undocumented S4 methods:
  generic '%in%' and siglist 'flowFrame,multiRangeGate'
  generic 'show' and siglist 'multiRangeGate'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.1/site-library/flowCore/libs/flowCore.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘srand’, possibly from ‘srand’ (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 nor [v]sprintf. 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
filterResultList-class 6.477  0.160   6.664
flowFrame-class        5.256  0.087   5.355
* 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 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/flowCore.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL flowCore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘flowCore’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Hyperlog.cpp -o Hyperlog.o
Hyperlog.cpp: In constructor ‘Hyperlog::IllegalArgument::IllegalArgument(double)’:
Hyperlog.cpp:47:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=]
   47 |     snprintf(buffer, sizeof(buffer), "Illegal argument value %.17g", value);
      |                                       ~~~~~~~~^~~~~~~~~~~~~~~
Hyperlog.cpp:47:38: note: assuming directive output of 23 bytes
   47 |     snprintf(buffer, sizeof(buffer), "Illegal argument value %.17g", value);
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Hyperlog.cpp:47:13: note: ‘snprintf’ output between 25 and 48 bytes into a destination of size 8
   47 |     snprintf(buffer, sizeof(buffer), "Illegal argument value %.17g", value);
      |     ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Hyperlog.cpp: In constructor ‘Hyperlog::IllegalArgument::IllegalArgument(int)’:
Hyperlog.cpp:53:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=]
   53 |     snprintf(buffer, sizeof(buffer), "Illegal argument value %d", value);
      |                                       ~~~~~~~~^~~~~~~~~~~~~~~
Hyperlog.cpp:53:13: note: ‘snprintf’ output between 25 and 35 bytes into a destination of size 8
   53 |     snprintf(buffer, sizeof(buffer), "Illegal argument value %d", value);
      |     ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Logicle.cpp -o Logicle.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c biexponential.cpp -o biexponential.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c convertRawBytes.cpp -o convertRawBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c fcsTextParse.cpp -o fcsTextParse.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from fcsTextParse.cpp:9:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string.hpp:23,
                 from fcsTextParse.cpp:9:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/classification.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/trim.hpp:23,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from fcsTextParse.cpp:9:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from fcsTextParse.cpp:13:
/home/biocbuild/R/R-4.3.1/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/R/R-4.3.1/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
fcsTextParse.cpp: In function ‘cpp11::writable::doubles_matrix<> string_to_spill(std::string)’:
fcsTextParse.cpp:21:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   21 |   for (auto j = 0; j < spillover.n_cols; j++) {
      |                    ~~^~~~~~~~~~~~~~~~~~
fcsTextParse.cpp:22:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   22 |     for (auto i = 0; i < spillover.n_rows; i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~
fcsTextParse.cpp: In function ‘cpp11::sexp fcsTextParse(std::string, bool)’:
fcsTextParse.cpp:142:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |     for (int i = 0; i < pairs.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c hyperlogTransform.cpp -o hyperlogTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c inPolygon.cpp -o inPolygon.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c inPolytope.cpp -o inPolytope.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c logicleTransform.cpp -o logicleTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c sortBytes.cpp -o sortBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c uint2double.cpp -o uint2double.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o biexponential.o convertRawBytes.o cpp11.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /home/biocbuild/R/R-4.3.1/site-library/cytolib/lib/libcytolib.a -L/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-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
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
Warning message:
replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats' 
> 
> 
> test_check("flowCore")
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, 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")'.

[ FAIL 0 | WARN 2 | SKIP 3 | PASS 324 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• dir.exists(dataPath) is not TRUE (1): 'test-IO-internal.R:4:1'
• file.exists(filename) is not TRUE (2): 'test-IO.R:32:3', 'test-IO.R:40:3'

[ FAIL 0 | WARN 2 | SKIP 3 | PASS 324 ]
> 
> #devtools::test("~/rglab/workspace/flowCore")
> 
> proc.time()
   user  system elapsed 
 27.448   0.709  28.208