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This page was generated on 2023-11-02 11:40:41 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 724/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 2.14.0  (landing page)
Mike Jiang
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/flowCore
git_branch: RELEASE_3_18
git_last_commit: 77dbcc8
git_last_commit_date: 2023-10-24 09:37:29 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

INSTALL results for flowCore on kunpeng2


To the developers/maintainers of the flowCore package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCore.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: flowCore
Version: 2.14.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL flowCore
StartedAt: 2023-11-01 20:15:14 -0000 (Wed, 01 Nov 2023)
EndedAt: 2023-11-01 20:16:18 -0000 (Wed, 01 Nov 2023)
EllapsedTime: 63.9 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### 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)