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) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:41 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (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 724/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowCore 2.14.0 (landing page) Mike Jiang
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| 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 |
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL flowCore
###
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##############################################################################
* 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)