Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:40 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the flowCore package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 647/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowCore 2.4.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: flowCore |
Version: 2.4.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings flowCore_2.4.0.tar.gz |
StartedAt: 2021-10-14 09:52:07 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:53:53 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 106.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowCore.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings flowCore_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/flowCore.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘2.4.0’ * 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 14.4Mb sub-directories of 1Mb or more: data 5.0Mb extdata 1.1Mb libs 6.8Mb * 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 File ‘/home/biocbuild/bbs-3.13-bioc/R/library/flowCore/libs/flowCore.so’: Found ‘rand’, possibly from ‘rand’ (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. 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-3.13-bioc/meat/flowCore.Rcheck/00check.log’ for details.
flowCore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL flowCore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘flowCore’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/bbs-3.13-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-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from /home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from /home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from /home/biocbuild/bbs-3.13-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++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: /home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/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) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from fcsTextParse.cpp:8: /home/biocbuild/bbs-3.13-bioc/R/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++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from fcsTextParse.cpp:10: /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: /home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/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) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: /home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from /home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from /home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: /home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/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) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/libcytolib.a -L/home/biocbuild/bbs-3.13-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-3.13-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)
flowCore.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" 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 10 | SKIP 3 | PASS 334 ] > > #devtools::test("~/rglab/workspace/flowCore") > > proc.time() user system elapsed 16.206 1.214 17.422
flowCore.Rcheck/flowCore-Ex.timings
name | user | system | elapsed | |
EHtrans-class | 0.025 | 0.016 | 0.041 | |
FCSTransTransform | 0.539 | 0.028 | 0.568 | |
Subset-methods | 0.161 | 0.004 | 0.165 | |
arcsinhTransform | 0.036 | 0.000 | 0.036 | |
asinht-class | 0.015 | 0.000 | 0.015 | |
asinhtGml2-class | 0.018 | 0.000 | 0.018 | |
biexponentialTransform | 2.217 | 0.068 | 2.285 | |
boundaryFilter-class | 0.056 | 0.000 | 0.057 | |
characterOrNumeric-class | 0.002 | 0.000 | 0.002 | |
characterOrParameters-class | 0.001 | 0.000 | 0.001 | |
characterOrTransformation-class | 0.001 | 0.000 | 0.001 | |
coerce | 0.026 | 0.008 | 0.034 | |
collapse_desc | 0.634 | 0.036 | 0.670 | |
compensatedParameter-class | 0.087 | 0.000 | 0.090 | |
compensation-class | 0.201 | 0.011 | 0.213 | |
decompensate | 0.032 | 0.001 | 0.033 | |
dg1polynomial-class | 0.016 | 0.000 | 0.016 | |
each_col | 0.02 | 0.00 | 0.02 | |
ellipsoidGate-class | 0.047 | 0.000 | 0.047 | |
exponential-class | 0.016 | 0.000 | 0.016 | |
expressionFilter-class | 0.063 | 0.000 | 0.063 | |
filter-methods | 0.587 | 0.028 | 0.615 | |
filter-on-methods | 0.062 | 0.000 | 0.062 | |
filterList-class | 0.004 | 0.000 | 0.004 | |
filterResult-class | 0.001 | 0.000 | 0.001 | |
filterResultList-class | 3.654 | 0.132 | 3.786 | |
filterSummary-class | 0.062 | 0.007 | 0.068 | |
filterSummaryList-class | 0.606 | 0.032 | 0.638 | |
flowFrame-class | 3.153 | 0.064 | 3.217 | |
flowSet-class | 1.953 | 0.112 | 2.065 | |
fr_append_cols | 0.504 | 0.055 | 0.560 | |
fsApply | 0.101 | 0.001 | 0.101 | |
getIndexSort | 0.010 | 0.003 | 0.014 | |
hyperlog-class | 0.695 | 0.004 | 0.699 | |
hyperlogtGml2-class | 0.019 | 0.001 | 0.019 | |
identifier-methods | 0.015 | 0.000 | 0.014 | |
inverseLogicleTransform | 0.551 | 0.028 | 0.579 | |
invsplitscale-class | 0.015 | 0.004 | 0.018 | |
keyword-methods | 0.540 | 0.019 | 0.561 | |
kmeansFilter-class | 0.104 | 0.001 | 0.104 | |
linearTransform | 0.022 | 0.000 | 0.022 | |
lintGml2-class | 0.023 | 0.000 | 0.023 | |
lnTransform | 1.107 | 0.060 | 1.167 | |
logTransform | 0.018 | 0.004 | 0.021 | |
logarithm-class | 0.016 | 0.000 | 0.017 | |
logicalFilterResult-class | 0.001 | 0.000 | 0.000 | |
logicleTransform | 0.530 | 0.028 | 0.558 | |
logicletGml2-class | 0.032 | 0.004 | 0.035 | |
logtGml2-class | 0.019 | 0.000 | 0.019 | |
manyFilterResult-class | 0.001 | 0.000 | 0.001 | |
markernames | 0.500 | 0.019 | 0.521 | |
multipleFilterResult-class | 0.001 | 0.001 | 0.000 | |
parameters-methods | 0.013 | 0.003 | 0.017 | |
polygonGate-class | 0.046 | 0.005 | 0.050 | |
quadGate-class | 0.114 | 0.011 | 0.125 | |
quadratic-class | 0.016 | 0.000 | 0.015 | |
quadraticTransform | 0.020 | 0.001 | 0.020 | |
ratio-class | 0.02 | 0.00 | 0.02 | |
ratiotGml2-class | 0.015 | 0.000 | 0.015 | |
read.FCS | 0.051 | 0.000 | 0.051 | |
read.FCSheader | 0.006 | 0.000 | 0.007 | |
read.flowSet | 0.057 | 0.003 | 0.060 | |
rectangleGate-class | 0.069 | 0.001 | 0.068 | |
rotate_gate | 0 | 0 | 0 | |
sampleFilter-class | 0.033 | 0.004 | 0.037 | |
scaleTransform | 0.021 | 0.000 | 0.020 | |
scale_gate | 0.001 | 0.000 | 0.000 | |
shift_gate | 0.001 | 0.000 | 0.000 | |
singleParameterTransform-class | 0.002 | 0.000 | 0.001 | |
sinht-class | 0.017 | 0.000 | 0.017 | |
split-methods | 1.162 | 0.027 | 1.190 | |
splitScaleTransform | 0.764 | 0.013 | 0.776 | |
splitscale-class | 0.024 | 0.000 | 0.023 | |
squareroot-class | 0.017 | 0.000 | 0.017 | |
timeFilter-class | 1.423 | 0.044 | 1.466 | |
transform-class | 0.001 | 0.000 | 0.002 | |
transform | 0.819 | 0.019 | 0.840 | |
transformFilter-class | 0.109 | 0.001 | 0.110 | |
transformList-class | 0.508 | 0.039 | 0.547 | |
transformMap-class | 0.001 | 0.000 | 0.001 | |
transform_gate | 0.001 | 0.000 | 0.000 | |
truncateTransform | 0.02 | 0.00 | 0.02 | |
unitytransform-class | 0.010 | 0.003 | 0.013 | |
write.FCS | 0.030 | 0.001 | 0.029 | |
write.flowSet | 0.619 | 0.051 | 0.671 | |