Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:05 -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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowCore_2.4.0.tar.gz |
StartedAt: 2021-10-14 23:12:43 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:17:15 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 272.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowCore.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowCore_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 whether package 'flowCore' can be installed ... OK * checking installed package size ... NOTE installed size is 15.3Mb sub-directories of 1Mb or more: R 1.1Mb data 5.0Mb extdata 1.1Mb help 1.4Mb libs 5.6Mb * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE Output for data("GvHD", package = "flowCore"): There were 36 warnings (use warnings() to see them) * 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 for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowCore/libs/i386/flowCore.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowCore/libs/x64/flowCore.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biexponentialTransform 5.63 0.03 5.65 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biexponentialTransform 5.75 0.08 5.83 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.Rcheck/00check.log' for details.
flowCore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowCore_2.4.0.tar.gz && rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowCore_2.4.0.zip && rm flowCore_2.4.0.tar.gz flowCore_2.4.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 43 8843k 43 3860k 0 0 5351k 0 0:00:01 --:--:-- 0:00:01 5353k 100 8843k 100 8843k 0 0 7045k 0 0:00:01 0:00:01 --:--:-- 7052k install for i386 * installing *source* package 'flowCore' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastLogicle.cpp -o FastLogicle.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Hyperlog.cpp -o Hyperlog.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Logicle.cpp -o Logicle.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/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] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/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: C:/Users/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] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/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: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/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 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/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 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/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 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biexponential.cpp -o biexponential.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convertRawBytes.cpp -o convertRawBytes.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fcsTextParse.cpp -o fcsTextParse.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/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] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from fcsTextParse.cpp:8: C:/Users/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] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from fcsTextParse.cpp:10: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/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 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/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 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/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 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hyperlogTransform.cpp -o hyperlogTransform.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolygon.cpp -o inPolygon.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolytope.cpp -o inPolytope.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logicleTransform.cpp -o logicleTransform.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/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] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/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] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/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 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/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 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/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 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c poly_centroid.cpp -o poly_centroid.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sortBytes.cpp -o sortBytes.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uint2double.cpp -o uint2double.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zeroin.cpp -o zeroin.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def 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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lstdc++fs -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.buildbin-libdir/00LOCK-flowCore/00new/flowCore/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'flowCore' finding HTML links ... done CytoExploreR_exports html EHtrans-class html FCSTransTransform html GvHD html Subset-methods html arcsinhTransform html asinht-class html asinhtGml2-class html biexponentialTransform html boundaryFilter-class html characterOrNumeric-class html characterOrParameters-class html characterOrTransformation-class html checkOffset html coerce html collapse_desc html compensatedParameter-class html compensation-class html complementFilter-class html concreteFilter-class html decompensate html dg1polynomial-class html each_col html ellipsoidGate-class html estimateMedianLogicle html exponential-class html expressionFilter-class html filter-and-methods html filter-class html filter-in-methods html filter-methods html filter-on-methods html filterDetails-methods html filterList-class html filterReference-class html filterResult-class html filterResultList-class html filterSummary-class html filterSummaryList-class html filters-class html flowCore-package html flowFrame-class html flowSet-class html flowSet_to_list html fr_append_cols html fsApply html getChannelMarker html getIndexSort html hyperlog-class html hyperlogtGml2-class html identifier-methods html intersectFilter-class html inverseLogicleTransform html invsplitscale-class html keyword-methods html kmeansFilter-class html linearTransform html lintGml2-class html lnTransform html logTransform html logarithm-class html logicalFilterResult-class html logicleTransform html logicletGml2-class html logtGml2-class html manyFilterResult-class html markernames html multipleFilterResult-class html normalization-class html nullParameter-class html parameterFilter-class html parameterTransform-class html parameters-class html parameters-methods html polygonGate-class html polytopeGate-class html quadGate-class html quadratic-class html quadraticTransform html randomFilterResult-class html ratio-class html ratiotGml2-class html read.FCS html read.FCSheader html read.flowSet html rectangleGate-class html rotate_gate html sampleFilter-class html scaleTransform html scale_gate html setOperationFilter-class html shift_gate html singleParameterTransform-class html sinht-class html split-methods html splitScaleTransform html splitscale-class html squareroot-class html subsetFilter-class html summarizeFilter-methods html timeFilter-class html transform-class html transform html transformFilter-class html transformList-class html transformMap-class html transformReference-class html transform_gate html transformation-class html truncateTransform html unionFilter-class html unitytransform-class html updateTransformKeywords html validFilters html write.FCS html write.flowSet html ** building package indices ** installing vignettes 'HowTo-flowCore.Rnw' using 'UTF-8' ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'flowCore' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastLogicle.cpp -o FastLogicle.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Hyperlog.cpp -o Hyperlog.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Logicle.cpp -o Logicle.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/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: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/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] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/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: C:/Users/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] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/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 long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/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 long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/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 long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biexponential.cpp -o biexponential.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convertRawBytes.cpp -o convertRawBytes.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fcsTextParse.cpp -o fcsTextParse.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/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] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from fcsTextParse.cpp:8: C:/Users/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] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from fcsTextParse.cpp:10: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/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 long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/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 long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/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 long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hyperlogTransform.cpp -o hyperlogTransform.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolygon.cpp -o inPolygon.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolytope.cpp -o inPolytope.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logicleTransform.cpp -o logicleTransform.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/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] failed ************ (boost::mpl::not_<Pred>::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/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] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/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 long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/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 long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/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 long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c poly_centroid.cpp -o poly_centroid.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sortBytes.cpp -o sortBytes.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uint2double.cpp -o uint2double.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zeroin.cpp -o zeroin.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def 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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lstdc++fs -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'flowCore' as flowCore_2.4.0.zip * DONE (flowCore) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'flowCore' successfully unpacked and MD5 sums checked
flowCore.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 190 | SKIP 3 | PASS 334 ] There were 36 warnings (use warnings() to see them) > > #devtools::test("~/rglab/workspace/flowCore") > > proc.time() user system elapsed 21.70 1.98 25.00 |
flowCore.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 190 | SKIP 3 | PASS 334 ] There were 36 warnings (use warnings() to see them) > > #devtools::test("~/rglab/workspace/flowCore") > > proc.time() user system elapsed 20.29 1.28 22.12 |
flowCore.Rcheck/examples_i386/flowCore-Ex.timings
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flowCore.Rcheck/examples_x64/flowCore-Ex.timings
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