Installation error in macOS

masato-ogishi commented 4 years ago

Describe the bug An installation from the github repository failed. The error code reads: make: *** [R_GatingSet.o] Error 1 ERROR: compilation failed for package ‘flowWorkspace’

To Reproduce library(devtools) install_github("RGLab/flowWorkspace")

SessionInfo: ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value
version R version 4.0.2 (2020-06-22) os macOS High Sierra 10.13.6
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-09-02

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── package version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0) backports 1.1.9 2020-08-24 [1] CRAN (R 4.0.2) callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0) cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0) curl 4.3 2019-12-02 [1] CRAN (R 4.0.0) desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0) devtools 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0) ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0) fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0) fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0) memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0) processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2) ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0) remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0) tinytex 0.25 2020-07-24 [1] CRAN (R 4.0.2) usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.0) withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0) xfun 0.16 2020-07-24 [1] CRAN (R 4.0.2)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

jacobpwagner commented 4 years ago

Can you provide any more of the compilation error itself or the compilation output in the console leading up to the error?

masato-ogishi commented 4 years ago

Here is the output. Thank you for your help!

library(devtools) Loading required package: usethis install_github("RGLab/flowWorkspace") Downloading GitHub repo RGLab/flowWorkspace@HEAD Skipping 11 packages ahead of CRAN: Rhdf5lib, RProtoBufLib, cytolib, BiocGenerics, Biobase, zlibbioc, flowCore, graph, ncdfFlow, Rgraphviz, RBGL ✓ checking for file ‘/private/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T/RtmpxNAvLl/remotes1279bad853c9/RGLab-flowWorkspace-9f0fcfb/DESCRIPTION’ ... ─ preparing ‘flowWorkspace’: (562ms) ✓ checking DESCRIPTION meta-information ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories WARNING: Removing directory ‘flowWorkspace/Meta’ which should only occur in an installed package NB: this package now depends on R (>= 3.5.0) WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘flowWorkspace/tests/testthat/expect_result/empty_pop.rds’ ─ building ‘flowWorkspace_4.1.9.tar.gz’

installing source package ‘flowWorkspace’ ... using staged installation libs /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_API.cpp -o RAPI.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/transformation.hpp:18, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:15, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/gate.hpp:12, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14, from R_API.cpp:9: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed **** (Pred::**** ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_notarg' [-Wparentheses] failed **** (boost::mpl::not::**** ^ In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/gate.hpp:12, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14, from R_API.cpp:9: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){


/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
   ~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                           ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/transformation.hpp:18,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:15,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/gate.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14,
             from R_GatingHierarchy.cpp:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/gate.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14,
             from R_GatingHierarchy.cpp:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
  ~~~~~~~~~~~~~~^~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
   ~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                           ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/transformation.hpp:18,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:15,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/gate.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14,
             from ../inst/include/flowWorkspace.h:5,
             from R_GatingSet.cpp:10:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/gate.hpp:12,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/populationTree.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14,
             from ../inst/include/flowWorkspace.h:5,
             from R_GatingSet.cpp:10:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
  ~~~~~~~~~~~~~~^~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
   ~~~~~~~~~~~~~~^~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                           ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/flowWorkspace.h:6,
             from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/pairVectorRcppWrap.h: In function 'T Rcpp::as(SEXP) [with T = cytolib::FCS_READ_PARAM; SEXP = SEXPREC*]':
../inst/include/flowWorkspace/pairVectorRcppWrap.h:78:71: error: no match for 'operator=' (operand types are 'std::vector<long int>' and 'std::vector<long long int, std::allocator<long long int> >')
   config.data.which_lines = as<vector<int64_t>>(cfg["which.lines"]);
                                                                   ^
In file included from /usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/vector:69,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:14,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14,
             from ../inst/include/flowWorkspace.h:5,
             from R_GatingSet.cpp:10:
/usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/bits/vector.tcc:186:5: note: candidate: 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = long int; _Alloc = std::allocator<long int>]'
 vector<_Tp, _Alloc>::
 ^~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/bits/vector.tcc:186:5: note:   no known conversion for argument 1 from 'std::vector<long long int, std::allocator<long long int> >' to 'const std::vector<long int>&'
In file included from /usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/vector:64,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:14,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14,
             from ../inst/include/flowWorkspace.h:5,
             from R_GatingSet.cpp:10:
/usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/bits/stl_vector.h:596:7: note: candidate: 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = long int; _Alloc = std::allocator<long int>]'
   operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
   ^~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/bits/stl_vector.h:596:7: note:   no known conversion for argument 1 from 'std::vector<long long int, std::allocator<long long int> >' to 'std::vector<long int>&&'
/usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/bits/stl_vector.h:617:7: note: candidate: 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = long int; _Alloc = std::allocator<long int>]'
   operator=(initializer_list<value_type> __l)
   ^~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/include/c++/8.4.0/bits/stl_vector.h:617:7: note:   no known conversion for argument 1 from 'std::vector<long long int, std::allocator<long long int> >' to 'std::initializer_list<long int>'
make: *** [R_GatingSet.o] Error 1
ERROR: compilation failed for package ‘flowWorkspace’

removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace’ Error: Failed to install 'flowWorkspace' from GitHub: (converted from warning) installation of package ‘/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T//RtmpxNAvLl/file1279b568ae024/flowWorkspace_4.1.9.tar.gz’ had non-zero exit status

jacobpwagner commented 4 years ago

I can't see your cytolib version (maybe attach the output of packageVersion("cytolib") just to verify) but by your error this is almost definitely just because you haven't picked up a recent change in cytolib corresponding to this change in flowWorkspace. Re-install cytolib from the current GitHub master branch and then try again. You'll need to do the same for CytoML if you use it:

devtools::install_github("RGLab/cytolib")
devtools::install_github("RGLab/flowWorkspace")
devtools::install_github("RGLab/CytoML")

jacobpwagner commented 4 years ago

The cytolib version dependency has now also been incremented so the cause should be clear moving forward (instead of a compilation error you'll get prompted to update cytolib).

masato-ogishi commented 4 years ago

Thanks. But now I encountered another error when installing cytolib. I don't figure out what to do. Thanks for your help!!

remotes::install_github("RGLab/cytolib") Downloading GitHub repo RGLab/cytolib@HEAD Skipping 2 packages ahead of CRAN: Rhdf5lib, RProtoBufLib ✓ checking for file ‘/private/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T/Rtmpp09PWI/remotes13dac10ed0983/RGLab-cytolib-6846d09/DESCRIPTION’ ... ─ preparing ‘cytolib’: (336ms) ✓ checking DESCRIPTION meta-information ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts (479ms) ─ checking for empty or unneeded directories ─ building ‘cytolib_2.1.18.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h’

installing source package ‘cytolib’ ... using staged installation checking for a sed that does not truncate output... /usr/bin/sed checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config knows TileDB... no checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking tiledb/tiledb.h usability... no checking tiledb/tiledb.h presence... no checking for tiledb/tiledb.h... no configure: No tiledb is found, build without tiledb... configure: Parsing cytolib version info ... configure: CYTOLIB_VERSION=2.1.18 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars libs /usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTOPTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrame.cpp -o CytoFrame.o In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux/na_assert.hpp:23, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19, from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19, from ../inst/include/cytolib/transformation.hpp:18, from ../inst/include/cytolib/compensation.hpp:15, from ../inst/include/cytolib/CytoFrame.hpp:16, from CytoFrame.cpp:3: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed **** (Pred::**** ^ /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_notarg' [-Wparentheses] failed **** (boost::mpl::not::**** ^ In file included from ../inst/include/cytolib/CytoFrame.hpp:16, from CytoFrame.cpp:3: ../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': ../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){


../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
   ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                           ~~^~~~~~~~~~~~~~~~~~~~~
CytoFrame.cpp: In member function 'void cytolib::CytoFrame::append_columns(const std::vector<std::__cxx11::basic_string<char> >&, const EVENT_DATA_VEC&)':
CytoFrame.cpp:152:31: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
new_mins.fill(-arma::math::inf());
                           ^~~
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo:123,
             from ../inst/include/cytolib/CytoFrame.hpp:12,
             from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
arma_deprecated static eT inf()       { return eT(Datum<eT>::inf); }  // use datum::inf instead
                         ^~~
CytoFrame.cpp:152:35: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
new_mins.fill(-arma::math::inf());
                               ^
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo:123,
             from ../inst/include/cytolib/CytoFrame.hpp:12,
             from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
arma_deprecated static eT inf()       { return eT(Datum<eT>::inf); }  // use datum::inf instead
                         ^~~
CytoFrame.cpp:152:35: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
new_mins.fill(-arma::math::inf());
                               ^
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo:123,
             from ../inst/include/cytolib/CytoFrame.hpp:12,
             from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
arma_deprecated static eT inf()       { return eT(Datum<eT>::inf); }  // use datum::inf instead
                         ^~~
CytoFrame.cpp:154:30: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
new_maxs.fill(arma::math::inf());
                          ^~~
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo:123,
             from ../inst/include/cytolib/CytoFrame.hpp:12,
             from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
arma_deprecated static eT inf()       { return eT(Datum<eT>::inf); }  // use datum::inf instead
                         ^~~
CytoFrame.cpp:154:34: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
new_maxs.fill(arma::math::inf());
                              ^
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo:123,
             from ../inst/include/cytolib/CytoFrame.hpp:12,
             from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
arma_deprecated static eT inf()       { return eT(Datum<eT>::inf); }  // use datum::inf instead
                         ^~~
CytoFrame.cpp:154:34: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
new_maxs.fill(arma::math::inf());
                              ^
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo:123,
             from ../inst/include/cytolib/CytoFrame.hpp:12,
             from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
arma_deprecated static eT inf()       { return eT(Datum<eT>::inf); }  // use datum::inf instead
                         ^~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CytoFrameView.cpp -o CytoFrameView.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
             from ../inst/include/cytolib/transformation.hpp:18,
             from ../inst/include/cytolib/compensation.hpp:15,
             from ../inst/include/cytolib/CytoFrame.hpp:16,
             from ../inst/include/cytolib/MemCytoFrame.hpp:12,
             from ../inst/include/cytolib/CytoFrameView.hpp:12,
             from CytoFrameView.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
             from ../inst/include/cytolib/MemCytoFrame.hpp:12,
             from ../inst/include/cytolib/CytoFrameView.hpp:12,
             from CytoFrameView.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
  ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
   ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                           ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CytoVFS.cpp -o CytoVFS.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
             from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16,
             from ../inst/include/cytolib/CytoVFS.hpp:15,
             from CytoVFS.cpp:8:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
                 ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 CytoVFS.cpp:8:
../inst/include/cytolib/CytoVFS.hpp:31:3: error: 'shared_ptr' does not name a type; did you mean 'char16_t'?
shared_ptr<void> ctxptr_;
^~~~~~~~~~
char16_t
../inst/include/cytolib/CytoVFS.hpp:39:4: error: 'shared_ptr' does not name a type; did you mean 'char16_t'?
shared_ptr<void> get_ctxptr() const{return ctxptr_;};
^~~~~~~~~~
char16_t
../inst/include/cytolib/CytoVFS.hpp:51:3: error: 'shared_ptr' does not name a type; did you mean 'char16_t'?
shared_ptr<void> vfsptr_;
^~~~~~~~~~
char16_t
make: *** [CytoVFS.o] Error 1
ERROR: compilation failed for package ‘cytolib’

removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’ Error: Failed to install 'cytolib' from GitHub: (converted from warning) installation of package ‘/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T//Rtmpp09PWI/file13dac52b80c98/cytolib_2.1.18.tar.gz’ had non-zero exit status

masato-ogishi commented 4 years ago

packageVersion("cytolib") [1] ‘2.1.17’ packageVersion("CytoML") [1] ‘2.1.11’ packageVersion("flowWorkspace") [1] ‘4.1.4’

jacobpwagner commented 4 years ago

Try installing cytolib again now after this.

GeroKn commented 4 years ago

I am getting the same errors on MacOS. Unfortunately, I have no idea on how to find the error.

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggforce_0.3.2               gplots_3.0.4                RColorBrewer_1.1-2         
 [4] sva_3.37.0                  BiocParallel_1.23.2         genefilter_1.71.0          
 [7] mgcv_1.8-33                 nlme_3.1-149                pheatmap_1.0.12            
[10] rlist_0.4.6.1               ggplot2_3.3.2               fgsea_1.15.0               
[13] DESeq2_1.29.13              SummarizedExperiment_1.19.6 DelayedArray_0.15.7        
[16] matrixStats_0.56.0          Matrix_1.2-18               Biobase_2.49.0             
[19] GenomicRanges_1.41.6        GenomeInfoDb_1.25.10        IRanges_2.23.10            
[22] S4Vectors_0.27.12           BiocGenerics_0.35.4        
`

`> devtools::install_github("RGLab/cytolib")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo RGLab/cytolib@HEAD
Skipping 1 packages ahead of CRAN: Rhdf5lib
✓  checking for file ‘/private/var/folders/9n/dfskvf3n3n7dz6w_5qk3kt6c0000gn/T/RtmpqdlMrG/remotes240c143161c3/RGLab-cytolib-b3931f3/DESCRIPTION’ ...
─  preparing ‘cytolib’: (341ms)
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (500ms)
─  checking for empty or unneeded directories
─  building ‘cytolib_2.1.18.tar.gz’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h’

* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /usr/bin/sed
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config knows TileDB... no
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking tiledb/tiledb.h usability... no
checking tiledb/tiledb.h presence... no
checking for tiledb/tiledb.h... no
configure: No tiledb is found, build without tiledb...
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.1.18
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c CytoFrame.cpp -o CytoFrame.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c CytoFrameView.cpp -o CytoFrameView.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/CytoFrameView.hpp:12,
                 from CytoFrameView.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/CytoFrameView.hpp:12,
                 from CytoFrameView.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c CytoVFS.cpp -o CytoVFS.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16,
                 from ../inst/include/cytolib/CytoVFS.hpp:16,
                 from CytoVFS.cpp:8:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from GatingHierarchy.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from GatingHierarchy.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c GatingSet.cpp -o GatingSet.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/cytolib/compensation.hpp:19,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
../inst/include/cytolib/global.hpp: In constructor 'cytolib::GatingSet::GatingSet(std::string, bool, bool, std::vector<std::__cxx11::basic_string<char> >, bool, cytolib::CytoCtx)':
../inst/include/cytolib/global.hpp:29:3: warning: 'fmt' may be used uninitialized in this function [-Wmaybe-uninitialized]
   29 |   switch(fmt)
      |   ^~~~~~
GatingSet.cpp:30:14: note: 'fmt' was declared here
   30 |   FileFormat fmt;
      |              ^~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c GatingSet.pb.cc -o GatingSet.pb.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c H5CytoFrame.cpp -o H5CytoFrame.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/H5CytoFrame.hpp:12,
                 from H5CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/H5CytoFrame.hpp:12,
                 from H5CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c MemCytoFrame.cpp -o MemCytoFrame.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from MemCytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from MemCytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c POPINDICES.cpp -o POPINDICES.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from POPINDICES.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from POPINDICES.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c calibrationTable.cpp -o calibrationTable.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/foreach.hpp:76,
                 from calibrationTable.cpp:5:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c compensation.cpp -o compensation.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from compensation.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 compensation.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c dummy.cpp -o dummy.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c ellipse2points.cpp -o ellipse2points.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c gate.cpp -o gate.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from gate.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from gate.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c global.cpp -o global.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16,
                 from ../inst/include/cytolib/CytoVFS.hpp:16,
                 from ../inst/include/cytolib/global.hpp:21,
                 from global.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
global.cpp: In function 'std::string cytolib::s3_to_http(std::string)':
global.cpp:46:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   46 |   for(int i = 1; i < tokens.size(); i++)
      |                  ~~^~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c in_polygon.cpp -o in_polygon.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c nodeProperties.cpp -o nodeProperties.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/compensation.hpp:15,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from nodeProperties.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from nodeProperties.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   50 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   54 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   60 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c spline.cpp -o spline.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c trans_group.cpp -o trans_group.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from ../inst/include/cytolib/trans_group.hpp:13,
                 from trans_group.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c transformation.cpp -o transformation.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
                 from ../inst/include/cytolib/transformation.hpp:18,
                 from transformation.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/directory.hpp:26,
                 from boost/libs/filesystem/src/directory.cpp:28:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/exception.cpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/operations.cpp:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/path.cpp:28:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from boost/libs/filesystem/src/portability.cpp:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
                 from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25,
                 from boost/libs/filesystem/src/unique_path.cpp:16:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/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>::************
      |                     ^
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
/usr/local/bin/g++-9 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
/usr/local/bin/g++-9 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/local/lib/gcc5/ -o cytolib.so CytoFrame.o CytoFrameView.o CytoVFS.o GatingHierarchy.o GatingSet.o GatingSet.pb.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o dummy.o ellipse2points.o gate.o global.o in_polygon.o nodeProperties.o spline.o trans_group.o transformation.o -L/opt/local/lib/gcc5/ -lgomp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/local/lib/gcc5/'
ld: warning: directory not found for option '-L/opt/local/lib/gcc5/'
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘cytolib’:
 .onLoad failed in loadNamespace() for 'cytolib', details:
  call: dyn.load(cytolib, local = FALSE, now = TRUE)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN2H515DSetAccPropList7DEFAULTE
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’
Error: Failed to install 'cytolib' from GitHub:
  (converted from warning) installation of package ‘/var/folders/9n/dfskvf3n3n7dz6w_5qk3kt6c0000gn/T//RtmpqdlMrG/file240c36095390/cytolib_2.1.18.tar.gz’ had non-zero exit status

jacobpwagner commented 4 years ago

@GeroKn , can you give me the output of packageVersion("Rhdf5lib")?

GeroKn commented 4 years ago

Thanks for your help!

> packageVersion("Rhdf5lib") [1] ‘1.11.3’

jacobpwagner commented 4 years ago

@GeroKn , I'm not actually seeing any linker flag for libhdf5. Can you give me the output of this as well (from a terminal):

Rscript -e 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'

Or, from within an R session:

Rhdf5lib::pkgconfig("PKG_CXX_LIBS")

GeroKn commented 4 years ago

Hi Jacob,

Rscript -e 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")' "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5.a" "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libsz.a" -lz

jacobpwagner commented 4 years ago

Hey @GeroKn , I'd suggest following @gfinak 's general advice here regarding making sure the versions you have of each of the packages are built from source using the same compiler, or just using the binaries from Bioconductor using BiocManager::install.

In your case in particular, it looks like a compiler discrepancy between Rhdf5lib (probably from the binaries on Bioconductor using clang++ -mmacosx-version-min=10.13) and cytolib (using g++9 by your output above) may be to blame. Although, I am not entirely sure why during compilation it seems to not be getting those Rhdf5lib linking paths at all.

Either way, a decent first thing to try would be removing the installation directories of Rhdf5lib, RProtoBufLib, cytolib, and flowWorkspace and then installing them all from the same source. That is, use either BiocManager::install, or devtools::install_github to build from source, but do the same for all of those packages.

GeroKn commented 4 years ago

Hi Jacob,

It works now. There were many issues, I don't know what solved the problem and basically I have no idea what I did besides googling one error message after the other, but it's running :D First of all, there was a Makevars on my system, which defined g++9 as the compiler. Afterwards, it was using clang as the compiler, however it still not worked, complaining about some missing -lgfortran library. I installed fortran, still did not work. After reinstalling Rcpp with install.packages("Rcpp", type = "source") the compilation of flowWorkspace was finally successful (type="source" was required for it to work).

Best! Gero

jacobpwagner commented 4 years ago

Closing this, as the installation issues for both users appear to be solved.

masato-ogishi commented 4 years ago

Unfortunately it's not actually solved for my Mac. As I also have a Windows PC and the packages work perfectly, I decided to switch to Windows. Thanks anyway for your debugging and maintenance for those amazing set of tools.

jacobpwagner commented 4 years ago

@masato-ogishi , sorry. I misread that. I'll look back and see if I can figure out the residual mac issues.

RGLab / flowWorkspace

Installation error in macOS #347