Mike Jiang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/cytolib |
| git_branch: RELEASE_3_13 |
| git_last_commit: 652ea2c |
| git_last_commit_date: 2021-05-19 12:29:37 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the cytolib package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cytolib.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 433/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cytolib 2.4.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: cytolib |
| Version: 2.4.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cytolib_2.4.0.tar.gz |
| StartedAt: 2021-10-14 09:27:54 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:28:08 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 14.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cytolib.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cytolib_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cytolib.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytolib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytolib’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cytolib’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 40.3Mb
sub-directories of 1Mb or more:
lib 40.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CxxFlags: no visible global function definition for ‘cytolibCxxFlags’
Undefined global functions or variables:
cytolibCxxFlags
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/cytolib.Rcheck/00check.log’
for details.
cytolib.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cytolib
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* 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
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.4.0
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/exception.cpp:15:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/directory.hpp:26,
from boost/libs/filesystem/src/directory.cpp:16:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/path.cpp:19:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/operations.hpp:26,
from boost/libs/filesystem/src/operations.cpp:17:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/operations.hpp:26,
from boost/libs/filesystem/src/unique_path.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/portability.cpp:14:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c CytoFrameView.cpp -o CytoFrameView.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from ../inst/include/cytolib/populationTree.hpp:14,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from GatingHierarchy.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c spline.cpp -o spline.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c trans_group.cpp -o trans_group.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/trans_group.hpp:13,
from trans_group.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5CytoFrame.cpp -o H5CytoFrame.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c ellipse2points.cpp -o ellipse2points.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c transformation.cpp -o transformation.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from transformation.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c GatingSet.cpp -o GatingSet.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from ../inst/include/cytolib/populationTree.hpp:14,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from GatingSet.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
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>, std::allocator<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;
| ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c POPINDICES.cpp -o POPINDICES.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c CytoVFS.cpp -o CytoVFS.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem.hpp:16,
from ../inst/include/cytolib/CytoVFS.hpp:17,
from CytoVFS.cpp:8:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c MemCytoFrame.cpp -o MemCytoFrame.o
MemCytoFrame.cpp:538: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
538 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c calibrationTable.cpp -o calibrationTable.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:76,
from calibrationTable.cpp:5:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c CytoFrame.cpp -o CytoFrame.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from CytoFrame.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c global.cpp -o global.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem/path.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/filesystem.hpp:16,
from ../inst/include/cytolib/CytoVFS.hpp:17,
from ../inst/include/cytolib/global.hpp:21,
from global.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
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++)
| ~~^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c in_polygon.cpp -o in_polygon.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gate.cpp -o gate.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c nodeProperties.cpp -o nodeProperties.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../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:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from ../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:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c compensation.cpp -o compensation.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from compensation.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from compensation.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
mkdir -p "/home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-cytolib/00new/cytolib/lib"
ar rs "/home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-cytolib/00new/cytolib/lib/libcytolib.a" CytoFrameView.o GatingHierarchy.o spline.o trans_group.o H5CytoFrame.o ellipse2points.o transformation.o GatingSet.o dummy.o POPINDICES.o CytoVFS.o MemCytoFrame.o calibrationTable.o CytoFrame.o global.o in_polygon.o gate.o nodeProperties.o compensation.o boost/libs/filesystem/src/path_traits.o boost/libs/filesystem/src/codecvt_error_category.o boost/libs/filesystem/src/utf8_codecvt_facet.o boost/libs/filesystem/src/windows_file_codecvt.o boost/libs/filesystem/src/exception.o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/path.o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/unique_path.o boost/libs/filesystem/src/portability.o boost/libs/system/src/error_code.o
ar: creating /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-cytolib/00new/cytolib/lib/libcytolib.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o cytolib.so dummy.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cytolib)