Mike Jiang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/flowCore |
| git_branch: RELEASE_3_14 |
| git_last_commit: 947b975 |
| git_last_commit_date: 2021-10-26 11:50:30 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:21 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the flowCore package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCore.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 657/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowCore 2.6.0 (landing page) Mike Jiang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: flowCore |
| Version: 2.6.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowCore_2.6.0.tar.gz |
| StartedAt: 2022-04-12 07:28:06 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 07:29:57 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 111.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowCore.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowCore_2.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/flowCore.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘2.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowCore’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 22.1Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 5.0Mb
extdata 1.1Mb
libs 14.0Mb
* 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
eval,compensatedParameter-missing : <anonymous>: no visible binding for
global variable ‘mat’
eval,compensatedParameter-missing : <anonymous>: no visible binding for
global variable ‘msv’
show,flowFrame: no visible global function definition for
‘capture.output’
Undefined global functions or variables:
capture.output mat msv
Consider adding
importFrom("utils", "capture.output")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.14-bioc/R/library/flowCore/libs/flowCore.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘srand’, possibly from ‘srand’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.14-bioc/meat/flowCore.Rcheck/00check.log’
for details.
flowCore.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL flowCore
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘flowCore’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c Hyperlog.cpp -o Hyperlog.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c Logicle.cpp -o Logicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from flowCore_types.h:12,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from flowCore_types.h:12,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from /home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
from /home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from flowCore_types.h:12,
from RcppExports.cpp:4:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from flowCore_types.h:12,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c biexponential.cpp -o biexponential.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c convertRawBytes.cpp -o convertRawBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c fcsTextParse.cpp -o fcsTextParse.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from fcsTextParse.cpp:8:
/home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from fcsTextParse.cpp:8:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from fcsTextParse.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from fcsTextParse.cpp:10:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c hyperlogTransform.cpp -o hyperlogTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c inPolygon.cpp -o inPolygon.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c inPolytope.cpp -o inPolytope.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c logicleTransform.cpp -o logicleTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
/home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from /home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
from /home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c poly_centroid.cpp -o poly_centroid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c sortBytes.cpp -o sortBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c uint2double.cpp -o uint2double.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c zeroin.cpp -o zeroin.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/lib/libcytolib.a -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-flowCore/00new/flowCore/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘HowTo-flowCore.Rnw’ using ‘UTF-8’
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowCore)
flowCore.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(flowCore)
> library(flowStats)
>
>
> test_check("flowCore")
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object is masked from 'package:flowStats':
normalize
The following object is masked from 'package:flowCore':
normalize
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[ FAIL 0 | WARN 2 | SKIP 3 | PASS 334 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• dir.exists(dataPath) is not TRUE (1)
• file.exists(filename) is not TRUE (2)
[ FAIL 0 | WARN 2 | SKIP 3 | PASS 334 ]
>
> #devtools::test("~/rglab/workspace/flowCore")
>
> proc.time()
user system elapsed
15.918 0.905 16.826
flowCore.Rcheck/flowCore-Ex.timings
| name | user | system | elapsed | |
| EHtrans-class | 0.040 | 0.004 | 0.045 | |
| FCSTransTransform | 0.642 | 0.036 | 0.679 | |
| Subset-methods | 0.182 | 0.000 | 0.182 | |
| arcsinhTransform | 0.04 | 0.00 | 0.04 | |
| asinht-class | 0.017 | 0.000 | 0.018 | |
| asinhtGml2-class | 0.019 | 0.000 | 0.020 | |
| biexponentialTransform | 2.432 | 0.064 | 2.496 | |
| boundaryFilter-class | 0.058 | 0.000 | 0.059 | |
| characterOrNumeric-class | 0.001 | 0.000 | 0.001 | |
| characterOrParameters-class | 0.000 | 0.000 | 0.001 | |
| characterOrTransformation-class | 0.001 | 0.000 | 0.001 | |
| coerce | 0.035 | 0.000 | 0.034 | |
| collapse_desc | 0.688 | 0.032 | 0.720 | |
| compensatedParameter-class | 0.098 | 0.000 | 0.101 | |
| compensation-class | 0.238 | 0.000 | 0.239 | |
| decompensate | 0.030 | 0.004 | 0.034 | |
| dg1polynomial-class | 0.015 | 0.000 | 0.016 | |
| each_col | 0.019 | 0.000 | 0.020 | |
| ellipsoidGate-class | 0.048 | 0.000 | 0.048 | |
| exponential-class | 0.016 | 0.000 | 0.016 | |
| expressionFilter-class | 0.065 | 0.000 | 0.065 | |
| filter-methods | 0.631 | 0.036 | 0.667 | |
| filter-on-methods | 0.071 | 0.000 | 0.070 | |
| filterList-class | 0.004 | 0.000 | 0.003 | |
| filterResult-class | 0 | 0 | 0 | |
| filterResultList-class | 4.178 | 0.164 | 4.343 | |
| filterSummary-class | 0.066 | 0.000 | 0.067 | |
| filterSummaryList-class | 0.676 | 0.020 | 0.696 | |
| flowFrame-class | 3.287 | 0.071 | 3.358 | |
| flowSet-class | 2.032 | 0.152 | 2.184 | |
| fr_append_cols | 0.552 | 0.061 | 0.611 | |
| fsApply | 0.104 | 0.000 | 0.103 | |
| getIndexSort | 0.017 | 0.000 | 0.016 | |
| hyperlog-class | 0.716 | 0.027 | 0.744 | |
| hyperlogtGml2-class | 0.023 | 0.001 | 0.023 | |
| identifier-methods | 0.012 | 0.003 | 0.016 | |
| inverseLogicleTransform | 1.104 | 0.081 | 1.184 | |
| invsplitscale-class | 0.019 | 0.000 | 0.019 | |
| keyword-methods | 0.539 | 0.040 | 0.578 | |
| kmeansFilter-class | 0.101 | 0.000 | 0.100 | |
| linearTransform | 0.026 | 0.003 | 0.031 | |
| lintGml2-class | 0.018 | 0.001 | 0.019 | |
| lnTransform | 1.209 | 0.040 | 1.250 | |
| logTransform | 0.023 | 0.000 | 0.022 | |
| logarithm-class | 0.018 | 0.000 | 0.018 | |
| logicalFilterResult-class | 0.001 | 0.000 | 0.000 | |
| logicleTransform | 0.578 | 0.032 | 0.609 | |
| logicletGml2-class | 0.039 | 0.011 | 0.051 | |
| logtGml2-class | 0.02 | 0.00 | 0.02 | |
| manyFilterResult-class | 0.001 | 0.000 | 0.000 | |
| markernames | 0.557 | 0.020 | 0.577 | |
| multipleFilterResult-class | 0.000 | 0.000 | 0.001 | |
| parameters-methods | 0.017 | 0.000 | 0.018 | |
| polygonGate-class | 0.052 | 0.000 | 0.053 | |
| quadGate-class | 0.115 | 0.004 | 0.119 | |
| quadratic-class | 0.014 | 0.004 | 0.017 | |
| quadraticTransform | 0.022 | 0.000 | 0.022 | |
| ratio-class | 0.024 | 0.000 | 0.025 | |
| ratiotGml2-class | 0.017 | 0.000 | 0.018 | |
| read.FCS | 0.056 | 0.000 | 0.056 | |
| read.FCSheader | 0.004 | 0.000 | 0.004 | |
| read.flowSet | 0.07 | 0.00 | 0.07 | |
| rectangleGate-class | 0.069 | 0.004 | 0.072 | |
| rotate_gate | 0 | 0 | 0 | |
| sampleFilter-class | 0.038 | 0.000 | 0.038 | |
| scaleTransform | 0.022 | 0.000 | 0.022 | |
| scale_gate | 0.000 | 0.000 | 0.001 | |
| shift_gate | 0 | 0 | 0 | |
| singleParameterTransform-class | 0.001 | 0.000 | 0.001 | |
| sinht-class | 0.019 | 0.000 | 0.019 | |
| split-methods | 1.221 | 0.099 | 1.320 | |
| splitScaleTransform | 0.867 | 0.032 | 0.898 | |
| splitscale-class | 0.021 | 0.001 | 0.022 | |
| squareroot-class | 0.020 | 0.000 | 0.019 | |
| timeFilter-class | 1.573 | 0.035 | 1.609 | |
| transform-class | 0.000 | 0.000 | 0.001 | |
| transform | 0.874 | 0.048 | 0.922 | |
| transformFilter-class | 0.113 | 0.000 | 0.112 | |
| transformList-class | 0.532 | 0.052 | 0.585 | |
| transformMap-class | 0 | 0 | 0 | |
| transform_gate | 0 | 0 | 0 | |
| truncateTransform | 0.023 | 0.000 | 0.023 | |
| unitytransform-class | 0.011 | 0.003 | 0.016 | |
| write.FCS | 0.036 | 0.000 | 0.036 | |
| write.flowSet | 0.688 | 0.028 | 0.715 | |