| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:59 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 264/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CancerInSilico 2.20.0 (landing page) Thomas D. Sherman
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK |  | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the CancerInSilico package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CancerInSilico.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CancerInSilico |
| Version: 2.20.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CancerInSilico.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CancerInSilico_2.20.0.tar.gz |
| StartedAt: 2023-10-16 00:14:47 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 00:15:49 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 62.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CancerInSilico.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CancerInSilico.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CancerInSilico_2.20.0.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/CancerInSilico.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CancerInSilico/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CancerInSilico' version '2.20.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CancerInSilico' can be installed ... WARNING
Found the following significant warnings:
CellModels/../OffLatticeModel/../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
CellModels/../OffLatticeModel/../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
OffLatticeModel/../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
OffLatticeModel/../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
Tests/Core/../../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
Tests/Core/../../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
See 'F:/biocbuild/bbs-3.17-bioc/meat/CancerInSilico.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... OK
* 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 ... OK
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/CancerInSilico/libs/x64/CancerInSilico.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 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: 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc/meat/CancerInSilico.Rcheck/00check.log'
for details.
CancerInSilico.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL CancerInSilico
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'CancerInSilico' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RunModel.cpp -o RunModel.o
In file included from CellModels/../OffLatticeModel/../Core/Lattice.h:19,
from CellModels/../OffLatticeModel/../Core/SquareLattice.h:10,
from CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:7,
from CellModels/DrasdoHohmeModel.h:7,
from RunModel.cpp:4:
CellModels/../OffLatticeModel/../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
49 | struct iequal_to : std::binary_function<Point<int>, Point<int>, bool>
| ^~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from RunModel.cpp:1:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
CellModels/../OffLatticeModel/../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
58 | struct ihash : std::unary_function<Point<int>, std::size_t>
| ^~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o
In file included from CellModels/../OffLatticeModel/../Core/Lattice.h:19,
from CellModels/../OffLatticeModel/../Core/SquareLattice.h:10,
from CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:7,
from CellModels/DrasdoHohmeModel.h:7,
from CellModels/DrasdoHohmeModel.cpp:1:
CellModels/../OffLatticeModel/../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
49 | struct iequal_to : std::binary_function<Point<int>, Point<int>, bool>
| ^~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from CellModels/../OffLatticeModel/../Core/CellBasedModel.h:6,
from CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
CellModels/../OffLatticeModel/../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
58 | struct ihash : std::unary_function<Point<int>, std::size_t>
| ^~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o
In file included from OffLatticeModel/OffLatticeCell.h:36,
from OffLatticeModel/OffLatticeCell.cpp:4:
OffLatticeModel/../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
49 | struct iequal_to : std::binary_function<Point<int>, Point<int>, bool>
| ^~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from OffLatticeModel/OffLatticeCell.cpp:2:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
OffLatticeModel/../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
58 | struct ihash : std::unary_function<Point<int>, std::size_t>
| ^~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c OffLatticeModel/OffLatticeCellBasedModel.cpp -o OffLatticeModel/OffLatticeCellBasedModel.o
In file included from OffLatticeModel/../Core/Lattice.h:19,
from OffLatticeModel/../Core/SquareLattice.h:10,
from OffLatticeModel/OffLatticeCellBasedModel.h:7,
from OffLatticeModel/OffLatticeCellBasedModel.cpp:1:
OffLatticeModel/../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
49 | struct iequal_to : std::binary_function<Point<int>, Point<int>, bool>
| ^~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from OffLatticeModel/../Core/CellBasedModel.h:6,
from OffLatticeModel/OffLatticeCellBasedModel.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
OffLatticeModel/../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
58 | struct ihash : std::unary_function<Point<int>, std::size_t>
| ^~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Core/Cell.cpp -o Core/Cell.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Core/CellType.cpp -o Core/CellType.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Core/Drug.cpp -o Core/Drug.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Core/Random.cpp -o Core/Random.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/size.hpp:21,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/random.hpp:70,
from Core/Random.cpp:3:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
F:/biocbuild/bbs-3.17-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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Tests/Core/test-CellType.cpp -o Tests/Core/test-CellType.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Tests/Core/test-Drug.cpp -o Tests/Core/test-Drug.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Tests/Core/test-Point.cpp -o Tests/Core/test-Point.o
In file included from Tests/Core/test-Point.cpp:3:
Tests/Core/../../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
49 | struct iequal_to : std::binary_function<Point<int>, Point<int>, bool>
| ^~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Tests/Core/../catch.h:11,
from Tests/Core/test-Point.cpp:1:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
Tests/Core/../../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
58 | struct ihash : std::unary_function<Point<int>, std::size_t>
| ^~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Tests/Core/test-Random.cpp -o Tests/Core/test-Random.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Tests/Core/test-SquareLattice.cpp -o Tests/Core/test-SquareLattice.o
In file included from Tests/Core/../../Core/Lattice.h:19,
from Tests/Core/../../Core/SquareLattice.h:10,
from Tests/Core/test-SquareLattice.cpp:4:
Tests/Core/../../Core/Point.h:49:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
49 | struct iequal_to : std::binary_function<Point<int>, Point<int>, bool>
| ^~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Tests/Core/test-SquareLattice.cpp:1:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
Tests/Core/../../Core/Point.h:58:21: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
58 | struct ihash : std::unary_function<Point<int>, std::size_t>
| ^~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o CancerInSilico.dll tmp.def RunModel.o RcppExports.o CellModels/DrasdoHohmeModel.o OffLatticeModel/OffLatticeCell.o OffLatticeModel/OffLatticeCellBasedModel.o OffLatticeModel/OffLatticeRadiusSolver.o Core/Cell.o Core/CellBasedModel.o Core/CellType.o Core/Drug.o Core/Random.o test-runner.o Tests/Core/test-CellType.o Tests/Core/test-Drug.o Tests/Core/test-Point.o Tests/Core/test-Random.o Tests/Core/test-SquareLattice.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-CancerInSilico/00new/CancerInSilico/libs/x64
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CancerInSilico)
CancerInSilico.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(CancerInSilico)
Loading required package: Rcpp
>
> test_check("CancerInSilico")
time = 0.00
size = 2
time = 1.00
size = 2
time = 0.00
size = 3
time = 100.00
size = 18
time = 0.00
size = 1000
time = 1.00
size = 1040
===============================================================================
All tests passed (56 assertions in 5 test cases)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 64 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test-GeneExpressionSimulation.R:31:1',
'test-GeneExpressionSimulation.R:47:1', 'test-cpp.R:3:1'
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 64 ]
>
> proc.time()
user system elapsed
2.01 0.23 2.23
CancerInSilico.Rcheck/CancerInSilico-Ex.timings
| name | user | system | elapsed | |
| cellSummary-methods | 0.10 | 0.02 | 0.11 | |
| checkDataSet | 0.00 | 0.00 | 0.02 | |
| getAxisAngle-methods | 0.08 | 0.00 | 0.08 | |
| getAxisLength-methods | 0.09 | 0.00 | 0.09 | |
| getCellDistance-methods | 0.10 | 0.01 | 0.11 | |
| getCellPhase-methods | 0.07 | 0.02 | 0.10 | |
| getCellType-methods | 0.06 | 0.00 | 0.06 | |
| getCoordinates-methods | 0.08 | 0.00 | 0.08 | |
| getCycleLength-methods | 0.06 | 0.00 | 0.07 | |
| getDensity-methods | 0.07 | 0.00 | 0.06 | |
| getLocalDensity-methods | 0.07 | 0.00 | 0.08 | |
| getNumberOfCells-methods | 0.07 | 0.00 | 0.06 | |
| getRadius-methods | 0.06 | 0.00 | 0.07 | |
| getTrialAcceptRate-methods | 0.06 | 0.00 | 0.06 | |
| inSilicoCellModel | 0.06 | 0.00 | 0.07 | |
| plotCells-methods | 0.08 | 0.00 | 0.08 | |
| run-methods | 0.21 | 0.00 | 0.20 | |