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This page was generated on 2023-01-02 09:00:22 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for CancerInSilico on palomino5


To the developers/maintainers of the CancerInSilico package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 246/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerInSilico 2.19.0  (landing page)
Thomas D. Sherman
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/CancerInSilico
git_branch: master
git_last_commit: 7affe4f
git_last_commit_date: 2022-11-01 11:14:34 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: CancerInSilico
Version: 2.19.0
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_2.19.0.tar.gz
StartedAt: 2022-12-28 22:14:02 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 22:14:58 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 55.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CancerInSilico.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/CancerInSilico.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '2.19.0'
* 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-rtools43/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-rtools43/meat/CancerInSilico.Rcheck/00check.log'
for details.

Installation output

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++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RunModel.cpp -o RunModel.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered/unordered_map.hpp:18,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered_map.hpp:17,
                 from CellModels/../OffLatticeModel/../Core/Lattice.h:10,
                 from CellModels/../OffLatticeModel/../Core/SquareLattice.h:10,
                 from CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:7,
                 from CellModels/DrasdoHohmeModel.h:7,
                 from RunModel.cpp:4:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  132 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
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:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from CellModels/../OffLatticeModel/../Core/Lattice.h:19:
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>
      |                         ^~~~~~~~~~~~~~~
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++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11  -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:/rtools42/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 F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered/unordered_map.hpp:18,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered_map.hpp:17,
                 from CellModels/../OffLatticeModel/../Core/Lattice.h:10,
                 from CellModels/../OffLatticeModel/../Core/SquareLattice.h:10,
                 from CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:7,
                 from CellModels/DrasdoHohmeModel.h:7,
                 from CellModels/DrasdoHohmeModel.cpp:1:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  132 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
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:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from CellModels/../OffLatticeModel/../Core/Lattice.h:19:
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>
      |                         ^~~~~~~~~~~~~~~
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++11  -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:/rtools42/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 F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from OffLatticeModel/../Core/Point.h:9,
                 from OffLatticeModel/OffLatticeCell.h:36,
                 from OffLatticeModel/OffLatticeCell.cpp:4:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  132 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
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:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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>
      |                         ^~~~~~~~~~~~~~~
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++11  -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:/rtools42/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 F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered/unordered_map.hpp:18,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered_map.hpp:17,
                 from OffLatticeModel/../Core/Lattice.h:10,
                 from OffLatticeModel/../Core/SquareLattice.h:10,
                 from OffLatticeModel/OffLatticeCellBasedModel.h:7,
                 from OffLatticeModel/OffLatticeCellBasedModel.cpp:1:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  132 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
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:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from OffLatticeModel/../Core/Lattice.h:19:
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>
      |                         ^~~~~~~~~~~~~~~
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++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
g++ -std=gnu++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Core/Cell.cpp -o Core/Cell.o
g++ -std=gnu++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
g++ -std=gnu++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Core/CellType.cpp -o Core/CellType.o
g++ -std=gnu++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Core/Drug.cpp -o Core/Drug.o
g++ -std=gnu++11  -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:/rtools42/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++11  -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:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11  -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:/rtools42/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++11  -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:/rtools42/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++11  -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:/rtools42/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 F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from Tests/Core/../../Core/Point.h:9,
                 from Tests/Core/test-Point.cpp:3:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  132 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
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:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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>
      |                         ^~~~~~~~~~~~~~~
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++11  -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:/rtools42/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++11  -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:/rtools42/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 F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered/unordered_map.hpp:18,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/unordered_map.hpp:17,
                 from Tests/Core/../../Core/Lattice.h:10,
                 from Tests/Core/../../Core/SquareLattice.h:10,
                 from Tests/Core/test-SquareLattice.cpp:4:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  132 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
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:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from Tests/Core/../../Core/Lattice.h:19:
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>
      |                         ^~~~~~~~~~~~~~~
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++11 -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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/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)

Tests output

CancerInSilico.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64 (64-bit)

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> 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 ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
   1.64    0.18    1.79

Example timings

CancerInSilico.Rcheck/CancerInSilico-Ex.timings

nameusersystemelapsed
cellSummary-methods0.090.000.10
checkDataSet0.000.000.01
getAxisAngle-methods0.060.010.08
getAxisLength-methods0.060.000.06
getCellDistance-methods0.070.020.08
getCellPhase-methods0.060.010.08
getCellType-methods0.060.000.06
getCoordinates-methods0.060.020.08
getCycleLength-methods0.070.000.06
getDensity-methods0.060.020.08
getLocalDensity-methods0.080.000.08
getNumberOfCells-methods0.060.010.08
getRadius-methods0.060.000.06
getTrialAcceptRate-methods0.080.000.08
inSilicoCellModel0.060.000.06
plotCells-methods0.080.000.08
run-methods0.270.000.26