Multiple platform build/check report for BioC 3.19 - CHECK results for CancerInSilico on palomino3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4494
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4508
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4466
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4362
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*

CHECK results for CancerInSilico on palomino3

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.

raw results

Summary

Package: CancerInSilico

Version: 2.24.0

Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CancerInSilico.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CancerInSilico_2.24.0.tar.gz

StartedAt: 2024-06-26 23:43:52 -0400 (Wed, 26 Jun 2024)

EndedAt: 2024-06-26 23:45:09 -0400 (Wed, 26 Jun 2024)

EllapsedTime: 76.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: CancerInSilico.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CancerInSilico.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CancerInSilico_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/CancerInSilico.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '2.24.0'
* 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-3.19-bioc/meat/CancerInSilico.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'simulatePathwayActivity.Rd':
  'sampleSize'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.19-bioc/R/library/CancerInSilico/libs/x64/CancerInSilico.dll':
  Found '_exit', possibly from '_exit' (C)
  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 ... 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, 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/CancerInSilico.Rcheck/00check.log'
for details.

Installation output

CancerInSilico.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL CancerInSilico
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'CancerInSilico' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/hashtable.h:37,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unordered_map.h:33,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/unordered_map:41,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RunModel.cpp:1:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/hashtable.h:37,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unordered_map.h:33,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/unordered_map:41,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from CellModels/../OffLatticeModel/../Core/CellBasedModel.h:6,
                 from CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:6:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/hashtable.h:37,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unordered_map.h:33,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/unordered_map:41,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from OffLatticeModel/OffLatticeCell.cpp:2:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/hashtable.h:37,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unordered_map.h:33,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/unordered_map:41,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from OffLatticeModel/../Core/CellBasedModel.h:6,
                 from OffLatticeModel/OffLatticeCellBasedModel.h:6:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/range/size.hpp:21,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/random.hpp:70,
                 from Core/Random.cpp:3:
F:/biocbuild/bbs-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/hashtable.h:37,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unordered_map.h:33,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/unordered_map:41,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Tests/Core/../catch.h:11,
                 from Tests/Core/test-Point.cpp:1:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/hashtable.h:37,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/unordered_map.h:33,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/unordered_map:41,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Tests/Core/test-SquareLattice.cpp:1:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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
Warning in fun(libname, pkgname) :
  Package 'CancerInSilico' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'CancerInSilico' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (CancerInSilico)

Tests output

CancerInSilico.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

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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
Warning message:
In fun(libname, pkgname) :
  Package 'CancerInSilico' is deprecated and will be removed from
  Bioconductor version 3.20
> 
> 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 
   2.09    0.26    2.40

Example timings

CancerInSilico.Rcheck/CancerInSilico-Ex.timings

name	user	system	elapsed
cellSummary-methods	0.10	0.00	0.09
checkDataSet	0.00	0.00	0.01
getAxisAngle-methods	0.09	0.00	0.09
getAxisLength-methods	0.11	0.00	0.11
getCellDistance-methods	0.08	0.00	0.08
getCellPhase-methods	0.09	0.01	0.11
getCellType-methods	0.09	0.02	0.11
getCoordinates-methods	0.11	0.00	0.11
getCycleLength-methods	0.08	0.02	0.09
getDensity-methods	0.08	0.01	0.10
getLocalDensity-methods	0.14	0.02	0.17
getNumberOfCells-methods	0.08	0.00	0.08
getRadius-methods	0.08	0.00	0.07
getTrialAcceptRate-methods	0.09	0.00	0.10
inSilicoCellModel	0.05	0.00	0.08
plotCells-methods	0.09	0.00	0.09
run-methods	0.31	0.00	0.31