Thomas D. Sherman
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CancerInSilico |
| Branch: master |
| Last Commit: c5b1f65 |
| Last Changed Date: 2019-10-29 13:42:08 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:46:20 -0500 (Thu, 16 Jan 2020).
| Package 220/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CancerInSilico 2.7.0 Thomas D. Sherman
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CancerInSilico |
| Version: 2.7.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerInSilico.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerInSilico_2.7.0.tar.gz |
| StartedAt: 2020-01-16 02:28:40 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:29:38 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 57.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CancerInSilico.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerInSilico.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerInSilico_2.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CancerInSilico.Rcheck’ * using R Under development (unstable) (2019-12-14 r77572) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CancerInSilico/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CancerInSilico’ version ‘2.7.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CancerInSilico’ can be installed ... OK * 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 is not available File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/CancerInSilico/libs/CancerInSilico.so’: Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking 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 NOTE See ‘/Users/biocbuild/bbs-3.11-bioc/meat/CancerInSilico.Rcheck/00check.log’ for details.
CancerInSilico.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CancerInSilico
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CancerInSilico’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RunModel.cpp -o RunModel.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c OffLatticeModel/OffLatticeCellBasedModel.cpp -o OffLatticeModel/OffLatticeCellBasedModel.o
In file included from OffLatticeModel/OffLatticeCellBasedModel.cpp:1:
In file included from OffLatticeModel/OffLatticeCellBasedModel.h:6:
In file included from OffLatticeModel/../Core/CellBasedModel.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'OffLatticeCell' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<OffLatticeCell>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang8/bin/../include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<OffLatticeCell> >::__destroy<OffLatticeCell>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/local/clang8/bin/../include/c++/v1/vector:427:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<OffLatticeCell> >::destroy<OffLatticeCell>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/local/clang8/bin/../include/c++/v1/vector:370:29: note: in instantiation of member function 'std::__1::__vector_base<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/local/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::clear' requested here
clear();
^
/usr/local/clang8/bin/../include/c++/v1/vector:496:5: note: in instantiation of member function 'std::__1::__vector_base<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::~__vector_base' requested here
vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
^
OffLatticeModel/OffLatticeCellBasedModel.cpp:26:33: note: in instantiation of member function 'std::__1::vector<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::vector' requested here
std::vector<OffLatticeCell> defaultCells;
^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Core/Cell.cpp -o Core/Cell.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Core/CellType.cpp -o Core/CellType.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Core/Drug.cpp -o Core/Drug.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Core/Random.cpp -o Core/Random.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c test-runner.cpp -o test-runner.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-CellType.cpp -o Tests/Core/test-CellType.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-Drug.cpp -o Tests/Core/test-Drug.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-Point.cpp -o Tests/Core/test-Point.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-Random.cpp -o Tests/Core/test-Random.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-SquareLattice.cpp -o Tests/Core/test-SquareLattice.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CancerInSilico.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-CancerInSilico/00new/CancerInSilico/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CancerInSilico)
CancerInSilico.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 64 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
4.259 0.400 4.605
CancerInSilico.Rcheck/CancerInSilico-Ex.timings
| name | user | system | elapsed | |
| cellSummary-methods | 0.127 | 0.021 | 0.149 | |
| checkDataSet | 0.003 | 0.002 | 0.006 | |
| getAxisAngle-methods | 0.103 | 0.009 | 0.113 | |
| getAxisLength-methods | 0.090 | 0.013 | 0.104 | |
| getCellDistance-methods | 0.098 | 0.016 | 0.114 | |
| getCellPhase-methods | 0.103 | 0.015 | 0.119 | |
| getCellType-methods | 0.112 | 0.015 | 0.128 | |
| getCoordinates-methods | 0.108 | 0.015 | 0.122 | |
| getCycleLength-methods | 0.109 | 0.018 | 0.127 | |
| getDensity-methods | 0.103 | 0.016 | 0.120 | |
| getLocalDensity-methods | 0.117 | 0.011 | 0.129 | |
| getNumberOfCells-methods | 0.116 | 0.021 | 0.136 | |
| getRadius-methods | 0.101 | 0.014 | 0.115 | |
| getTrialAcceptRate-methods | 0.106 | 0.016 | 0.123 | |
| inSilicoCellModel | 0.105 | 0.002 | 0.107 | |
| plotCells-methods | 0.106 | 0.018 | 0.124 | |
| run-methods | 0.422 | 0.019 | 0.441 | |