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CHECK report for CancerInSilico on veracruz1

This page was generated on 2018-04-12 13:43:45 -0400 (Thu, 12 Apr 2018).

Package 176/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerInSilico 1.4.0
Thomas D. Sherman , Elana J. Fertig
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CancerInSilico
Branch: RELEASE_3_6
Last Commit: deafd0f
Last Changed Date: 2017-10-30 12:41:22 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerInSilico
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerInSilico_1.4.0.tar.gz
StartedAt: 2018-04-12 01:16:24 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:18:02 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 97.9 seconds
RetCode: 0
Status:  OK 
CheckDir: CancerInSilico.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerInSilico_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CancerInSilico.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 loading without being on the library search path ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/CancerInSilico.Rcheck/00check.log’
for details.

Installation output

CancerInSilico.Rcheck/00install.out

* installing *source* package ‘CancerInSilico’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Cell.cpp -o Cell.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c CellModel.cpp -o CellModel.o
In file included from CellModel.cpp:2:
In file included from ./Simulation.h:4:
In file included from ./CellPopulation.h:10:
In file included from ./SpatialHash.h:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c CellPopulation.cpp -o CellPopulation.o
In file included from CellPopulation.cpp:4:
In file included from ./CellPopulation.h:10:
In file included from ./SpatialHash.h:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Parameters.cpp -o Parameters.o
In file included from Parameters.cpp:7:
./Parameters.h:14:9: warning: private field 'm_initial_num_cells' is not used [-Wunused-private-field]
    int m_initial_num_cells;
        ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Simulation.cpp -o Simulation.o
In file included from Simulation.cpp:1:
In file included from ./Simulation.h:4:
In file included from ./CellPopulation.h:10:
In file included from ./SpatialHash.h:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-Cell.cpp -o test-Cell.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-CellPopulation.cpp -o test-CellPopulation.o
In file included from test-CellPopulation.cpp:4:
In file included from ./CellPopulation.h:10:
In file included from ./SpatialHash.h:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-Parameters.cpp -o test-Parameters.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-SpatialHash.cpp -o test-SpatialHash.o
In file included from test-SpatialHash.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from test-SpatialHash.cpp:8:
In file included from ./SpatialHash.h:12:
In file included from ./ExceptionHandling.h:22:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:138:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/exceptions.h:106:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
test-SpatialHash.cpp:224:23: warning: equality comparison result unused [-Wunused-comparison]
            full_iter == hash.end();
            ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
test-SpatialHash.cpp:224:23: note: use '=' to turn this equality comparison into an assignment
            full_iter == hash.end();
                      ^˜
                      =
3 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++ -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 Cell.o CellModel.o CellPopulation.o Parameters.o RcppExports.o Simulation.o test-Cell.o test-CellPopulation.o test-Parameters.o test-SpatialHash.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/CancerInSilico.Rcheck/CancerInSilico/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CancerInSilico)

Tests output

CancerInSilico.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 = 5
time = 1.00
size = 6
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.320   0.058   1.386

Example timings

CancerInSilico.Rcheck/CancerInSilico-Ex.timings

nameusersystemelapsed
getCycleLengths0.0680.0010.068
getDensity0.1060.0030.110
getNumberOfCells0.0640.0000.065
getParameters0.0660.0010.067
plotCells0.7960.0020.804
runCancerSim0.3840.0010.388
show-CellModel-method0.0690.0000.070