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CHECK report for CancerInSilico on nebbiolo1

This page was generated on 2020-09-19 10:17:37 -0400 (Sat, 19 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CancerInSilico PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 221/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerInSilico 2.9.0
Thomas D. Sherman
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/CancerInSilico
Branch: master
Last Commit: e1cdc81
Last Changed Date: 2020-04-27 15:02:23 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerInSilico
Version: 2.9.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CancerInSilico.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CancerInSilico_2.9.0.tar.gz
StartedAt: 2020-09-18 21:30:46 -0400 (Fri, 18 Sep 2020)
EndedAt: 2020-09-18 21:31:21 -0400 (Fri, 18 Sep 2020)
EllapsedTime: 35.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CancerInSilico.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CancerInSilico.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CancerInSilico_2.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CancerInSilico.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘2.9.0’
* 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 ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   6.8Mb
* 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 ‘/home/biocbuild/bbs-3.12-bioc/R/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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/CancerInSilico.Rcheck/00check.log’
for details.



Installation output

CancerInSilico.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CancerInSilico
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CancerInSilico’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RunModel.cpp -o RunModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c OffLatticeModel/OffLatticeCellBasedModel.cpp -o OffLatticeModel/OffLatticeCellBasedModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Core/Cell.cpp -o Core/Cell.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Core/CellType.cpp -o Core/CellType.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Core/Drug.cpp -o Core/Drug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Core/Random.cpp -o Core/Random.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/fpclassify.hpp:19,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:22,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/random.hpp:69,
                 from Core/Random.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.12-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>::************
      |                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Tests/Core/test-CellType.cpp -o Tests/Core/test-CellType.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Tests/Core/test-Drug.cpp -o Tests/Core/test-Drug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Tests/Core/test-Point.cpp -o Tests/Core/test-Point.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Tests/Core/test-Random.cpp -o Tests/Core/test-Random.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Tests/Core/test-SquareLattice.cpp -o Tests/Core/test-SquareLattice.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/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 -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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)

Tests output

CancerInSilico.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  3.231   0.188   3.411 

Example timings

CancerInSilico.Rcheck/CancerInSilico-Ex.timings

nameusersystemelapsed
cellSummary-methods0.0900.0120.102
checkDataSet0.0020.0000.002
getAxisAngle-methods0.0880.0040.091
getAxisLength-methods0.0820.0080.090
getCellDistance-methods0.0800.0080.088
getCellPhase-methods0.0830.0040.087
getCellType-methods0.0830.0080.091
getCoordinates-methods0.0880.0000.088
getCycleLength-methods0.0810.0120.093
getDensity-methods0.0870.0000.087
getLocalDensity-methods0.0940.0040.098
getNumberOfCells-methods0.0820.0040.086
getRadius-methods0.0820.0040.086
getTrialAcceptRate-methods0.0850.0040.089
inSilicoCellModel0.0330.0000.035
plotCells-methods0.1420.0120.154
run-methods0.3910.0160.407