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CHECK report for CancerInSilico on malbec1

This page was generated on 2021-02-22 12:28:50 -0500 (Mon, 22 Feb 2021).

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 229/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerInSilico 2.10.0
Thomas D. Sherman
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/CancerInSilico
Branch: RELEASE_3_12
Last Commit: 3419b7b
Last Changed Date: 2020-10-27 11:18:15 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CancerInSilico
Version: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2021-02-22 00:12:09 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 00:12:41 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 31.7 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_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CancerInSilico.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.10.0’
* 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 12.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   9.7Mb
* 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
###
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* 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
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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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)

══ Skipped tests ═══════════════════════════════════════════════════════════════
● empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
  2.464   0.080   2.544 

Example timings

CancerInSilico.Rcheck/CancerInSilico-Ex.timings

nameusersystemelapsed
cellSummary-methods0.1360.0000.138
checkDataSet0.000.000.01
getAxisAngle-methods0.1080.0040.114
getAxisLength-methods0.1040.0200.121
getCellDistance-methods0.1200.0000.118
getCellPhase-methods0.1120.0040.118
getCellType-methods0.1120.0040.114
getCoordinates-methods0.1120.0040.115
getCycleLength-methods0.1160.0040.120
getDensity-methods0.1120.0040.113
getLocalDensity-methods0.1240.0040.128
getNumberOfCells-methods0.1120.0040.114
getRadius-methods0.1120.0040.116
getTrialAcceptRate-methods0.1120.0000.112
inSilicoCellModel0.0400.0040.045
plotCells-methods0.1640.0000.167
run-methods0.5040.0000.508