BioC 3.5: CHECK report for CancerInSilico on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CancerInSilico_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CancerInSilico.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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 ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/CancerInSilico.Rcheck/00check.log’
for details.

* installing *source* package ‘CancerInSilico’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Cell.cpp -o Cell.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c CellModel.cpp -o CellModel.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c CellPopulation.cpp -o CellPopulation.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Parameters.cpp -o Parameters.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Simulation.cpp -o Simulation.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c test-Cell.cpp -o test-Cell.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c test-CellPopulation.cpp -o test-CellPopulation.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c test-Parameters.cpp -o test-Parameters.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c test-SpatialHash.cpp -o test-SpatialHash.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/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 -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)

name	user	system	elapsed
getCycleLengths	0.104	0.000	0.106
getDensity	0.144	0.000	0.145
getNumberOfCells	0.080	0.000	0.081
getParameters	0.080	0.000	0.078
plotCells	1.056	0.000	1.058
runCancerSim	0.476	0.000	0.477
show-CellModel-method	0.072	0.004	0.074

BioC 3.5: CHECK report for CancerInSilico on malbec2

Summary

Command output