Thomas D. Sherman
| 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) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:30 -0400 (Thu, 12 Apr 2018).
| Package 176/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CancerInSilico 1.4.0 Thomas D. Sherman
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: CancerInSilico |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CancerInSilico_1.4.0.tar.gz |
| StartedAt: 2018-04-11 21:59:35 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:00:50 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 75.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CancerInSilico.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CancerInSilico_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CancerInSilico.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
libs 7.0Mb
* 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-3.6-bioc/meat/CancerInSilico.Rcheck/00check.log’
for details.
CancerInSilico.Rcheck/00install.out
* installing *source* package ‘CancerInSilico’ ... ** libs g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Cell.cpp -o Cell.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c CellModel.cpp -o CellModel.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c CellPopulation.cpp -o CellPopulation.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Parameters.cpp -o Parameters.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c Simulation.cpp -o Simulation.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/testthat/include" -I"/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/lib -lR installing to /home/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)
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-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 = 5
time = 1.00
size = 6
══ testthat results ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
1.240 0.024 1.257
CancerInSilico.Rcheck/CancerInSilico-Ex.timings
| name | user | system | elapsed | |
| getCycleLengths | 0.072 | 0.000 | 0.073 | |
| getDensity | 0.100 | 0.000 | 0.098 | |
| getNumberOfCells | 0.068 | 0.000 | 0.071 | |
| getParameters | 0.068 | 0.000 | 0.069 | |
| plotCells | 1.040 | 0.000 | 1.038 | |
| runCancerSim | 0.412 | 0.000 | 0.414 | |
| show-CellModel-method | 0.072 | 0.000 | 0.070 | |