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BioC 3.5: CHECK report for CancerInSilico on tokay2

This page was generated on 2017-10-18 14:26:32 -0400 (Wed, 18 Oct 2017).

Package 168/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerInSilico 1.2.0
Thomas D. Sherman , Elana J. Fertig
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/CancerInSilico
Branch: RELEASE_3_5
Last Commit: 0f5f857
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerInSilico
Version: 1.2.0
Command: rm -rf CancerInSilico.buildbin-libdir CancerInSilico.Rcheck && mkdir CancerInSilico.buildbin-libdir CancerInSilico.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CancerInSilico.buildbin-libdir CancerInSilico_1.2.0.tar.gz >CancerInSilico.Rcheck\00install.out 2>&1 && cp CancerInSilico.Rcheck\00install.out CancerInSilico-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CancerInSilico.buildbin-libdir --install="check:CancerInSilico-install.out" --force-multiarch --no-vignettes --timings CancerInSilico_1.2.0.tar.gz
StartedAt: 2017-10-17 22:29:38 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:32:23 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 166.0 seconds
RetCode: 0
Status:  OK  
CheckDir: CancerInSilico.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CancerInSilico.buildbin-libdir CancerInSilico.Rcheck && mkdir CancerInSilico.buildbin-libdir CancerInSilico.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CancerInSilico.buildbin-libdir CancerInSilico_1.2.0.tar.gz >CancerInSilico.Rcheck\00install.out 2>&1 && cp CancerInSilico.Rcheck\00install.out CancerInSilico-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CancerInSilico.buildbin-libdir --install="check:CancerInSilico-install.out" --force-multiarch --no-vignettes --timings CancerInSilico_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CancerInSilico.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CancerInSilico.buildbin-libdir/CancerInSilico/libs/i386/CancerInSilico.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/CancerInSilico.Rcheck/00check.log'
for details.


CancerInSilico.Rcheck/00install.out:


install for i386

* installing *source* package 'CancerInSilico' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Cell.cpp -o Cell.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellModel.cpp -o CellModel.o
CellModel.cpp: In function 'Rcpp::List CellModel(int, int, double, double, double, double, double, double, int, int, Rcpp::NumericVector, bool, double, double)':
CellModel.cpp:27:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (unsigned int i = 0; i < growthRates.length(); ++i) {
                                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellPopulation.cpp -o CellPopulation.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Parameters.cpp -o Parameters.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Simulation.cpp -o Simulation.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-Cell.cpp -o test-Cell.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-CellPopulation.cpp -o test-CellPopulation.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-Parameters.cpp -o test-Parameters.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-SpatialHash.cpp -o test-SpatialHash.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CancerInSilico.dll tmp.def 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 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CancerInSilico.buildbin-libdir/CancerInSilico/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'CancerInSilico' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Cell.cpp -o Cell.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellModel.cpp -o CellModel.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellPopulation.cpp -o CellPopulation.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Parameters.cpp -o Parameters.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Simulation.cpp -o Simulation.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-Cell.cpp -o test-Cell.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-CellPopulation.cpp -o test-CellPopulation.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-Parameters.cpp -o test-Parameters.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-SpatialHash.cpp -o test-SpatialHash.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/testthat/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CancerInSilico.dll tmp.def 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 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CancerInSilico.buildbin-libdir/CancerInSilico/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CancerInSilico' as CancerInSilico_1.2.0.zip
* DONE (CancerInSilico)

CancerInSilico.Rcheck/examples_i386/CancerInSilico-Ex.timings:

nameusersystemelapsed
getCycleLengths0.370.000.37
getDensity0.330.000.33
getNumberOfCells0.290.000.30
getParameters0.320.000.31
plotCells3.060.003.07
runCancerSim1.630.011.64
show-CellModel-method0.280.000.28

CancerInSilico.Rcheck/examples_x64/CancerInSilico-Ex.timings:

nameusersystemelapsed
getCycleLengths0.170.000.17
getDensity0.190.000.19
getNumberOfCells0.100.000.11
getParameters0.110.000.11
plotCells1.50.01.5
runCancerSim0.710.000.70
show-CellModel-method0.110.000.11