CancerInSilico 1.0.0
Thomas D. Sherman , Elana J. Fertig
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/CancerInSilico | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CancerInSilico_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CancerInSilico.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.0’
* 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 ... 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
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/CancerInSilico.Rcheck/00check.log’
for details.
* installing *source* package ‘CancerInSilico’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c Cell.cpp -o Cell.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c CellModel.cpp -o CellModel.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c CellPopulation.cpp -o CellPopulation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c Parameters.cpp -o Parameters.o
In file included from Parameters.cpp:7:
./Parameters.h:14:9: warning: private field 'm_initial_num_cells' is not used [-Wunused-private-field]
int m_initial_num_cells;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c Simulation.cpp -o Simulation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c test-Cell.cpp -o test-Cell.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c test-CellPopulation.cpp -o test-CellPopulation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c test-Parameters.cpp -o test-Parameters.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c test-SpatialHash.cpp -o test-SpatialHash.o
test-SpatialHash.cpp:224:23: warning: equality comparison result unused [-Wunused-comparison]
full_iter == hash.end();
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
test-SpatialHash.cpp:224:23: note: use '=' to turn this equality comparison into an assignment
full_iter == hash.end();
^˜
=
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/testthat/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c test-runner.cpp -o test-runner.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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)