Multiple platform build/check report for BioC 3.9 - CHECK report for ternarynet on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ternarynet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ternarynet_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ternarynet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* this is package ‘ternarynet’ version ‘1.28.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ternarynet’ 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 ... 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘ternarynet’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotFit: no visible global function definition for ‘plot’
plotPost: no visible global function definition for ‘plot’
plotTraces: no visible global function definition for ‘par’
plotTraces: no visible global function definition for ‘plot’
ternaryFit: no visible global function definition for ‘new’
ternaryFitParameters: no visible global function definition for ‘new’
ternaryPost: no visible global function definition for ‘new’
tnetfit: no visible global function definition for ‘runif’
tnetpost: no visible global function definition for ‘runif’
backupStage<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
beta0<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
chi0<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
degreeObjMin<-,ternaryFit: no visible global function definition for
  ‘validObject’
degreeObjs<-,ternaryPost: no visible global function definition for
  ‘validObject’
delta<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
edgePenalty<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
epsilon<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
experimentNames<-,ternaryFit: no visible global function definition for
  ‘validObject’
experimentNames<-,ternaryPost: no visible global function definition
  for ‘validObject’
finalTemperature<-,ternaryFit: no visible global function definition
  for ‘validObject’
geneNames<-,ternaryFit: no visible global function definition for
  ‘validObject’
geneNames<-,ternaryPost: no visible global function definition for
  ‘validObject’
graphObjMin<-,ternaryFit: no visible global function definition for
  ‘validObject’
graphObjs<-,ternaryPost: no visible global function definition for
  ‘validObject’
inputParams<-,ternaryFit: no visible global function definition for
  ‘validObject’
inputParams<-,ternaryPost: no visible global function definition for
  ‘validObject’
m0<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
maxDegree<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
maxStage<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
maxTransition<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
minScore<-,ternaryFit: no visible global function definition for
  ‘validObject’
ne<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
neighborDegree<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
newScore<-,ternaryFit: no visible global function definition for
  ‘validObject’
pAddParent<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
pExchangeParent<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
pNeighborhood<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
perturbationObj<-,ternaryFit: no visible global function definition for
  ‘validObject’
perturbationObj<-,ternaryPost: no visible global function definition
  for ‘validObject’
perturbationType<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
rho<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
scoreType<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
scores<-,ternaryPost: no visible global function definition for
  ‘validObject’
stageCount<-,ternaryFit: no visible global function definition for
  ‘validObject’
steadyStateObj<-,ternaryFit: no visible global function definition for
  ‘validObject’
steadyStateObj<-,ternaryPost: no visible global function definition for
  ‘validObject’
tableObjMin<-,ternaryFit: no visible global function definition for
  ‘validObject’
tableObjs<-,ternaryPost: no visible global function definition for
  ‘validObject’
traces<-,ternaryFit: no visible global function definition for
  ‘validObject’
xSeed<-,ternaryFit: no visible global function definition for
  ‘validObject’
Undefined global functions or variables:
  new par plot runif validObject
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
predictAttractor  7.578  0.009   7.586
plotPost          7.562  0.010   7.571
plotFit           7.369  0.016   7.384
tnetpost          7.235  0.010   7.246
attractorSummary  7.159  0.011   7.171
ternaryFit-class  7.117  0.009   7.125
plotTraces        7.010  0.010   7.020
graphPosterior    6.821  0.017   6.838
tnetfit           6.562  0.009   6.570
ternaryPost-class 6.023  0.007   6.030
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ternarynet.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ternarynet
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c tnetfit.cc -o tnetfit.o
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
    int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
                                      ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable]
int tableWidth = powi(nOutcomes,maxDegree);
    ^
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
    ^
tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable]
        int ipause; 
            ^
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
        int m1, m2, i;
                    ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c tnetpost.cc -o tnetpost.o
tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                                ^
tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                         ^
tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                                        ^
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
    double newScore, oldScore, minScore, finalScore;
                                         ^
tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
            ^
tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
        ^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
    int m0fit;
        ^
tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable]
    int ipause;
        ^
8 warnings generated.
clang++ -std=gnu++11 -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 ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-ternarynet/00new/ternarynet/libs
** R
** 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 (ternarynet)

CHECK report for ternarynet on celaya2

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
attractorSummary	7.159	0.011	7.171
graphPosterior	6.821	0.017	6.838
plotFit	7.369	0.016	7.384
plotPost	7.562	0.010	7.571
plotTraces	7.01	0.01	7.02
predictAttractor	7.578	0.009	7.586
simulateSteadyState	0.003	0.000	0.003
ternaryFit-class	7.117	0.009	7.125
ternaryFitParameters-class	0.002	0.001	0.004
ternaryPost-class	6.023	0.007	6.030
tnetfit	6.562	0.009	6.570
tnetpost	7.235	0.010	7.246