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CHECK report for ternarynet on merida2

This page was generated on 2018-10-17 08:50:17 -0400 (Wed, 17 Oct 2018).

Package 1474/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ternarynet 1.24.0
Matthew N. McCall
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ternarynet
Branch: RELEASE_3_7
Last Commit: 7834600
Last Changed Date: 2018-04-30 10:35:23 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ternarynet
Version: 1.24.0
Command: /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_1.24.0.tar.gz
StartedAt: 2018-10-17 00:23:32 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:25:09 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 96.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ternarynet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ternarynet.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.24.0’
* 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
plotPost          6.878  0.009   6.973
attractorSummary  6.811  0.010   6.882
ternaryPost-class 6.792  0.008   6.875
plotTraces        6.676  0.008   6.754
predictAttractor  6.653  0.008   6.736
tnetfit           6.641  0.007   6.713
tnetpost          6.606  0.007   6.685
plotFit           6.583  0.011   6.654
graphPosterior    6.476  0.008   6.538
ternaryFit-class  6.447  0.008   6.531
* 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-3.7-bioc/meat/ternarynet.Rcheck/00check.log’
for details.



Installation output

ternarynet.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ternarynet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ternarynet’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -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++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
    ^
tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable]
int tableWidth = powi(nOutcomes,maxDegree);
    ^
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
        int m1, m2, i;
                    ^
tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable]
        int ipause; 
            ^
4 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tnetpost.cc -o tnetpost.o
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
    double newScore, oldScore, minScore, finalScore;
                                         ^
tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
        ^
tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
            ^
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:25:9: warning: unused variable 'ipause' [-Wunused-variable]
    int ipause;
        ^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
    int m0fit;
        ^
8 warnings generated.
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 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/3.5/Resources/library/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
* DONE (ternarynet)

Tests output


Example timings

ternarynet.Rcheck/ternarynet-Ex.timings

nameusersystemelapsed
attractorSummary6.8110.0106.882
graphPosterior6.4760.0086.538
plotFit6.5830.0116.654
plotPost6.8780.0096.973
plotTraces6.6760.0086.754
predictAttractor6.6530.0086.736
simulateSteadyState0.0030.0000.004
ternaryFit-class6.4470.0086.531
ternaryFitParameters-class0.0060.0000.006
ternaryPost-class6.7920.0086.875
tnetfit6.6410.0076.713
tnetpost6.6060.0076.685