ternarynet 1.19.0
Matthew N. McCall
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ternarynet | | Last Changed Rev: 122712 / Revision: 129046 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / 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 ternarynet_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ternarynet.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* this is package ‘ternarynet’ version ‘1.19.0’
* 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 loading without being on the library search path ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotPost 6.651 0.014 8.887
attractorSummary 5.954 0.015 6.789
plotFit 5.744 0.012 8.107
graphPosterior 5.698 0.012 8.338
tnetfit 5.661 0.010 6.442
predictAttractor 5.626 0.011 6.374
tnetpost 5.605 0.010 6.314
ternaryPost-class 5.594 0.011 6.356
ternaryFit-class 5.593 0.010 5.858
plotTraces 5.527 0.011 7.797
* 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
‘/Users/biocbuild/bbs-3.5-bioc/meat/ternarynet.Rcheck/00check.log’
for details.
* installing *source* package ‘ternarynet’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tnetpost.cc -o tnetpost.o
tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
int m0fit;
^
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: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:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
double newScore, oldScore, minScore, finalScore;
^
tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
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 /Users/biocbuild/bbs-3.5-bioc/meat/ternarynet.Rcheck/ternarynet/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 (ternarynet)