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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ternarynet_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ternarynet.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* this is package ‘ternarynet’ version ‘1.20.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
‘/home/biocbuild/bbs-3.5-bioc/meat/ternarynet.Rcheck/00check.log’
for details.
* installing *source* package ‘ternarynet’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tnetfit.cc -o tnetfit.o
tnetfit.cc: In function ‘SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
tnetfit.cc:24:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage, maxStage, maxTransition;
^
tnetfit.cc:24:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage, maxStage, maxTransition;
^
tnetfit.cc:24:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage, maxStage, maxTransition;
^
tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable]
int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
^
tnetfit.cc:311:19: warning: ‘newScore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
^
tnetfit.cc:207:25: warning: ‘muci_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
convergence = (muci-muci_old)/sigma0;
^
tnetfit.cc:202:36: warning: ‘sigmaci’ may be used uninitialized in this function [-Wmaybe-uninitialized]
sigmaci = rho*sigmaRaw + (1-rho)*sigmaci;
^
tnetfit.cc:207:42: warning: ‘sigma0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
convergence = (muci-muci_old)/sigma0;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc: In function ‘double AttractorDistanceForced(int, int, int, int, double, int*, int*, int*, const double*, const int*)’:
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: In function ‘double initialTemp(double, int, int, int, int, int, double, double, double, int, const double*, int*, int*, int*, const double*, const int*)’:
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;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tnetpost.cc -o tnetpost.o
tnetpost.cc: In function ‘SEXPREC* tnetpost(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
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:28:32: warning: variable ‘minScore’ set but not used [-Wunused-but-set-variable]
double newScore, oldScore, minScore, finalScore;
^
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:30:26: warning: unused variable ‘tempi’ [-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:30:41: warning: unused variable ‘nTransition’ [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
tnetpost.cc:36:21: warning: variable ‘xSeedFit’ set but not used [-Wunused-but-set-variable]
int m0, mdelta, xSeedFit;
^
tnetpost.cc:38:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:38:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:38:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:39:9: warning: variable ‘maxStage’ set but not used [-Wunused-but-set-variable]
int maxStage, maxTransition;
^
tnetpost.cc:39:19: warning: variable ‘maxTransition’ set but not used [-Wunused-but-set-variable]
int maxStage, maxTransition;
^
tnetpost.cc:40:12: warning: variable ‘epsilon’ set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
tnetpost.cc:40:21: warning: variable ‘chi0’ set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
tnetpost.cc:40:27: warning: variable ‘delta’ set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
tnetpost.cc:40:34: warning: variable ‘rho’ set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
In file included from tnetpost.cc:14:0:
/home/biocbuild/bbs-3.5-bioc/R/include/Rmath.h:228:15: warning: variable ‘Rf_beta’ set but not used [-Wunused-but-set-variable]
#define beta Rf_beta
^
tnetpost.cc:41:9: note: in expansion of macro ‘beta’
int beta;
^
tnetpost.cc:44:9: warning: variable ‘ne’ set but not used [-Wunused-but-set-variable]
int ne, maxDegree;
^
tnetpost.cc:150:10: warning: variable ‘minDump’ set but not used [-Wunused-but-set-variable]
bool minDump = true;
^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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)
