##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf ternarynet.buildbin-libdir ternarynet.Rcheck && mkdir ternarynet.buildbin-libdir ternarynet.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ternarynet.buildbin-libdir ternarynet_1.17.0.tar.gz >ternarynet.Rcheck\00install.out 2>&1 && cp ternarynet.Rcheck\00install.out ternarynet-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ternarynet.buildbin-libdir --install="check:ternarynet-install.out" --force-multiarch --no-vignettes --timings ternarynet_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/ternarynet.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ternarynet/DESCRIPTION' ... OK
* this is package 'ternarynet' version '1.17.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/i386/ternarynet.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
attractorSummary 6.49 0 6.52
** running examples for arch 'x64' ... 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: 5 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/ternarynet.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ternarynet' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:311:53: 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;
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:
D:/biocbld/BBS-3˜1.4-B/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;
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ternarynet.dll tmp.def tnetfit.o tnetfuncs.o tnetpost.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'ternarynet' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:311:53: 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;
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:
D:/biocbld/BBS-3˜1.4-B/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;
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ternarynet.dll tmp.def tnetfit.o tnetfuncs.o tnetpost.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ternarynet' as ternarynet_1.17.0.zip
* DONE (ternarynet)
