ternarynet 1.30.0
Matthew N. McCall
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ternarynet |
| Branch: RELEASE_3_10 |
| Last Commit: 3617d67 |
| Last Changed Date: 2019-10-29 13:08:27 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ternarynet
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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:207:18: warning: ‘sigma0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
convergence = (muci-muci_old)/sigma0;
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include/Rmath.h:212:15: 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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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)