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INSTALL report for ternarynet on tokay1

This page was generated on 2019-04-13 11:22:02 -0400 (Sat, 13 Apr 2019).

Package 1553/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ternarynet 1.26.0
Matthew N. McCall
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/ternarynet
Branch: RELEASE_3_8
Last Commit: 846cf9e
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ternarynet
Version: 1.26.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ternarynet_1.26.0.tar.gz && rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ternarynet.buildbin-libdir ternarynet_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ternarynet_1.26.0.zip && rm ternarynet_1.26.0.tar.gz ternarynet_1.26.0.zip
StartedAt: 2019-04-12 18:56:07 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 18:56:47 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 40.4 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ternarynet_1.26.0.tar.gz && rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ternarynet.buildbin-libdir ternarynet_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ternarynet_1.26.0.zip && rm ternarynet_1.26.0.tar.gz ternarynet_1.26.0.zip
###
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100 25928  100 25928    0     0   653k      0 --:--:-- --:--:-- --:--:--  723k

install for i386

* installing *source* package 'ternarynet' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/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;
          ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ternarynet.dll tmp.def tnetfit.o tnetfuncs.o tnetpost.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ternarynet'
    finding HTML links ... done
    attractorSummary                        html  
    graphPosterior                          html  
    plotFit                                 html  
    plotPost                                html  
    plotTraces                              html  
    predictAttractor                        html  
    simulateSteadyState                     html  
    ternaryFit-class                        html  
    ternaryFitParameters-class              html  
    ternaryPost-class                       html  
    tnetfit                                 html  
    tnetpost                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ternarynet' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/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;
          ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ternarynet.dll tmp.def tnetfit.o tnetfuncs.o tnetpost.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ternarynet' as ternarynet_1.26.0.zip
* DONE (ternarynet)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ternarynet' successfully unpacked and MD5 sums checked
In R CMD INSTALL