Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S [T] U  V  W  X  Y  Z 

BioC 3.2: CHECK report for ternarynet on linux1.bioconductor.org

This page was generated on 2015-10-27 17:25:21 -0400 (Tue, 27 Oct 2015).

Package 1049/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ternarynet 1.14.0
Matthew N. McCall
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ternarynet
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ternarynet
Version: 1.14.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ternarynet_1.14.0.tar.gz
StartedAt: 2015-10-27 08:42:36 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 08:43:22 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 46.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ternarynet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ternarynet_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ternarynet.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.14.0’
* 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 ... [3s/3s] 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 ... OK
* 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 ... OK
* 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 ... [28s/28s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ternarynet.Rcheck/00check.log’
for details.


ternarynet.Rcheck/00install.out:

* installing *source* package ‘ternarynet’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-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:311:53: 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; 
                                          ^
g++ -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-bioc/R/include/Rmath.h:217:15: 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-3.2-bioc/R/lib -L/usr/local/lib -o ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)

ternarynet.Rcheck/ternarynet-Ex.timings:

nameusersystemelapsed
attractorSummary3.7530.0003.755
graphPosterior2.6750.0002.676
plotFit2.7960.0042.803
plotPost3.1580.0003.158
plotTraces2.7680.0002.775
predictAttractor2.4700.0002.472
simulateSteadyState0.0010.0000.002
ternaryFit-class2.2060.0002.206
ternaryFitParameters-class0.0020.0000.002
ternaryPost-class2.1800.0002.179
tnetfit2.9040.0002.907
tnetpost2.3190.0002.320