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BioC 2.14: CHECK report for ternarynet on zin2

This page was generated on 2014-10-08 08:49:25 -0700 (Wed, 08 Oct 2014).

Package 778/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ternarynet 1.8.0
Matthew N. McCall
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ternarynet
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ternarynet
Version: 1.8.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ternarynet_1.8.0.tar.gz
StartedAt: 2014-10-08 03:14:34 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 03:15:34 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ternarynet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ternarynet_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ternarynet.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* this is package ‘ternarynet’ version ‘1.8.0’
* 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/ternarynet.Rcheck/00check.log’
for details.

ternarynet.Rcheck/00install.out:

* installing *source* package ‘ternarynet’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-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]
tnetfit.cc:24:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
tnetfit.cc:24:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable]
tnetfit.cc:311:53: warning: ‘newScore’ may be used uninitialized in this function [-Wuninitialized]
tnetfit.cc:207:42: warning: ‘muci_old’ may be used uninitialized in this function [-Wuninitialized]
tnetfit.cc:202:44: warning: ‘sigmaci’ may be used uninitialized in this function [-Wuninitialized]
tnetfit.cc:207:42: warning: ‘sigma0’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.14-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:469:5: warning: unused variable ‘tableWidth’ [-Wunused-variable]
tnetfuncs.cc:477:5: warning: unused variable ‘ipause’ [-Wunused-variable]
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:567:6: warning: unused variable ‘ipause’ [-Wunused-variable]
tnetfuncs.cc:571:16: warning: unused variable ‘i’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.14-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]
tnetpost.cc:27:9: warning: unused variable ‘m0fit’ [-Wunused-variable]
tnetpost.cc:28:32: warning: variable ‘minScore’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:28:42: warning: unused variable ‘finalScore’ [-Wunused-variable]
tnetpost.cc:30:9: warning: unused variable ‘l0’ [-Wunused-variable]
tnetpost.cc:30:13: warning: unused variable ‘stage_count’ [-Wunused-variable]
tnetpost.cc:30:26: warning: unused variable ‘tempi’ [-Wunused-variable]
tnetpost.cc:30:33: warning: unused variable ‘jtrans’ [-Wunused-variable]
tnetpost.cc:30:41: warning: unused variable ‘nTransition’ [-Wunused-variable]
tnetpost.cc:36:21: warning: variable ‘xSeedFit’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:38:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:38:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:38:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:39:9: warning: variable ‘maxStage’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:39:19: warning: variable ‘maxTransition’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:12: warning: variable ‘epsilon’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:21: warning: variable ‘chi0’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:27: warning: variable ‘delta’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:34: warning: variable ‘rho’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:41:9: warning: variable ‘Rf_beta’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:44:9: warning: variable ‘ne’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:150:10: warning: variable ‘minDump’ set but not used [-Wunused-but-set-variable]
g++ -shared -L/usr/local/lib -o ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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
attractorSummary3.9280.0003.930
graphPosterior3.9360.0003.949
plotFit3.8800.0003.885
plotPost3.9450.0043.953
plotTraces4.0080.0004.015
predictAttractor4.080.004.09
simulateSteadyState0.0000.0040.004
ternaryFit-class4.0040.0004.012
ternaryFitParameters-class0.0040.0000.003
ternaryPost-class4.0250.0004.030
tnetfit4.1880.0044.214
tnetpost3.9760.0003.983