BioC 3.2: CHECK report for ternarynet on moscato1

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### Running command:
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###   rm -rf ternarynet.buildbin-libdir ternarynet.Rcheck && mkdir ternarynet.buildbin-libdir ternarynet.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ternarynet.buildbin-libdir ternarynet_1.14.0.tar.gz >ternarynet.Rcheck\00install.out 2>&1 && cp ternarynet.Rcheck\00install.out ternarynet-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ternarynet.buildbin-libdir --install="check:ternarynet-install.out" --force-multiarch --no-vignettes --timings ternarynet_1.14.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ternarynet.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.14.0'
* 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 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 ... OK
** 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 ... 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 ... 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-3.2-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/i386/ternarynet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/x64/ternarynet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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' ... [99s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
attractorSummary  11.60      0   11.60
graphPosterior    10.84      0   10.84
plotFit           10.58      0   10.60
predictAttractor  10.48      0   10.49
ternaryFit-class   9.75      0    9.75
ternaryPost-class  9.59      0    9.60
tnetpost           9.34      0    9.35
tnetfit            9.22      0    9.23
plotPost           8.89      0    8.89
plotTraces         7.79      0    7.78
** running examples for arch 'x64' ... [82s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
tnetpost          8.99      0    8.99
predictAttractor  8.71      0    8.70
plotFit           8.57      0    8.57
plotTraces        8.40      0    8.41
attractorSummary  8.29      0    8.29
plotPost          8.02      0    8.02
ternaryPost-class 7.89      0    7.89
ternaryFit-class  7.80      0    7.80
tnetfit           7.33      0    7.33
graphPosterior    7.03      0    7.03
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/ternarynet.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ternarynet' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/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]
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++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/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]
tnetfuncs.cc:435:5: 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:517:6: warning: unused variable 'ipause' [-Wunused-variable]
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/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]
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++ -m32 -shared -s -static-libgcc -o ternarynet.dll tmp.def tnetfit.o tnetfuncs.o tnetpost.o -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-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
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/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]
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++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/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]
tnetfuncs.cc:435:5: 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:517:6: warning: unused variable 'ipause' [-Wunused-variable]
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/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]
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++ -m64 -shared -s -static-libgcc -o ternarynet.dll tmp.def tnetfit.o tnetfuncs.o tnetpost.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ternarynet' as ternarynet_1.14.0.zip
* DONE (ternarynet)

name	user	system	elapsed
attractorSummary	11.6	0.0	11.6
graphPosterior	10.84	0.00	10.84
plotFit	10.58	0.00	10.60
plotPost	8.89	0.00	8.89
plotTraces	7.79	0.00	7.78
predictAttractor	10.48	0.00	10.49
simulateSteadyState	0	0	0
ternaryFit-class	9.75	0.00	9.75
ternaryFitParameters-class	0.02	0.00	0.01
ternaryPost-class	9.59	0.00	9.60
tnetfit	9.22	0.00	9.23
tnetpost	9.34	0.00	9.35

BioC 3.2: CHECK report for ternarynet on moscato1

Summary

Command output