CNORode 1.18.0
David Henriques
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/CNORode | | Branch: RELEASE_3_5 | | Last Commit: b68c4f8 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf CNORode.buildbin-libdir CNORode.Rcheck && mkdir CNORode.buildbin-libdir CNORode.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNORode.buildbin-libdir CNORode_1.18.0.tar.gz >CNORode.Rcheck\00install.out 2>&1 && cp CNORode.Rcheck\00install.out CNORode-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CNORode.buildbin-libdir --install="check:CNORode-install.out" --force-multiarch --no-vignettes --timings CNORode_1.18.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNORode.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNORode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORode' version '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'MEIGOR'
* 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 'CNORode' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'MEIGOR' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'CellNOptR' 'genalg'
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 ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
createLBodeContPars: no visible global function definition for 'runif'
getLBodeContObjFunction: no visible global function definition for
'compatCNOlist'
getLBodeContObjFunction: no visible global function definition for
'indexFinder'
getLBodeDataSim: no visible global function definition for
'compatCNOlist'
getLBodeDataSim: no visible global function definition for
'indexFinder'
getLBodeMINLPObjFunction: no visible global function definition for
'compatCNOlist'
getLBodeMINLPObjFunction: no visible global function definition for
'indexFinder'
getLBodeModelSim: no visible global function definition for
'compatCNOlist'
getLBodeModelSim: no visible global function definition for
'indexFinder'
minlpLBodeSSm: no visible global function definition for
'compatCNOlist'
minlpLBodeSSm: no visible global function definition for 'essR'
minlpLBodeSSm: no visible global function definition for 'runif'
parEstimationLBode: no visible global function definition for
'compatCNOlist'
parEstimationLBodeGA: no visible global function definition for
'compatCNOlist'
parEstimationLBodeGA: no visible global function definition for
'indexFinder'
parEstimationLBodeGA: no visible global function definition for
'plot.new'
parEstimationLBodeGA : monitor_func: no visible global function
definition for 'par'
parEstimationLBodeGA : monitor_func: no visible global function
definition for 'plot'
parEstimationLBodeGA : monitor_func: no visible global function
definition for 'lines'
parEstimationLBodeGA: no visible global function definition for 'rbga'
parEstimationLBodeSSm: no visible global function definition for
'compatCNOlist'
parEstimationLBodeSSm: no visible global function definition for
'indexFinder'
parEstimationLBodeSSm: no visible global function definition for 'essR'
plotLBodeFitness: no visible global function definition for
'compatCNOlist'
plotLBodeFitness: no visible global function definition for
'indexFinder'
plotLBodeFitness: no visible global function definition for
'plotOptimResults'
plotLBodeFitness: no visible global function definition for
'plotOptimResultsPan'
plotLBodeFitness: no visible global function definition for 'CNOlist'
plotLBodeModelSim: no visible global function definition for
'compatCNOlist'
plotLBodeModelSim: no visible global function definition for
'indexFinder'
plotLBodeModelSim: no visible global function definition for
'plotCNOlistLarge'
plotLBodeModelSim: no visible global function definition for 'CNOlist'
plotLBodeModelSim: no visible global function definition for
'plotCNOlist'
simdata2cnolist: no visible global function definition for
'compatCNOlist'
simdata2cnolist: no visible global function definition for 'CNOlist'
simulate: no visible global function definition for 'compatCNOlist'
simulate: no visible global function definition for 'indexFinder'
Undefined global functions or variables:
CNOlist compatCNOlist essR indexFinder lines par plot plot.new
plotCNOlist plotCNOlistLarge plotOptimResults plotOptimResultsPan
rbga runif
Consider adding
importFrom("graphics", "lines", "par", "plot", "plot.new")
importFrom("stats", "runif")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/i386/CNORode.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
parEstimationLBode 117.14 0.08 117.22
parEstimationLBodeGA 52.17 0.02 52.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
parEstimationLBode 31.68 0.03 31.74
parEstimationLBodeGA 8.85 0.03 8.89
* 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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNORode.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'CNORode' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodea.c -o cvodea.o
cvodea.c: In function 'CVAhermiteStorePnt':
cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
int is, retval;
^
cvodea.c: In function 'CVArhsQ':
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
int flag, retval;
^
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2572:7: warning: 'ySd0' may be used uninitialized in this function [-Wmaybe-uninitialized]
N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]);
^
cvodea.c:2591:5: warning: 'yS0' may be used uninitialized in this function [-Wmaybe-uninitialized]
N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
^
cvodea.c: In function 'CVodeB':
cvodea.c:1263:13: warning: 'flag' may be used uninitialized in this function [-Wmaybe-uninitialized]
int sign, flag;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodea_io.c -o cvodea_io.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes.c -o cvodes.o
cvodes.c: In function 'cvQuadSensRhs1InternalDQ':
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
realtype Deltap, rDeltap;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_band.c -o cvodes_band.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_bandpre.c -o cvodes_bandpre.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_dense.c -o cvodes_dense.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_diag.c -o cvodes_diag.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_direct.c -o cvodes_direct.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_io.c -o cvodes_io.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_spgmr.c -o cvodes_spgmr.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_spils.c -o cvodes_spils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c decimal2binary.c -o decimal2binary.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c findStates.c -o findStates.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c fnvector_serial.c -o fnvector_serial.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c getNumBits.c -o getNumBits.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c getNumInputs.c -o getNumInputs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c getStateIndex.c -o getStateIndex.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function 'getTruthTables':
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
int i,j,k,m,n,counter1,input,miniterm;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c get_count_bits.c -o get_count_bits.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c get_input_index.c -o get_input_index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function 'get_support_truth_tables':
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c get_truth_tables_index.c -o get_truth_tables_index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c hill_function.c -o hill_function.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c linear_transfer_function.c -o linear_transfer_function.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c normHill.c -o normHill.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c nvector_serial.c -o nvector_serial.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c printAdjMat.c -o printAdjMat.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c printInterMat.c -o printInterMat.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c printNminiTerms.c -o printNminiTerms.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c printTruthTables.c -o printTruthTables.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c rhsODE.c -o rhsODE.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sim_logic_ode.c -o sim_logic_ode.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150:4: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^
simulateODE.c:32:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_band.c -o sundials_band.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_dense.c -o sundials_dense.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_direct.c -o sundials_direct.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_iterative.c -o sundials_iterative.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_math.c -o sundials_math.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_nvector.c -o sundials_nvector.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_spbcgs.c -o sundials_spbcgs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c: In function 'SpgmrFree':
sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=core2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/i386
** R
** data
** 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 'CNORode' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodea.c -o cvodea.o
cvodea.c: In function 'CVAhermiteStorePnt':
cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
int is, retval;
^
cvodea.c: In function 'CVArhsQ':
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
int flag, retval;
^
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2572:7: warning: 'ySd0' may be used uninitialized in this function [-Wmaybe-uninitialized]
N_VLinearSum(ONE, YS[0][is], -delta, ySd0[is], YS[0][is]);
^
cvodea.c:2591:5: warning: 'yS0' may be used uninitialized in this function [-Wmaybe-uninitialized]
N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
^
cvodea.c: In function 'CVodeB':
cvodea.c:1263:13: warning: 'flag' may be used uninitialized in this function [-Wmaybe-uninitialized]
int sign, flag;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodea_io.c -o cvodea_io.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes.c -o cvodes.o
cvodes.c: In function 'cvQuadSensRhs1InternalDQ':
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
realtype Deltap, rDeltap;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_band.c -o cvodes_band.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_bandpre.c -o cvodes_bandpre.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_dense.c -o cvodes_dense.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_diag.c -o cvodes_diag.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_direct.c -o cvodes_direct.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_io.c -o cvodes_io.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_spgmr.c -o cvodes_spgmr.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_spils.c -o cvodes_spils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c decimal2binary.c -o decimal2binary.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c findStates.c -o findStates.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c fnvector_serial.c -o fnvector_serial.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c getNumBits.c -o getNumBits.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c getNumInputs.c -o getNumInputs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c getStateIndex.c -o getStateIndex.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c getTruthTables.c -o getTruthTables.o
getTruthTables.c: In function 'getTruthTables':
getTruthTables.c:17:14: warning: unused variable 'n' [-Wunused-variable]
int i,j,k,m,n,counter1,input,miniterm;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c get_count_bits.c -o get_count_bits.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c get_input_index.c -o get_input_index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c get_support_truth_tables.c -o get_support_truth_tables.o
get_support_truth_tables.c: In function 'get_support_truth_tables':
get_support_truth_tables.c:16:10: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c get_truth_tables_index.c -o get_truth_tables_index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c hill_function.c -o hill_function.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c linear_transfer_function.c -o linear_transfer_function.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c normHill.c -o normHill.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c nvector_serial.c -o nvector_serial.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c printAdjMat.c -o printAdjMat.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c printInterMat.c -o printInterMat.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c printNminiTerms.c -o printNminiTerms.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c printTruthTables.c -o printTruthTables.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c rhsODE.c -o rhsODE.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sim_logic_ode.c -o sim_logic_ode.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150:4: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
flag = CVDense(cvode_mem, neq);
^
simulateODE.c:32:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
int i,j,neq,counter,flag;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_band.c -o sundials_band.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_dense.c -o sundials_dense.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_direct.c -o sundials_direct.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_iterative.c -o sundials_iterative.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_math.c -o sundials_math.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_nvector.c -o sundials_nvector.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_spbcgs.c -o sundials_spbcgs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c: In function 'SpgmrFree':
sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
realtype **Hes, *givens, *yg;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=core2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CNORode.dll tmp.def cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNORode.buildbin-libdir/CNORode/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNORode' as CNORode_1.18.0.zip
* DONE (CNORode)