Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:36:01 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 381/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORode 1.42.0  (landing page)
Attila Gabor
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CNORode
git_branch: RELEASE_3_17
git_last_commit: 9d3b4b3
git_last_commit_date: 2023-04-25 10:24:23 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for CNORode on palomino3


To the developers/maintainers of the CNORode package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNORode.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CNORode
Version: 1.42.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNORode.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CNORode_1.42.0.tar.gz
StartedAt: 2023-10-16 00:46:11 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:47:33 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 82.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CNORode.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNORode.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CNORode_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CNORode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNORode' version '1.42.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CNORode' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'knitr'
  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'
crossvalidateODE: no visible global function definition for 'error'
minlpLBodeSSm: no visible global function definition for 'essR'
minlpLBodeSSm: no visible global function definition for 'runif'
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 'lines'
runCNORode: no visible global function definition for 'pdf'
runCNORode: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off error essR lines par pdf plot.new runif
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/CNORode/libs/x64/CNORode.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  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 use Fortran I/O
nor system RNGs nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
parEstimationLBode 8.67   0.37    9.14
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck/00check.log'
for details.



Installation output

CNORode.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL CNORode
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'CNORode' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FG_transfer_function.c -o FG_transfer_function.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
 2445 |   int is, retval;
      |           ^~~~~~
cvodea.c: In function 'CVArhsQ':
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
 2941 |   int flag, retval;
      |       ^~~~
cvodea.c: In function 'CVAhermiteGetY':
cvodea.c:2591:5: warning: 'ySd0' may be used uninitialized [-Wmaybe-uninitialized]
 2591 |     N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cvodea.c:2507:19: note: 'ySd0' was declared here
 2507 |   N_Vector *yS0, *ySd0, *yS1, *ySd1;
      |                   ^~~~
cvodea.c:2591:5: warning: 'yS0' may be used uninitialized [-Wmaybe-uninitialized]
 2591 |     N_VLinearSum(ONE, yS0[is], factor1, ySd0[is], yS[is]);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cvodea.c:2507:13: note: 'yS0' was declared here
 2507 |   N_Vector *yS0, *ySd0, *yS1, *ySd1;
      |             ^~~
cvodea.c: In function 'CVodeB':
cvodea.c:1263:13: warning: 'flag' may be used uninitialized [-Wmaybe-uninitialized]
 1263 |   int sign, flag;
      |             ^~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodea_io.c -o cvodea_io.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes.c -o cvodes.o
cvodes.c: In function 'cvHin':
cvodes.c:4318:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4318 |       if (count1 <= 2)
      |       ^~
cvodes.c:4320:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4320 |         if (retval == QRHSFUNC_RECVR) return(CV_REPTD_QRHSFUNC_ERR);
      |         ^~
cvodes.c: In function 'cvQuadSensRhs1InternalDQ':
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
 8834 |   realtype Deltap, rDeltap;
      |                    ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_band.c -o cvodes_band.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_dense.c -o cvodes_dense.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_diag.c -o cvodes_diag.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_direct.c -o cvodes_direct.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_io.c -o cvodes_io.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_spils.c -o cvodes_spils.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c decimal2binary.c -o decimal2binary.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findStates.c -o findStates.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fnvector_serial.c -o fnvector_serial.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getNumBits.c -o getNumBits.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getNumInputs.c -o getNumInputs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getStateIndex.c -o getStateIndex.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getTruthTables.c -o getTruthTables.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_count_bits.c -o get_count_bits.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_input_index.c -o get_input_index.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_support_truth_tables.c -o get_support_truth_tables.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hill_function.c -o hill_function.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c linear_transfer_function.c -o linear_transfer_function.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c normHill.c -o normHill.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c normHill_mod.c -o normHill_mod.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nvector_serial.c -o nvector_serial.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printAdjMat.c -o printAdjMat.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printInterMat.c -o printInterMat.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printNminiTerms.c -o printNminiTerms.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c printTruthTables.c -o printTruthTables.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rhsODE.c -o rhsODE.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sim_logic_ode.c -o sim_logic_ode.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:37:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   37 |         int i,j,neq,counter,flag;
      |                     ^~~~~~~
simulateODE.c:257:4: warning: 'tout' may be used uninitialized [-Wmaybe-uninitialized]
  257 |    rhsODEF(tout,y0,ydot0, data);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
simulateODE.c:38:18: note: 'tout' was declared here
   38 |         realtype tout, ti, tf;
      |                  ^~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_band.c -o sundials_band.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_dense.c -o sundials_dense.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_direct.c -o sundials_direct.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_iterative.c -o sundials_iterative.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_math.c -o sundials_math.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_nvector.c -o sundials_nvector.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
  439 |   realtype **Hes, *givens, *yg;
      |                             ^~
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
  439 |   realtype **Hes, *givens, *yg;
      |                    ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I./include    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -shared -s -static-libgcc -o CNORode.dll tmp.def FG_transfer_function.o 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 normHill_mod.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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-CNORode/00new/CNORode/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNORode)

Tests output


Example timings

CNORode.Rcheck/CNORode-Ex.timings

nameusersystemelapsed
createLBodeContPars0.020.000.01
getLBodeContObjFunction0.010.010.04
getLBodeDataSim0.020.000.02
getLBodeMINLPObjFunction0.020.010.03
getLBodeModelSim0.010.020.03
minlpLBodeSSm000
parEstimationLBode8.670.379.14
parEstimationLBodeGA2.860.112.98
parEstimationLBodeSSm000
plotLBodeFitness0.630.000.63
plotLBodeModelSim0.320.000.31
runCNORode000
simdata2cnolist0.010.000.01
simulate0.020.000.02