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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CNORode_1.41.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CNORode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORode’ version ‘1.41.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNORode’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 loading without being on the library search path ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/CNORode/libs/CNORode.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘__vsprintf_chk’, possibly from ‘vsprintf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CNORode-vignette.Rnw’ using ‘UTF-8’... failed
 WARNING
Errors in running code in vignettes:
when running code in ‘CNORode-vignette.Rnw’
  ...

> options(width = 70, useFancyQuotes = "UTF-8", prompt = " ", 
+     continue = "  ")

> BiocManager::install("MEIGOR")

  When sourcing ‘CNORode-vignette.R’:
Error: there is no package called ‘BiocManager’
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘CNORode-vignette.Rnw’ using Sweave

Error: processing vignette 'CNORode-vignette.Rnw' failed with diagnostics:
 chunk 3 (label = installMEIGOR) 
Error in loadNamespace(x) : there is no package called ‘BiocManager’

--- failed re-building ‘CNORode-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘CNORode-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CNORode
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘CNORode’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c FG_transfer_function.c -o FG_transfer_function.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -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:2572:7: warning: ‘ySd0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2572 |       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]
 2591 |     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]
 1263 |   int sign, flag;
      |             ^~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodea_io.c -o cvodea_io.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -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"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_band.c -o cvodes_band.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_dense.c -o cvodes_dense.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_diag.c -o cvodes_diag.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_direct.c -o cvodes_direct.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_io.c -o cvodes_io.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_spils.c -o cvodes_spils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c decimal2binary.c -o decimal2binary.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c findStates.c -o findStates.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c fnvector_serial.c -o fnvector_serial.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c getNumBits.c -o getNumBits.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c getNumInputs.c -o getNumInputs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c getStateIndex.c -o getStateIndex.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c getTruthTables.c -o getTruthTables.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c get_count_bits.c -o get_count_bits.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c get_input_index.c -o get_input_index.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c get_support_truth_tables.c -o get_support_truth_tables.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c hill_function.c -o hill_function.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c linear_transfer_function.c -o linear_transfer_function.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c normHill.c -o normHill.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c normHill_mod.c -o normHill_mod.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c nvector_serial.c -o nvector_serial.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c printAdjMat.c -o printAdjMat.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c printInterMat.c -o printInterMat.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c printNminiTerms.c -o printNminiTerms.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c printTruthTables.c -o printTruthTables.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c rhsODE.c -o rhsODE.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sim_logic_ode.c -o sim_logic_ode.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -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 in this function [-Wmaybe-uninitialized]
  257 |    rhsODEF(tout,y0,ydot0, data);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_band.c -o sundials_band.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_dense.c -o sundials_dense.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_direct.c -o sundials_direct.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_iterative.c -o sundials_iterative.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_math.c -o sundials_math.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_nvector.c -o sundials_nvector.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -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"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -I./include  -fpic  -g -O2  -Wall -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o CNORode.so 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 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-CNORode/00new/CNORode/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNORode)