Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:20:06 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for CNORode on nebbiolo1


To the developers/maintainers of the CNORode package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 362/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORode 1.38.0  (landing page)
Attila Gabor
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/CNORode
git_branch: RELEASE_3_15
git_last_commit: a08ee26
git_last_commit_date: 2022-04-26 11:12:20 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CNORode
Version: 1.38.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNORode_1.38.0.tar.gz
StartedAt: 2022-10-18 19:06:57 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:07:57 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 60.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CNORode.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CNORode_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CNORode.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNORode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORode’ version ‘1.38.0’
* 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 for sufficient/correct file permissions ... 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 ... 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 is not available
File ‘/home/biocbuild/bbs-3.15-bioc/R/library/CNORode/libs/CNORode.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (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. 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/CNORode.Rcheck/00check.log’
for details.



Installation output

CNORode.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CNORode
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘CNORode’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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:37:14: 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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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)

Tests output


Example timings

CNORode.Rcheck/CNORode-Ex.timings

nameusersystemelapsed
createLBodeContPars0.0050.0010.005
getLBodeContObjFunction0.0100.0000.011
getLBodeDataSim0.0080.0000.007
getLBodeMINLPObjFunction0.010.000.01
getLBodeModelSim0.0080.0000.007
minlpLBodeSSm000
parEstimationLBode4.5790.0784.658
parEstimationLBodeGA1.8110.0321.844
parEstimationLBodeSSm0.0010.0010.000
plotLBodeFitness0.5160.0110.527
plotLBodeModelSim0.3190.0040.323
runCNORode000
simdata2cnolist0.0060.0040.010
simulate0.0080.0010.008