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This page was generated on 2023-01-29 16:33:40 -0000 (Sun, 29 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4021
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CHECK results for CNORode on kunpeng1


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 360/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNORode 1.41.0  (landing page)
Attila Gabor
Snapshot Date: 2023-01-27 13:09:27 -0000 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/CNORode
git_branch: master
git_last_commit: d730517
git_last_commit_date: 2022-11-01 15:07:28 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    WARNINGS  

Summary

Package: CNORode
Version: 1.41.0
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/library --timings CNORode_1.41.0.tar.gz
StartedAt: 2023-01-28 20:12:56 -0000 (Sat, 28 Jan 2023)
EndedAt: 2023-01-28 20:17:09 -0000 (Sat, 28 Jan 2023)
EllapsedTime: 252.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CNORode.Rcheck
Warnings: 2

Command output

##############################################################################
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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/library --timings CNORode_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CNORode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORode’ version ‘1.41.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in .bibentry_check_bibentry1(rval): A bibentry of bibtype ‘Manual’ has to specify the field: title
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'CNORode' was found
* 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 ... WARNING
Error in library(CNORode, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘CNORode’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* 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’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/CNORode.Rcheck/00check.log’
for details.



Installation output

CNORode.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CNORode
###
##############################################################################
##############################################################################


* 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)

Tests output


Example timings