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This page was generated on 2021-06-21 14:05:02 -0400 (Mon, 21 Jun 2021).

CHECK results for rsbml on nebbiolo1

To the developers/maintainers of the rsbml package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rsbml.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1635/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.50.0  (landing page)
Michael Lawrence
Snapshot Date: 2021-06-20 06:50:09 -0400 (Sun, 20 Jun 2021)
URL: https://git.bioconductor.org/packages/rsbml
Branch: RELEASE_3_13
Last Commit: 84b2f61
Last Changed Date: 2021-05-19 11:39:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    NA  
machv2macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: rsbml
Version: 2.50.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rsbml.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rsbml_2.50.0.tar.gz
StartedAt: 2021-06-20 13:29:50 -0400 (Sun, 20 Jun 2021)
EndedAt: 2021-06-20 13:30:25 -0400 (Sun, 20 Jun 2021)
EllapsedTime: 34.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rsbml.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rsbml.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rsbml_2.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/rsbml.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rsbml/DESCRIPTION’ ... OK
* this is package ‘rsbml’ version ‘2.50.0’
* 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:
  .BBSoptions
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 ‘rsbml’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘utils’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* 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
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘graph:::listLen’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.character.SBML as.character.SBMLDocument
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.simulate.SBML: no visible global function definition for ‘tail’
.simulate.SBML: no visible global function definition for ‘new’
.simulate.SBML: no visible global function definition for ‘is’
.simulate.SBML : <anonymous>: no visible global function definition for
  ‘head’
.simulate.SBML: no visible global function definition for ‘slotNames’
.simulate.SBML: no visible binding for global variable ‘new’
as.ts,SOSResult: no visible global function definition for ‘ts’
coerce,SBMLProblems-character: no visible binding for global variable
  ‘as’
describe,CompartmentGlyph: no visible global function definition for
  ‘callNextMethod’
describe,CubicBezier: no visible global function definition for
  ‘callNextMethod’
describe,ReactionGlyph: no visible global function definition for
  ‘callNextMethod’
describe,SpeciesGlyph: no visible global function definition for
  ‘callNextMethod’
describe,SpeciesReference: no visible global function definition for
  ‘callNextMethod’
describe,SpeciesReferenceGlyph: no visible global function definition
  for ‘callNextMethod’
describe,TextGlyph: no visible global function definition for
  ‘callNextMethod’
end<-,LineSegment: no visible binding for global variable ‘object’
glyphCurve<-,ReactionGlyph: no visible global function definition for
  ‘new’
glyphCurve<-,SpeciesReferenceGlyph: no visible global function
  definition for ‘new’
kineticLaw<-,Reaction: no visible global function definition for ‘new’
rsbml_graph,Model: no visible global function definition for ‘new’
rsbml_problems,SBMLDocument : makeProblems : <anonymous>: no visible
  binding for global variable ‘new’
rsbml_problems,SBMLDocument: no visible binding for global variable
  ‘new’
show,SBMLProblem: no visible global function definition for ‘as’
simulate,SBMLDocument: no visible global function definition for ‘tail’
simulate,SBMLDocument: no visible global function definition for ‘new’
simulate,SBMLDocument: no visible global function definition for ‘is’
simulate,SBMLDocument : <anonymous>: no visible global function
  definition for ‘head’
simulate,SBMLDocument: no visible global function definition for
  ‘slotNames’
simulate,SBMLDocument: no visible binding for global variable ‘new’
simulate,SOSExperiment: no visible global function definition for
  ‘slotNames’
simulate,SOSExperiment : <anonymous>: no visible global function
  definition for ‘slot’
Undefined global functions or variables:
  as callNextMethod head is new object slot slotNames tail ts
Consider adding
  importFrom("methods", "as", "callNextMethod", "is", "new", "slot",
             "slotNames")
  importFrom("stats", "ts")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘asMath’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 1 WARNING, 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/rsbml.Rcheck/00check.log’
for details.



Installation output

rsbml.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL rsbml
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘rsbml’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML... yes
configure: === Begin local SOSLib build ===
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether gcc accepts -fpic... yes
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for autoconf... /usr/bin/autoconf
checking for aclocal... /usr/bin/aclocal
checking for make... /usr/bin/make
checking for ar... /usr/bin/ar
checking for swig... swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for SBML... no
configure: WARNING: libsbml 3.0 not found by pkg-config
checking for SBML Library headers... yes
checking for SBML Library... checking for correct functioning of SBML... no:
                   CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -I/usr/include -I/usr/include/sbml
                   LDFLAGS=  
                   LIBS=-lm -lstdc++ 
configure: error: Can not link to SBML Library:
		  Please, make sure to use libSBML version >= 3.0.2 or CVS
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c StringMap.c -o StringMap.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c check.c -o check.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c doc.c -o doc.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c dom.c -o dom.o
dom.c: In function ‘rsbml_build_dom_line_segment’:
dom.c:687:12: warning: comparison between ‘SBMLTypeCode_t’ {aka ‘enum <anonymous>’} and ‘enum <anonymous>’ [-Wenum-compare]
  687 |   if (type == SBML_LAYOUT_CUBICBEZIER) {
      |            ^~
dom.c:693:19: warning: comparison between ‘SBMLTypeCode_t’ {aka ‘enum <anonymous>’} and ‘enum <anonymous>’ [-Wenum-compare]
  693 |   } else if (type == SBML_LAYOUT_LINESEGMENT)
      |                   ^~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c io.c -o io.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c layoutWrappers.cpp -o layoutWrappers.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c mathml.c -o mathml.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include    -I/usr/local/include   -fpic  -g -O2  -Wall -c simulate.c -o simulate.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -lsbml -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs
** R
** 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 (rsbml)

Tests output


Example timings

rsbml.Rcheck/rsbml-Ex.timings

nameusersystemelapsed
SBML-class0.0810.0000.082
SBMLDocument-class0.1120.0040.116
read0.1010.0000.101