Package: rsbml

Version: 2.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rsbml.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rsbml_2.42.0.tar.gz

StartedAt: 2019-10-16 06:26:50 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:28:00 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 69.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: rsbml.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rsbml.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rsbml_2.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rsbml.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rsbml/DESCRIPTION’ ... OK
* this is package ‘rsbml’ version ‘2.42.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rsbml’ can be installed ... WARNING
Found the following significant warnings:
  dom.c:687:12: warning: comparison of constant 'SBML_LAYOUT_CUBICBEZIER' (102) with expression of type 'SBMLTypeCode_t' is always false [-Wtautological-constant-out-of-range-compare]
  dom.c:693:19: warning: comparison of constant 'SBML_LAYOUT_LINESEGMENT' (107) with expression of type 'SBMLTypeCode_t' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/rsbml.Rcheck/00install.out’ for details.
* 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 : : 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 : : 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 : : 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 : : 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* 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: 2 WARNINGs, 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/rsbml.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rsbml
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘rsbml’ ...
** using staged installation
checking for pkg-config... /usr/local/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... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin15.6.0
checking host system type... i386-apple-darwin15.6.0
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/local/bin/autoconf
checking for aclocal... /usr/local/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/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for SBML... yes
checking for correct functioning of SBML... yes
checking for SUNDIALS Library headers... checking for SUNDIALS Library... checking correct functioning of SUNDIALS... no:
                   CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 
                   LDFLAGS= 
                   LIBS= -lm -lstdc++
configure: error: Can not link to SUNDIALS Library
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c StringMap.c -o StringMap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c check.c -o check.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c doc.c -o doc.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c dom.c -o dom.o
dom.c:687:12: warning: comparison of constant 'SBML_LAYOUT_CUBICBEZIER' (102) with expression of type 'SBMLTypeCode_t' is always false [-Wtautological-constant-out-of-range-compare]
  if (type == SBML_LAYOUT_CUBICBEZIER) {
      ~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~~
dom.c:693:19: warning: comparison of constant 'SBML_LAYOUT_LINESEGMENT' (107) with expression of type 'SBMLTypeCode_t' is always false [-Wtautological-constant-out-of-range-compare]
  } else if (type == SBML_LAYOUT_LINESEGMENT)
             ~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~~
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c graph.c -o graph.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c io.c -o io.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c layoutWrappers.cpp -o layoutWrappers.o
In file included from layoutWrappers.cpp:1:
./rsbml.h:76:11: warning: struct 'LayoutModelPlugin' was previously declared as a class [-Wmismatched-tags]
  typedef struct LayoutModelPlugin LayoutModelPlugin_t;
          ^
/usr/local/include/sbml/packages/layout/extension/LayoutModelPlugin.h:58:22: note: previous use is here
class LIBSBML_EXTERN LayoutModelPlugin : public SBasePlugin
                     ^
./rsbml.h:76:11: note: did you mean class here?
  typedef struct LayoutModelPlugin LayoutModelPlugin_t;
          ^~~~~~
          class
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mathml.c -o mathml.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.8/include/libxml2 -I/usr/local/include      -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c simulate.c -o simulate.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -L/usr/local/lib -lsbml -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)

name	user	system	elapsed
SBML-class	0.278	0.019	0.337
SBMLDocument-class	0.493	0.012	0.525
read	0.343	0.009	0.371