BioC 3.3: CHECK report for rsbml on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rsbml_2.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/rsbml.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.30.0’
* 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 ... 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 ... 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
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 ... OK
* 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’
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 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 ... OK
* 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 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/rsbml.Rcheck/00check.log’
for details.

* installing *source* package ‘rsbml’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML3... 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... /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... /usr/bin/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... 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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c StringMap.c -o StringMap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c check.c -o check.o
In file included from check.c:1:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from check.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c doc.c -o doc.o
In file included from doc.c:1:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from doc.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
doc.c: In function ‘rsbml_build_doc_simple_species_reference’:
doc.c:453:8: warning: unused variable ‘tmp’ [-Wunused-variable]
   SEXP tmp = GET_SLOT(r_simple_species_reference, install("species"));
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c dom.c -o dom.o
In file included from dom.c:1:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from dom.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
dom.c: In function ‘rsbml_build_dom_line_segment’:
dom.c:792:12: warning: comparison between ‘SBMLTypeCode_t’ and ‘enum <anonymous>’ [-Wenum-compare]
   if (type == SBML_LAYOUT_CUBICBEZIER) {
            ^
dom.c:798:19: warning: comparison between ‘SBMLTypeCode_t’ and ‘enum <anonymous>’ [-Wenum-compare]
   } else if (type == SBML_LAYOUT_LINESEGMENT)
                   ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c graph.c -o graph.o
In file included from graph.c:1:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from graph.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
In file included from init.c:1:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from init.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c io.c -o io.o
In file included from io.c:1:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from io.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c layoutWrappers.cpp -o layoutWrappers.o
In file included from layoutWrappers.cpp:1:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from layoutWrappers.cpp:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c mathml.c -o mathml.o
In file included from mathml.c:3:0:
rsbml.h:8:0: warning: "USE_LAYOUT" redefined [enabled by default]
 #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
 ^
In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0,
                 from /usr/local/include/sbml/common/sbmlfwd.h:45,
                 from /usr/local/include/sbml/SBMLTypes.h:37,
                 from rsbml.h:1,
                 from mathml.c:3:
/usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition
 #define USE_LAYOUT 1
 ^
mathml.c: In function ‘rmathml_SEXP’:
mathml.c:56:12: warning: unused variable ‘closure’ [-Wunused-variable]
       SEXP closure, pargs;
            ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2    -DLIBSBML3 -I/usr/local/include    -fpic  -g -O2  -Wall -c simulate.c -o simulate.o
g++ -shared -L/home/biocbuild/bbs-3.3-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 -L/usr/local/lib -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/rsbml.Rcheck/rsbml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rsbml)

name	user	system	elapsed
SBML-class	0.248	0.004	0.286
SBMLDocument-class	0.520	0.001	0.529
read	0.384	0.000	0.384

BioC 3.3: CHECK report for rsbml on zin2

Summary

Command output