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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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

Package 1772/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.63.0  (landing page)
Michael Lawrence
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/rsbml
git_branch: devel
git_last_commit: 588dff4
git_last_commit_date: 2024-04-30 10:17:23 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kjohnson3macOS 13.6.5 Ventura / arm64... NOT SUPPORTED ...
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for rsbml on palomino6

To the developers/maintainers of the rsbml package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rsbml
Version: 2.63.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rsbml.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rsbml_2.63.0.tar.gz
StartedAt: 2024-07-16 03:32:14 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 03:36:18 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 243.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rsbml.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rsbml.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rsbml_2.63.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/rsbml.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rsbml/DESCRIPTION' ... OK
* this is package 'rsbml' version '2.63.0'
* 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 whether package 'rsbml' can be installed ... WARNING
Found the following significant warnings:
  C:/libsbml/x64/include/sbml/ListOf.h:111:27: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/rsbml.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 18.6Mb
  sub-directories of 1Mb or more:
    SBML_odeSolver-1.7.0beta   1.6Mb
    libs                      15.4Mb
* 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 code 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 whether startup messages can be suppressed ... 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'
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 ... NOTE
checkRd: (-1) SBML-class.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) SBML-class.Rd:76: Escaped LaTeX specials: \_
checkRd: (-1) SBML-class.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) SBML-class.Rd:80: Escaped LaTeX specials: \_
checkRd: (-1) SBML-class.Rd:82: Escaped LaTeX specials: \_
checkRd: (-1) SBMLDocument-class.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) SBMLDocument-class.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) SBMLDocument-class.Rd:38: Escaped LaTeX specials: \_
checkRd: (-1) SBMLDocument-class.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) SBMLDocument-class.Rd:42: Escaped LaTeX specials: \_
checkRd: (-1) SBMLDocument-class.Rd:44: Escaped LaTeX specials: \_
* 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 ... 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/rsbml/libs/x64/rsbml.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 nor [v]sprintf. 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 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 ... 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, 8 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/rsbml.Rcheck/00check.log'
for details.


Installation output

rsbml.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rsbml
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'rsbml' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c StringMap.c -o StringMap.o
In file included from C:/libsbml/x64/include/sbml/common/common.h:117,
                 from StringMap.c:52:
C:/libsbml/x64/include/sbml/util/util.h:369:7: warning: 'finite' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
  369 |   int finite (double d);
      |       ^~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c check.c -o check.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c doc.c -o doc.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dom.c -o dom.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c graph.c -o graph.o
graph.c: In function 'rsbml_build_graph':
graph.c:55:57: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
   55 |     StringMap_put(id_map, CHAR(STRING_ELT(r_nodes, i)), (void *)i);
      |                                                         ^
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c layoutWrappers.cpp -o layoutWrappers.o
In file included from C:/libsbml/x64/include/sbml/FunctionDefinition.h:136,
                 from C:/libsbml/x64/include/sbml/SBMLTransforms.h:52,
                 from C:/libsbml/x64/include/sbml/SBMLDocument.h:302,
                 from C:/libsbml/x64/include/sbml/SBMLTypes.h:43,
                 from rsbml.h:1,
                 from layoutWrappers.cpp:1:
C:/libsbml/x64/include/sbml/ListOf.h:111:27: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  111 | struct IdEq : public std::unary_function<SBase*, bool>
      |                           ^~~~~~~~~~~~~~
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/string:49,
                 from C:/libsbml/x64/include/sbml/util/util.h:49,
                 from C:/libsbml/x64/include/sbml/xml/XMLError.h:344,
                 from C:/libsbml/x64/include/sbml/SBMLError.h:461,
                 from C:/libsbml/x64/include/sbml/SBMLDocument.h:299:
C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mathml.c -o mathml.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IC:/Users/biocbuild/bbs-3.20-bioc/R/include -DLIBSBML3    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
g++ -std=gnu++17 -shared -s -static-libgcc -o rsbml.dll tmp.def StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -LC:/libsbml/x64/bin -lsbml -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
mkdir -p C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs//x64
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs/x64
** 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
** 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-class0.120.030.15
SBMLDocument-class0.200.020.22
read0.180.010.18