Michael Lawrence
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/rsbml |
| git_branch: RELEASE_3_17 |
| git_last_commit: 3dd92e2 |
| git_last_commit_date: 2023-04-25 09:45:58 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:35 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1771/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rsbml 2.58.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: rsbml |
| Version: 2.58.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rsbml.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings rsbml_2.58.0.tar.gz |
| StartedAt: 2023-10-16 06:16:04 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 06:21:29 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 325.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rsbml.Rcheck |
| Warnings: 2 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rsbml.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings rsbml_2.58.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/rsbml.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* 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 '2.58.0'
* 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 'F:/biocbuild/bbs-3.17-bioc/meat/rsbml.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 19.5Mb
sub-directories of 1Mb or more:
SBML_odeSolver-1.7.0beta 1.6Mb
libs 16.3Mb
* 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 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 'F:/biocbuild/bbs-3.17-bioc/R/library/rsbml/libs/x64/rsbml.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (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 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, 8 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc/meat/rsbml.Rcheck/00check.log'
for details.
rsbml.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL rsbml
###
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* installing to library 'F:/biocbuild/bbs-3.17-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) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check.c -o check.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doc.c -o doc.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dom.c -o dom.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48,
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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mathml.c -o mathml.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.17-bioc/R/include -DLIBSBML3 -I"C:/rtools43/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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
mkdir -p F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rsbml/00new/rsbml/libs//x64
installing to F:/biocbuild/bbs-3.17-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)
rsbml.Rcheck/rsbml-Ex.timings
| name | user | system | elapsed | |
| SBML-class | 0.14 | 0.01 | 0.16 | |
| SBMLDocument-class | 0.2 | 0.0 | 0.2 | |
| read | 0.18 | 0.00 | 0.19 | |