Michael Lawrence
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/rsbml |
| git_branch: devel |
| git_last_commit: 7671d4c |
| git_last_commit_date: 2025-04-15 09:41:01 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1817/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rsbml 2.67.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
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: 2.67.0 |
| Command: rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir rsbml_2.67.0.tar.gz |
| StartedAt: 2025-08-15 11:11:11 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 11:14:06 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 175.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: rsbml_2.67.0.zip |
| PackageFileSize: 6.517 MiB |
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### Running command:
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### rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir rsbml_2.67.0.tar.gz
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* installing *source* package 'rsbml' ...
** this is package 'rsbml' version '2.67.0'
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c check.c -o check.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c doc.c -o doc.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c dom.c -o dom.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/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:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/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:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c mathml.c -o mathml.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.22-bioc/R/include -DLIBSBML3 -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
mkdir -p F:/biocbuild/bbs-3.22-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll F:/biocbuild/bbs-3.22-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs//x64
installing to F:/biocbuild/bbs-3.22-bioc/meat/rsbml.buildbin-libdir/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
* MD5 sums
packaged installation of 'rsbml' as rsbml_2.67.0.zip
* DONE (rsbml)