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This page was generated on 2024-03-28 11:38:25 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1802/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.61.0  (landing page)
Michael Lawrence
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/rsbml
git_branch: devel
git_last_commit: ab3e650
git_last_commit_date: 2023-10-24 09:39:01 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

BUILD BIN results for rsbml on palomino3


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: 2.61.0
Command: rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir rsbml_2.61.0.tar.gz
StartedAt: 2024-03-28 09:18:48 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 09:20:20 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 91.4 seconds
RetCode: 0
Status:   OK  
PackageFile: rsbml_2.61.0.zip
PackageFileSize: 6.513 MiB

Command output

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###
### Running command:
###
###   rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=rsbml.buildbin-libdir rsbml_2.61.0.tar.gz
###
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* 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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -IC:/libsbml/x64/include -IC:/libsbml/x64/include/expat -IF:/biocbuild/bbs-3.19-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 -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
mkdir -p F:/biocbuild/bbs-3.19-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs/x64
cp C:/libsbml/x64/bin/*.dll F:/biocbuild/bbs-3.19-bioc/meat/rsbml.buildbin-libdir/00LOCK-rsbml/00new/rsbml/libs//x64
installing to F:/biocbuild/bbs-3.19-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_2.61.0.zip
* DONE (rsbml)