Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1754/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgoslin 1.8.0  (landing page)
Nils Hoffmann
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/rgoslin
git_branch: RELEASE_3_19
git_last_commit: 4152af5
git_last_commit_date: 2024-04-30 11:40:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


BUILD BIN results for rgoslin on palomino3

To the developers/maintainers of the rgoslin package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rgoslin.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: rgoslin
Version: 1.8.0
Command: rm -rf rgoslin.buildbin-libdir && mkdir rgoslin.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=rgoslin.buildbin-libdir rgoslin_1.8.0.tar.gz
StartedAt: 2024-06-17 17:32:29 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 17:36:00 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 211.0 seconds
RetCode: 0
Status:   OK  
PackageFile: rgoslin_1.8.0.zip
PackageFileSize: 1.246 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rgoslin.buildbin-libdir && mkdir rgoslin.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=rgoslin.buildbin-libdir rgoslin_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'rgoslin' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
The name of the shared library to be created is: rgoslin.dll
make[1]: Entering directory '/f/biocbuild/bbs-3.19-bioc/tmpdir/RtmpoPG5Fk/R.INSTALL228a412482097/rgoslin/src/cppgoslin'
rm -f "cppgoslin/parser/KnownGrammars.h"
rm -f "src/domain/LipidClasses.cpp"
rm -f "cppgoslin/domain/ClassesEnum.h"
rm -f cppgoslin/domain/*.o
rm -f cppgoslin/parser/*.o
rm -f cppgoslin/tests/*.o
rm -f libcppGoslin.dll
rm -f *Test
rm -f writeGrammarsHeader
rm -f writeLipidEnums
rm -f libcppGoslin.a
make[1]: Leaving directory '/f/biocbuild/bbs-3.19-bioc/tmpdir/RtmpoPG5Fk/R.INSTALL228a412482097/rgoslin/src/cppgoslin'
make[1]: Entering directory '/f/biocbuild/bbs-3.19-bioc/tmpdir/RtmpoPG5Fk/R.INSTALL228a412482097/rgoslin/src/cppgoslin'
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I . -o writeGrammarsHeader writeGrammarsHeader.cpp && ".\writeGrammarsHeader.exe" "cppgoslin/parser/KnownGrammars.h"
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I . -o writeLipidEnums writeLipidEnums.cpp src/domain/StringFunctions.cpp src/parser/SumFormulaParserEventHandler.cpp src/parser/ParserClasses.cpp && ".\writeLipidEnums.exe" "src/domain/LipidClasses.cpp"
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/Adduct.o -c src/domain/Adduct.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidMolecularSpecies.o -c src/domain/LipidMolecularSpecies.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidSnPosition.o -c src/domain/LipidSnPosition.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidStructureDefined.o -c src/domain/LipidStructureDefined.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/FattyAcid.o -c src/domain/FattyAcid.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidAdduct.o -c src/domain/LipidAdduct.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidSpecies.o -c src/domain/LipidSpecies.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidFullStructure.o -c src/domain/LipidFullStructure.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidCompleteStructure.o -c src/domain/LipidCompleteStructure.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidSpeciesInfo.o -c src/domain/LipidSpeciesInfo.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/StringFunctions.o -c src/domain/StringFunctions.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/LipidClasses.o -c src/domain/LipidClasses.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/DoubleBonds.o -c src/domain/DoubleBonds.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/FunctionalGroup.o -c src/domain/FunctionalGroup.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/Headgroup.o -c src/domain/Headgroup.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/Cycle.o -c src/domain/Cycle.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/domain/GenericDatastructures.o -c src/domain/GenericDatastructures.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/ParserClasses.o -c src/parser/ParserClasses.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/KnownParsers.o -c src/parser/KnownParsers.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/GoslinParserEventHandler.o -c src/parser/GoslinParserEventHandler.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/LipidMapsParserEventHandler.o -c src/parser/LipidMapsParserEventHandler.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/SwissLipidsParserEventHandler.o -c src/parser/SwissLipidsParserEventHandler.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/HmdbParserEventHandler.o -c src/parser/HmdbParserEventHandler.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/SumFormulaParserEventHandler.o -c src/parser/SumFormulaParserEventHandler.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/SumFormulaParser.o -c src/parser/SumFormulaParser.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/ShorthandParserEventHandler.o -c src/parser/ShorthandParserEventHandler.cpp
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/FattyAcidParserEventHandler.o -c src/parser/FattyAcidParserEventHandler.cpp
In file included from ./cppgoslin/domain/LipidAdduct.h:29,
                 from ./cppgoslin/parser/FattyAcidParserEventHandler.h:31,
                 from src/parser/FattyAcidParserEventHandler.cpp:26:
./cppgoslin/domain/FattyAcid.h:47:12: warning: 'virtual std::string FattyAcid::to_string(goslin::LipidLevel)' was hidden [-Woverloaded-virtual=]
   47 |     string to_string(LipidLevel level);
      |            ^~~~~~~~~
In file included from ./cppgoslin/domain/Headgroup.h:31,
                 from ./cppgoslin/domain/LipidStructureDefined.h:32,
                 from ./cppgoslin/domain/LipidFullStructure.h:31,
                 from ./cppgoslin/domain/LipidCompleteStructure.h:31,
                 from ./cppgoslin/domain/LipidAdduct.h:35:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: note:   by 'std::string LipidSpeciesInfo::to_string()'
   53 |     string to_string();
      |            ^~~~~~~~~
g++  -std=gnu++11 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -I. -fPIC -o src/parser/LipidBaseParserEventHandler.o -c src/parser/LipidBaseParserEventHandler.cpp
ar rcs libcppGoslin.a src/domain/Adduct.o src/domain/LipidMolecularSpecies.o src/domain/LipidSnPosition.o src/domain/LipidStructureDefined.o src/domain/FattyAcid.o src/domain/LipidAdduct.o src/domain/LipidSpecies.o src/domain/LipidFullStructure.o src/domain/LipidCompleteStructure.o src/domain/LipidSpeciesInfo.o src/domain/StringFunctions.o src/domain/LipidClasses.o src/domain/DoubleBonds.o src/domain/FunctionalGroup.o src/domain/Headgroup.o src/domain/Cycle.o src/domain/GenericDatastructures.o src/parser/ParserClasses.o src/parser/KnownParsers.o src/parser/GoslinParserEventHandler.o src/parser/LipidMapsParserEventHandler.o src/parser/SwissLipidsParserEventHandler.o src/parser/HmdbParserEventHandler.o src/parser/SumFormulaParserEventHandler.o src/parser/SumFormulaParser.o src/parser/ShorthandParserEventHandler.o src/parser/FattyAcidParserEventHandler.o src/parser/LipidBaseParserEventHandler.o
make[1]: Leaving directory '/f/biocbuild/bbs-3.19-bioc/tmpdir/RtmpoPG5Fk/R.INSTALL228a412482097/rgoslin/src/cppgoslin'
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rgoslin.cpp -o rgoslin.o
g++ -shared -s -static-libgcc -o rgoslin.dll tmp.def RcppExports.o rgoslin.o cppgoslin/libcppGoslin.a -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
installing to F:/biocbuild/bbs-3.19-bioc/meat/rgoslin.buildbin-libdir/00LOCK-rgoslin/00new/rgoslin/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 'rgoslin' as rgoslin_1.8.0.zip
* DONE (rgoslin)