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

This page was generated on 2024-07-16 17:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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: 2024-07-14 14:00 -0400 (Sun, 14 Jul 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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


CHECK results for rgoslin on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rgoslin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rgoslin_1.8.0.tar.gz
StartedAt: 2024-07-15 10:24:06 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 10:25:10 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 64.0 seconds
RetCode: 0
Status:   OK  
CheckDir: rgoslin.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rgoslin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rgoslin_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rgoslin.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgoslin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgoslin’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rgoslin’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rgoslin/libs/rgoslin.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)

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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/rgoslin.Rcheck/00check.log’
for details.


Installation output

rgoslin.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rgoslin
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘rgoslin’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
The name of the shared library to be created is: rgoslin.so
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.so
rm -f *Test
rm -f writeGrammarsHeader
rm -f writeLipidEnums
rm -f libcppGoslin.a
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I . -o writeGrammarsHeader writeGrammarsHeader.cpp && "./writeGrammarsHeader" "cppgoslin/parser/KnownGrammars.h"
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I . -o writeLipidEnums writeLipidEnums.cpp src/domain/StringFunctions.cpp src/parser/SumFormulaParserEventHandler.cpp src/parser/ParserClasses.cpp && "./writeLipidEnums" "src/domain/LipidClasses.cpp"
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/Adduct.o -c src/domain/Adduct.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidMolecularSpecies.o -c src/domain/LipidMolecularSpecies.cpp
In file included from src/domain/LipidMolecularSpecies.cpp:26:
In file included from ./cppgoslin/domain/LipidMolecularSpecies.h:32:
In file included from ./cppgoslin/domain/LipidSpecies.h:36:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidSnPosition.o -c src/domain/LipidSnPosition.cpp
In file included from src/domain/LipidSnPosition.cpp:26:
In file included from ./cppgoslin/domain/LipidSnPosition.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidStructureDefined.o -c src/domain/LipidStructureDefined.cpp
In file included from src/domain/LipidStructureDefined.cpp:26:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/FattyAcid.o -c src/domain/FattyAcid.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidAdduct.o -c src/domain/LipidAdduct.cpp
In file included from src/domain/LipidAdduct.cpp:26:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidSpecies.o -c src/domain/LipidSpecies.cpp
In file included from src/domain/LipidSpecies.cpp:26:
In file included from ./cppgoslin/domain/LipidSpecies.h:36:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidFullStructure.o -c src/domain/LipidFullStructure.cpp
In file included from src/domain/LipidFullStructure.cpp:26:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidCompleteStructure.o -c src/domain/LipidCompleteStructure.cpp
In file included from src/domain/LipidCompleteStructure.cpp:26:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidSpeciesInfo.o -c src/domain/LipidSpeciesInfo.cpp
In file included from src/domain/LipidSpeciesInfo.cpp:26:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/StringFunctions.o -c src/domain/StringFunctions.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidClasses.o -c src/domain/LipidClasses.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/DoubleBonds.o -c src/domain/DoubleBonds.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/FunctionalGroup.o -c src/domain/FunctionalGroup.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/Headgroup.o -c src/domain/Headgroup.cpp
In file included from src/domain/Headgroup.cpp:26:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/Cycle.o -c src/domain/Cycle.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/GenericDatastructures.o -c src/domain/GenericDatastructures.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/ParserClasses.o -c src/parser/ParserClasses.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/KnownParsers.o -c src/parser/KnownParsers.cpp
In file included from src/parser/KnownParsers.cpp:26:
In file included from ./cppgoslin/parser/KnownParsers.h:30:
In file included from ./cppgoslin/parser/FattyAcidParserEventHandler.h:31:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/GoslinParserEventHandler.o -c src/parser/GoslinParserEventHandler.cpp
In file included from src/parser/GoslinParserEventHandler.cpp:26:
In file included from ./cppgoslin/parser/GoslinParserEventHandler.h:31:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/LipidMapsParserEventHandler.o -c src/parser/LipidMapsParserEventHandler.cpp
In file included from src/parser/LipidMapsParserEventHandler.cpp:26:
In file included from ./cppgoslin/parser/LipidMapsParserEventHandler.h:31:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/SwissLipidsParserEventHandler.o -c src/parser/SwissLipidsParserEventHandler.cpp
In file included from src/parser/SwissLipidsParserEventHandler.cpp:26:
In file included from ./cppgoslin/parser/SwissLipidsParserEventHandler.h:32:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/HmdbParserEventHandler.o -c src/parser/HmdbParserEventHandler.cpp
In file included from src/parser/HmdbParserEventHandler.cpp:26:
In file included from ./cppgoslin/parser/HmdbParserEventHandler.h:31:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/SumFormulaParserEventHandler.o -c src/parser/SumFormulaParserEventHandler.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/SumFormulaParser.o -c src/parser/SumFormulaParser.cpp
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/ShorthandParserEventHandler.o -c src/parser/ShorthandParserEventHandler.cpp
In file included from src/parser/ShorthandParserEventHandler.cpp:26:
In file included from ./cppgoslin/parser/ShorthandParserEventHandler.h:32:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/FattyAcidParserEventHandler.o -c src/parser/FattyAcidParserEventHandler.cpp
In file included from src/parser/FattyAcidParserEventHandler.cpp:26:
In file included from ./cppgoslin/parser/FattyAcidParserEventHandler.h:31:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/LipidBaseParserEventHandler.o -c src/parser/LipidBaseParserEventHandler.cpp
In file included from src/parser/LipidBaseParserEventHandler.cpp:26:
In file included from ./cppgoslin/parser/LipidBaseParserEventHandler.h:31:
In file included from ./cppgoslin/domain/LipidAdduct.h:35:
In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31:
In file included from ./cppgoslin/domain/LipidFullStructure.h:31:
In file included from ./cppgoslin/domain/LipidStructureDefined.h:32:
In file included from ./cppgoslin/domain/Headgroup.h:31:
./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
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
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rgoslin.cpp -o rgoslin.o
In file included from rgoslin.cpp:3:
In file included from ./cppgoslin/cppgoslin/cppgoslin.h:37:
In file included from ./cppgoslin/cppgoslin/domain/Headgroup.h:31:
./cppgoslin/cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual]
    string to_string();
           ^
./cppgoslin/cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0)
    string to_string(LipidLevel level);
           ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o rgoslin.so RcppExports.o rgoslin.o cppgoslin/libcppGoslin.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-rgoslin/00new/rgoslin/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rgoslin)

Tests output

rgoslin.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rgoslin)
> 
> test_check("rgoslin")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 341 ]
> 
> proc.time()
   user  system elapsed 
  6.299   0.431   7.686 

Example timings

rgoslin.Rcheck/rgoslin-Ex.timings

nameusersystemelapsed
isValidLipidName0.1680.0080.200
listAvailableGrammars0.0010.0010.003
parseLipidNames1.3380.0861.667