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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1723/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgoslin 1.11.0  (landing page)
Nils Hoffmann
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/rgoslin
git_branch: devel
git_last_commit: f32d084
git_last_commit_date: 2024-10-29 11:09:15 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for rgoslin on kjohnson3

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: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2024-12-23 21:00:14 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 21:00:27 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 13.2 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rgoslin.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgoslin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgoslin’ version ‘1.11.0’
* 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 ... NOTE
Found the following non-portable file paths:
  rgoslin/src/cppgoslin/writeGrammarsHeader.dSYM/Contents/Resources/Relocations/aarch64/writeGrammarsHeader.yml
  rgoslin/src/cppgoslin/writeLipidEnums.dSYM/Contents/Resources/Relocations/aarch64/writeLipidEnums.yml

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rgoslin’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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/4.5-arm64/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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’
* installing *source* package ‘rgoslin’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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 arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I . -o writeGrammarsHeader writeGrammarsHeader.cpp && "./writeGrammarsHeader" "cppgoslin/parser/KnownGrammars.h"
clang++ -arch arm64 -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 arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/Adduct.o -c src/domain/Adduct.cpp
clang++ -arch arm64 -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 arm64 -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 arm64 -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 arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/FattyAcid.o -c src/domain/FattyAcid.cpp
clang++ -arch arm64 -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 arm64 -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 arm64 -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 arm64 -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 arm64 -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 arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/StringFunctions.o -c src/domain/StringFunctions.cpp
clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/LipidClasses.o -c src/domain/LipidClasses.cpp
clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/DoubleBonds.o -c src/domain/DoubleBonds.cpp
clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/FunctionalGroup.o -c src/domain/FunctionalGroup.cpp
clang++ -arch arm64 -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 arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/Cycle.o -c src/domain/Cycle.cpp
clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/domain/GenericDatastructures.o -c src/domain/GenericDatastructures.cpp
clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/ParserClasses.o -c src/parser/ParserClasses.cpp
clang++ -arch arm64 -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 arm64 -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 arm64 -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 arm64 -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 arm64 -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 arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/SumFormulaParserEventHandler.o -c src/parser/SumFormulaParserEventHandler.cpp
clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2  -I. -fPIC -o src/parser/SumFormulaParser.o -c src/parser/SumFormulaParser.cpp
clang++ -arch arm64 -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 arm64 -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 arm64 -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 arm64 -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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 arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.5-arm64/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


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Platform: aarch64-apple-darwin20

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> library(testthat)
> library(rgoslin)
> 
> test_check("rgoslin")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 341 ]
> 
> proc.time()
   user  system elapsed 
  0.839   0.073   0.910 

Example timings

rgoslin.Rcheck/rgoslin-Ex.timings

nameusersystemelapsed
isValidLipidName0.0310.0020.033
listAvailableGrammars000
parseLipidNames0.1880.0090.198