Nils Hoffmann
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/rgoslin |
| git_branch: RELEASE_3_17 |
| git_last_commit: 92d8ff1 |
| git_last_commit_date: 2023-04-25 11:36:36 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1702/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rgoslin 1.4.0 (landing page) Nils Hoffmann
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the rgoslin package: - 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: rgoslin |
| Version: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2023-10-18 18:45:55 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 18:46:45 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 50.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rgoslin.Rcheck |
| Warnings: 0 |
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###
### 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rgoslin.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgoslin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgoslin’ version ‘1.4.0’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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/4.3-arm64/Resources/library/rgoslin/libs/rgoslin.so’:
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rgoslin.Rcheck/00check.log’
for details.
rgoslin.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rgoslin
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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:52:12: 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/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -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/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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:52:12: 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 -single_module -multiply_defined suppress -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/4.3-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)
rgoslin.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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.
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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
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> library(testthat)
> library(rgoslin)
>
> test_check("rgoslin")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 333 ]
>
> proc.time()
user system elapsed
3.011 0.170 4.196
rgoslin.Rcheck/rgoslin-Ex.timings
| name | user | system | elapsed | |
| isValidLipidName | 0.089 | 0.004 | 0.128 | |
| listAvailableGrammars | 0.000 | 0.000 | 0.001 | |
| parseLipidNames | 0.701 | 0.050 | 0.978 | |