Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1736/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rgoslin 1.10.0 (landing page) Nils Hoffmann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: rgoslin |
Version: 1.10.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rgoslin.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rgoslin_1.10.0.tar.gz |
StartedAt: 2024-12-20 05:14:00 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:15:10 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 69.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rgoslin.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rgoslin.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rgoslin_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/rgoslin.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'rgoslin/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rgoslin' version '1.10.0' * 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 whether package 'rgoslin' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/rgoslin/libs/x64/rgoslin.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 'F:/biocbuild/bbs-3.20-bioc/meat/rgoslin.Rcheck/00check.log' for details.
rgoslin.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rgoslin ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'rgoslin' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++11 The name of the shared library to be created is: rgoslin.dll make[1]: Entering directory '/f/biocbuild/bbs-3.20-bioc/meat/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-3.20-bioc/meat/rgoslin/src/cppgoslin' make[1]: Entering directory '/f/biocbuild/bbs-3.20-bioc/meat/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 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-3.20-bioc/meat/rgoslin/src/cppgoslin' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'F:/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'F:/biocbuild/bbs-3.20-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-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/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 * DONE (rgoslin)
rgoslin.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 2.87 0.31 3.23
rgoslin.Rcheck/rgoslin-Ex.timings
name | user | system | elapsed | |
isValidLipidName | 0.16 | 0.01 | 0.21 | |
listAvailableGrammars | 0 | 0 | 0 | |
parseLipidNames | 0.63 | 0.02 | 0.64 | |