merida1 Summary
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Package: rgoslin |
Version: 0.99.9 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rgoslin |
BuildTime: 2 minutes 54.36 seconds |
CheckCommand: BiocCheckGitClone('rgoslin') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rgoslin_0.99.9.tar.gz && BiocCheck('rgoslin_0.99.9.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 15.10 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh rgoslin_0.99.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 2 minutes 37.46 seconds |
PackageFileSize: 1419.60 KiB |
BuildID:: rgoslin_20220322181524 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: rgoslin. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘rgoslin/DESCRIPTION’ ... OK
* preparing ‘rgoslin’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘rgoslin_0.99.9.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('rgoslin')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2485/62b02b2642d603eab399ca18ec2b08b902f72f04/rgoslin.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgoslin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgoslin’ version ‘0.99.9’
* 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 serialization versions ... OK
* checking whether package ‘rgoslin’ can be installed ... [157s/157s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [3s/3s]
[3s/3s] 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: OK
===============================
BiocCheck('rgoslin_0.99.9.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2485/62b02b2642d603eab399ca18ec2b08b902f72f04/rgoslin_0.99.9.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpBBu0TB/fileefd638c5d8d3/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of rgoslin...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/rgoslin.R (line 82, column 17)
R/rgoslin.R (line 106, column 17)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
parseLipidNames() (R/rgoslin.R, line 49): 73 lines
_anonymous_.69() (R/rgoslin.R, line 69): 25 lines
_anonymous_.93() (R/rgoslin.R, line 93): 25 lines
isValidLipidName() (R/rgoslin.R, line 19): 8 lines
rcpp_is_valid_lipid_name() (R/RcppExports.R, line 3): 3 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 61 lines (11%) are > 80 characters
long.
First 6 lines:
R/RcppExports.R:9 .Call(`_rgoslin_rcpp_parse_lipid_name_with_gramma...
R/rgoslin-package.R:2 #' rgoslin is the R implementation of the "gramma...
R/rgoslin-package.R:3 #' implementations for parsing of shorthand lipid...
man/rgoslin-package.Rd:9 The R implementation for the Grammar of Succin...
man/rgoslin-package.Rd:12 rgoslin is the R implementation of the "gramm...
man/rgoslin-package.Rd:13 implementations for parsing of shorthand lipi...
* NOTE: Consider multiples of 4 spaces for line indents, 4
lines(1%) are not.
First 4 lines:
man/rgoslin-package.Rd:21 \item \url{https://github.com/lifs-tools/rg...
man/rgoslin-package.Rd:22 \item Report bugs at \url{https://github.co...
man/rgoslin-package.Rd:31 \item Dominik Kopczynski \email{dominik.kop...
vignettes/introduction.Rmd:6 affiliation: Forschungszentrum Jülich, I...
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 4
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir rgoslin_0.99.9.tar.gz'
>>>>>>>
* installing *source* package ‘rgoslin’ ...
** using staged installation
** libs
The name of the shared library to be created is: rgoslin.so
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++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I . -o writeGrammarsHeader writeGrammarsHeader.cpp && ./writeGrammarsHeader "cppgoslin/parser/KnownGrammars.h"
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/Adduct.o -c src/domain/Adduct.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/FattyAcid.o -c src/domain/FattyAcid.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/StringFunctions.o -c src/domain/StringFunctions.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/LipidClasses.o -c src/domain/LipidClasses.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/DoubleBonds.o -c src/domain/DoubleBonds.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/FunctionalGroup.o -c src/domain/FunctionalGroup.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/Cycle.o -c src/domain/Cycle.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/domain/GenericDatastructures.o -c src/domain/GenericDatastructures.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/parser/ParserClasses.o -c src/parser/ParserClasses.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/parser/SumFormulaParserEventHandler.o -c src/parser/SumFormulaParserEventHandler.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -Wall -g -O2 -I. -fPIC -o src/parser/SumFormulaParser.o -c src/parser/SumFormulaParser.cpp
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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++ -mmacosx-version-min=10.13 -std=gnu++11 -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/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.
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++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -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/usr/local/lib -o rgoslin.so RcppExports.o rgoslin.o cppgoslin/libcppGoslin.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2485/62b02b2642d603eab399ca18ec2b08b902f72f04/libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/rgoslin/libs/rgoslin.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "libdir/rgoslin/libs/rgoslin.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/rgoslin/libs/rgoslin.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/rgoslin/libs/rgoslin.so"
nebbiolo1 Summary
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Package: rgoslin |
Version: 0.99.9 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rgoslin |
BuildTime: 2 minutes 8.66 seconds |
CheckCommand: BiocCheckGitClone('rgoslin') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings rgoslin_0.99.9.tar.gz && BiocCheck('rgoslin_0.99.9.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 12.38 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 627.15 KiB |
BuildID:: rgoslin_20220322181524 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: rgoslin. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘rgoslin/DESCRIPTION’ ... OK
* preparing ‘rgoslin’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘rgoslin_0.99.9.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('rgoslin')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2485/62b02b2642d603eab399ca18ec2b08b902f72f04/rgoslin.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgoslin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgoslin’ version ‘0.99.9’
* 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 serialization versions ... OK
* checking whether package ‘rgoslin’ can be installed ... [113s/114s] OK
* checking installed package size ... NOTE
installed size is 16.4Mb
sub-directories of 1Mb or more:
libs 15.6Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/2s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2485/62b02b2642d603eab399ca18ec2b08b902f72f04/rgoslin.Rcheck/00check.log’
for details.
===============================
BiocCheck('rgoslin_0.99.9.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2485/62b02b2642d603eab399ca18ec2b08b902f72f04/rgoslin_0.99.9.tar.gz" "/tmp/Rtmp66yZBI/file1703545ba1daf0/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of rgoslin...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/rgoslin.R (line 82, column 17)
R/rgoslin.R (line 106, column 17)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
parseLipidNames() (R/rgoslin.R, line 49): 73 lines
_anonymous_.69() (R/rgoslin.R, line 69): 25 lines
_anonymous_.93() (R/rgoslin.R, line 93): 25 lines
isValidLipidName() (R/rgoslin.R, line 19): 8 lines
rcpp_is_valid_lipid_name() (R/RcppExports.R, line 3): 3 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 61 lines (11%) are > 80 characters
long.
First 6 lines:
R/RcppExports.R:9 .Call(`_rgoslin_rcpp_parse_lipid_name_with_gramma...
R/rgoslin-package.R:2 #' rgoslin is the R implementation of the "gramma...
R/rgoslin-package.R:3 #' implementations for parsing of shorthand lipid...
man/rgoslin-package.Rd:9 The R implementation for the Grammar of Succin...
man/rgoslin-package.Rd:12 rgoslin is the R implementation of the "gramm...
man/rgoslin-package.Rd:13 implementations for parsing of shorthand lipi...
* NOTE: Consider multiples of 4 spaces for line indents, 4
lines(1%) are not.
First 4 lines:
man/rgoslin-package.Rd:21 \item \url{https://github.com/lifs-tools/rg...
man/rgoslin-package.Rd:22 \item Report bugs at \url{https://github.co...
man/rgoslin-package.Rd:31 \item Dominik Kopczynski \email{dominik.kop...
vignettes/introduction.Rmd:6 affiliation: Forschungszentrum Jülich, I...
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 4
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
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