Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the rsbml package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rsbml.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1635/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rsbml 2.50.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
Package: rsbml |
Version: 2.50.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rsbml.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rsbml_2.50.0.tar.gz |
StartedAt: 2021-10-14 11:25:33 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:26:08 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 34.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rsbml.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rsbml.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rsbml_2.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/rsbml.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rsbml/DESCRIPTION’ ... OK * this is package ‘rsbml’ version ‘2.50.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘rsbml’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocGenerics’ ‘utils’ A package should be listed in only one of these fields. * checking top-level files ... NOTE Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred. * 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 ... NOTE Namespace in Imports field not imported from: ‘utils’ All declared Imports should be used. Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘graph:::listLen’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: as.character.SBML as.character.SBMLDocument See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .simulate.SBML: no visible global function definition for ‘tail’ .simulate.SBML: no visible global function definition for ‘new’ .simulate.SBML: no visible global function definition for ‘is’ .simulate.SBML : <anonymous>: no visible global function definition for ‘head’ .simulate.SBML: no visible global function definition for ‘slotNames’ .simulate.SBML: no visible binding for global variable ‘new’ as.ts,SOSResult: no visible global function definition for ‘ts’ coerce,SBMLProblems-character: no visible binding for global variable ‘as’ describe,CompartmentGlyph: no visible global function definition for ‘callNextMethod’ describe,CubicBezier: no visible global function definition for ‘callNextMethod’ describe,ReactionGlyph: no visible global function definition for ‘callNextMethod’ describe,SpeciesGlyph: no visible global function definition for ‘callNextMethod’ describe,SpeciesReference: no visible global function definition for ‘callNextMethod’ describe,SpeciesReferenceGlyph: no visible global function definition for ‘callNextMethod’ describe,TextGlyph: no visible global function definition for ‘callNextMethod’ end<-,LineSegment: no visible binding for global variable ‘object’ glyphCurve<-,ReactionGlyph: no visible global function definition for ‘new’ glyphCurve<-,SpeciesReferenceGlyph: no visible global function definition for ‘new’ kineticLaw<-,Reaction: no visible global function definition for ‘new’ rsbml_graph,Model: no visible global function definition for ‘new’ rsbml_problems,SBMLDocument : makeProblems : <anonymous>: no visible binding for global variable ‘new’ rsbml_problems,SBMLDocument: no visible binding for global variable ‘new’ show,SBMLProblem: no visible global function definition for ‘as’ simulate,SBMLDocument: no visible global function definition for ‘tail’ simulate,SBMLDocument: no visible global function definition for ‘new’ simulate,SBMLDocument: no visible global function definition for ‘is’ simulate,SBMLDocument : <anonymous>: no visible global function definition for ‘head’ simulate,SBMLDocument: no visible global function definition for ‘slotNames’ simulate,SBMLDocument: no visible binding for global variable ‘new’ simulate,SOSExperiment: no visible global function definition for ‘slotNames’ simulate,SOSExperiment : <anonymous>: no visible global function definition for ‘slot’ Undefined global functions or variables: as callNextMethod head is new object slot slotNames tail ts Consider adding importFrom("methods", "as", "callNextMethod", "is", "new", "slot", "slotNames") importFrom("stats", "ts") importFrom("utils", "head", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘asMath’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * 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 * checking files in ‘vignettes’ ... OK * checking examples ... 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 WARNING, 8 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/rsbml.Rcheck/00check.log’ for details.
rsbml.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL rsbml ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘rsbml’ ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for LIBSBML... yes configure: === Begin local SOSLib build === checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking whether gcc accepts -fpic... yes checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for autoconf... /usr/bin/autoconf checking for aclocal... /usr/bin/aclocal checking for make... /usr/bin/make checking for ar... /usr/bin/ar checking for swig... swig checking for perl... /usr/bin/perl checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for SBML... no configure: WARNING: libsbml 3.0 not found by pkg-config checking for SBML Library headers... yes checking for SBML Library... checking for correct functioning of SBML... no: CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -I/usr/include -I/usr/include/sbml LDFLAGS= LIBS=-lm -lstdc++ configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 3.0.2 or CVS configure: === End local SOSLib build === configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c StringMap.c -o StringMap.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c check.c -o check.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c doc.c -o doc.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c dom.c -o dom.o dom.c: In function ‘rsbml_build_dom_line_segment’: dom.c:687:12: warning: comparison between ‘SBMLTypeCode_t’ {aka ‘enum <anonymous>’} and ‘enum <anonymous>’ [-Wenum-compare] 687 | if (type == SBML_LAYOUT_CUBICBEZIER) { | ^~ dom.c:693:19: warning: comparison between ‘SBMLTypeCode_t’ {aka ‘enum <anonymous>’} and ‘enum <anonymous>’ [-Wenum-compare] 693 | } else if (type == SBML_LAYOUT_LINESEGMENT) | ^~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c graph.c -o graph.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c io.c -o io.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c layoutWrappers.cpp -o layoutWrappers.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c mathml.c -o mathml.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c simulate.c -o simulate.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -lsbml -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-rsbml/00new/rsbml/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 (rsbml)
rsbml.Rcheck/rsbml-Ex.timings
name | user | system | elapsed | |
SBML-class | 0.077 | 0.004 | 0.086 | |
SBMLDocument-class | 0.102 | 0.012 | 0.115 | |
read | 0.102 | 0.000 | 0.103 | |