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This page was generated on 2021-08-05 12:06:07 -0400 (Thu, 05 Aug 2021).

INSTALL results for rsbml on nebbiolo2

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.

raw results

Package 1610/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.51.0  (landing page)
Michael Lawrence
Snapshot Date: 2021-08-04 14:50:10 -0400 (Wed, 04 Aug 2021)
URL: https://git.bioconductor.org/packages/rsbml
Branch: master
Last Commit: e69392a
Last Changed Date: 2021-05-19 11:39:45 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: rsbml
Version: 2.51.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rsbml
StartedAt: 2021-08-04 16:04:05 -0400 (Wed, 04 Aug 2021)
EndedAt: 2021-08-04 16:04:22 -0400 (Wed, 04 Aug 2021)
EllapsedTime: 17.7 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rsbml
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)