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This page was generated on 2022-06-24 11:05:47 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

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? 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 1686/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsbml 2.55.0  (landing page)
Michael Lawrence
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/rsbml
git_branch: master
git_last_commit: 52ab642
git_last_commit_date: 2022-04-26 11:00:24 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64... NOT SUPPORTED ...

Summary

Package: rsbml
Version: 2.55.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL rsbml
StartedAt: 2022-06-23 15:07:09 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 15:07:26 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 17.6 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL rsbml
###
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* installing to library ‘/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-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-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-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)