Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:08:09 -0400 (Thu, 12 Apr 2018).
Package 1217/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
rsbml 2.36.0 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | [ OK ] | OK | WARNINGS | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | ![]() |
Package: rsbml |
Version: 2.36.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL rsbml |
StartedAt: 2018-04-11 17:57:11 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 17:57:22 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 11.1 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL rsbml ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.6-bioc/R/library’ * installing *source* package ‘rsbml’ ... 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... /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... yes checking for correct functioning of SBML... yes checking for SUNDIALS Library headers... checking for SUNDIALS Library... checking correct functioning of SUNDIALS... no: CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 LDFLAGS= LIBS= -lm -lstdc++ configure: error: Can not link to SUNDIALS Library configure: === End local SOSLib build === configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c StringMap.c -o StringMap.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c check.c -o check.o In file included from check.c:1:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from check.c:1: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c doc.c -o doc.o In file included from doc.c:1:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from doc.c:1: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c dom.c -o dom.o In file included from dom.c:1:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from dom.c:1: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ 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] if (type == SBML_LAYOUT_CUBICBEZIER) { ^ dom.c:693:19: warning: comparison between ‘SBMLTypeCode_t {aka enum <anonymous>}’ and ‘enum <anonymous>’ [-Wenum-compare] } else if (type == SBML_LAYOUT_LINESEGMENT) ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c graph.c -o graph.o In file included from graph.c:1:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from graph.c:1: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o In file included from init.c:1:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from init.c:1: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c io.c -o io.o In file included from io.c:1:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from io.c:1: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c layoutWrappers.cpp -o layoutWrappers.o In file included from layoutWrappers.cpp:1:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from layoutWrappers.cpp:1: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c mathml.c -o mathml.o In file included from mathml.c:3:0: rsbml.h:8:0: warning: "USE_LAYOUT" redefined #define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT ^ In file included from /usr/local/include/sbml/common/libsbml-config.h:66:0, from /usr/local/include/sbml/common/sbmlfwd.h:45, from /usr/local/include/sbml/SBMLTypes.h:37, from rsbml.h:1, from mathml.c:3: /usr/local/include/sbml/common/libsbml-config-common.h:93:0: note: this is the location of the previous definition #define USE_LAYOUT 1 ^ gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c simulate.c -o simulate.o g++ -shared -L/home/biocbuild/bbs-3.6-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 -L/usr/local/lib -lxml2 -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/R/library/rsbml/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rsbml)