rsbml 2.0.0
Michael Lawrence
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/rsbml | | Last Changed Rev: 34841 / Revision: 38965 | | Last Changed Date: 2008-10-22 10:15:39 -0700 (Wed, 22 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/rsbml.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'rsbml/DESCRIPTION' ... OK
* this is package 'rsbml' version '2.0.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rsbml' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating rsbml-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating rsbml-manual.tex ... OK
* checking rsbml-manual.tex using pdflatex ... OK
* Installing *source* package 'rsbml' ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML3... 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... config/install-sh -c -d
checking for gawk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin9.6.0
checking host system type... i386-apple-darwin9.6.0
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... /usr/bin/swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/local/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
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c StringMap.c -o StringMap.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c check.c -o check.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c doc.c -o doc.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c dom.c -o dom.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c graph.c -o graph.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c io.c -o io.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c mathml.c -o mathml.o
mathml.c: In function 'rmathml_SEXP':
mathml.c:56: warning: unused variable 'closure'
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -g -O2 -Wall -c simulate.c -o simulate.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o mathml.o simulate.o -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
Loading required package: graph
** help
>>> Building/Updating help pages for package 'rsbml'
Formats: text html latex example
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** building package indices ...
* DONE (rsbml)