rsbml 2.9.1
Michael Lawrence
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rsbml | | Last Changed Rev: 50783 / Revision: 53255 | | Last Changed Date: 2010-11-10 05:31:14 -0800 (Wed, 10 Nov 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | N O T S U P P O R T E D |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | ERROR | skipped | skipped |
* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/rsbml.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rsbml/DESCRIPTION’ ... OK
* this is package ‘rsbml’ version ‘2.9.1’
* checking package name space information ... OK
* 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 whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'Event-class':
Slots for class 'Event'
Code: annotation cvTerms eventAssignments eventDelay id metaId name
notes sboTerm timeUnits trigger useValuesFromTriggerTime
Inherited: metaId notes annotation cvTerms sboTerm
Docs: annotation cvTerms eventAssignments eventDelay id metaId name
notes sboTerm timeUnits trigger
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
‘/loc/home/biocbuild/bbs-2.8-bioc/meat/rsbml.Rcheck/00check.log’
for details
* 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 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... /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... /usr/bin/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 -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c StringMap.c -o StringMap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c check.c -o check.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c doc.c -o doc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c dom.c -o dom.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c mathml.c -o mathml.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -fpic -g -O2 -c simulate.c -o simulate.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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 -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/rsbml.Rcheck/rsbml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (rsbml)