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Package 206/251HostnameOS / ArchBUILDCHECKBUILD BIN
rsbml 1.5.0
Michael Lawrence
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rsbml
Last Changed Rev: 28215 / Revision: 29143
Last Changed Date: 2007-10-24 23:39:53 -0700 (Wed, 24 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK [ WARNINGS ]
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  WARNINGS  OK 
Package: rsbml
Version: 1.5.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check rsbml_1.5.0.tar.gz
StartedAt: 2007-12-11 04:49:46 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 04:50:25 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 39.8 seconds
RetCode: 0
Status: WARNINGS
CheckDir: rsbml.Rcheck
Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/rsbml.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'rsbml/DESCRIPTION' ... OK
* this is package 'rsbml' version '1.5.0'
* 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 ... WARNING
Rd files without 'description':
  Species-class.Rd
These entries are required in an Rd file.

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './quick-start.tex' ...
Package natbib Warning: Citation `sbmlr' on page 1 undefined on input line 16.
Package natbib Warning: Citation `libsbml' on page 1 undefined on input line 17
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './quick-start.tex' ...
Package natbib Warning: Citation `sbmlr' on page 1 undefined on input line 16.
Package natbib Warning: Citation `libsbml' on page 1 undefined on input line 17
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './quick-start.tex' ...
* creating rsbml-manual.tex ... OK
* checking rsbml-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/rsbml.Rcheck/00check.log
for details

rsbml.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/rsbml.Rcheck
* Installing *source* package 'rsbml' ...
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking SBMLDocument.h usability... yes
checking SBMLDocument.h presence... yes
checking for SBMLDocument.h... yes
checking for SBMLDocument_create in -lsbml... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include    -fpic  -g -O2 -Wall -c check.c -o check.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include    -fpic  -g -O2 -Wall -c doc.c -o doc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include    -fpic  -g -O2 -Wall -c dom.c -o dom.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include    -fpic  -g -O2 -Wall -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include    -fpic  -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/include/sbml -I/usr/local/include/sbml -I/usr/local/include    -fpic  -g -O2 -Wall -c io.c -o io.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o rsbml.so check.o doc.o dom.o graph.o init.o io.o -lsbml   -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: graph
New generic for "curve" does not agree with implicit generic from package "graphics"; a new generic will be assigned with package "rsbml"
New generic for "delay" does not agree with implicit generic from package "base"; a new generic will be assigned with package "rsbml"
New generic for "scale" does not agree with implicit generic from package "base"; a new generic will be assigned with package "rsbml"
** help
Note: removing empty section \description
 >>> Building/Updating help pages for package 'rsbml'
     Formats: text html latex example 
  AlgebraicRule-class               text    html    latex
  AssignmentRule-class              text    html    latex
  BoundingBox-class                 text    html    latex
  Compartment-class                 text    html    latex
  CompartmentGlyph-class            text    html    latex
  CompartmentType-class             text    html    latex
  CompartmentVolumeRule-class       text    html    latex
  Constraint-class                  text    html    latex
  CubicBezier-class                 text    html    latex
  Curve-class                       text    html    latex
  Delay-class                       text    html    latex
  Dimensions-class                  text    html    latex
  Event-class                       text    html    latex
  EventAssignment-class             text    html    latex
  FunctionDefinition-class          text    html    latex
  GraphicalObject-class             text    html    latex
  InitialAssignment-class           text    html    latex
  KineticLaw-class                  text    html    latex
  Layout-class                      text    html    latex
  LineSegment-class                 text    html    latex
  Model-class                       text    html    latex
  ModifierSpeciesReference-class    text    html    latex
  Parameter-class                   text    html    latex
  ParameterRule-class               text    html    latex
  Point-class                       text    html    latex
  RateRule-class                    text    html    latex
  Reaction-class                    text    html    latex
  ReactionGlyph-class               text    html    latex
  Rule-class                        text    html    latex
  SBML-class                        text    html    latex   example
  SBMLDocument-class                text    html    latex   example
  SBase-class                       text    html    latex
  SimpleSpeciesReference-class      text    html    latex
  Species-class                     text    html    latex
  SpeciesConcentrationRule-class    text    html    latex
  SpeciesGlyph-class                text    html    latex
  SpeciesReference-class            text    html    latex
  SpeciesReferenceGlyph-class       text    html    latex
  SpeciesType-class                 text    html    latex
  StoichiometryMath-class           text    html    latex
  TextGlyph-class                   text    html    latex
  Trigger-class                     text    html    latex
  Unit-class                        text    html    latex
  UnitDefinition-class              text    html    latex
  read                              text    html    latex   example
** building package indices ...
* DONE (rsbml)