Package: Rredland

Version: 1.4.0

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check Rredland_1.4.0.tar.gz

RetCode: 1

Time: 102.5 seconds

Status: ERROR

CheckDir: Rredland.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.0-bioc/meat/Rredland.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'Rredland/DESCRIPTION' ... OK
* this is package 'Rredland' version '1.4.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rredland' 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 name space 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 data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating Rredland-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'Rredland-Ex.R' failed.
The error most likely occurred in:

> ### * readRDF
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: readRDF
> ### Title: read an RDF document identified by URI (or deserialize a redland
> ###   Berkeley DB representation) into a librdf model object
> ### Aliases: readRDF restoreBDB
> ### Keywords: models
> 
> ### ** Examples
> 
> # use character string URI 
> ii = readRDF(paste("file:", system.file("RDF/gopart.rdf", package="Rredland"),
+         sep=""))
> ii
redlModel object, status=open.
> freeRedl(ii)
>         # make a URI for a fragment from GO distributed with the package
> example(makeRedlURI)

mkRURI> fi <- system.file("RDF/gopart.rdf", package="Rredland")

mkRURI> uu <- makeRedlURI(paste("file:",fi,sep=""))

mkRURI> uu
redlURI object with URIstring:
 file:/extra/loc/biocbuild/bbs-2.0-bioc/meat/Rredland.Rcheck/Rredland/RDF/gopart.rdf 
>         # read from it with defaults
> mm = readRDF(uu)
> mm
redlModel object, status=open.
>         # excerpt after transformation to data.frame
> as(mm, "data.frame")[1:3,]
                          subject
1 urn:lsid:uniprot.org:go:0000001
2 urn:lsid:uniprot.org:go:0000001
3 urn:lsid:uniprot.org:go:0000001
                                        predicate
1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type
2      http://www.w3.org/2000/01/rdf-schema#label
3    http://www.w3.org/2000/01/rdf-schema#comment
                                                                                                                                                                                     object
1                                                                                                                                                     urn:lsid:uniprot.org:ontology:Concept
2                                                                                                                                                               "mitochondrion inheritance"
3 "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton."
>         # now we will do some disk operations with BDB
> curd = getwd()
> tt = tempdir()
>         # change dir
> setwd(tt)
>         # read contents of previous URI, but use external storage
> hh = readRDF(uu, storageType="bdb", storageName="gopart")
Error in readRDF(uu, storageType = "bdb", storageName = "gopart") : 
	failed to create new storage
Execution halted

* Installing *source* package 'Rredland' ...
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 ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... 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 for BerkeleyDB... yes
checking db.h usability... yes
checking db.h presence... yes
checking for db.h... yes
checking whether compiling/linking BerkeleyDB code works... yes
checking BerkeleyDB in /usr... ok
checking for pkg-config... /usr/bin/pkg-config
checking for redland-config... /usr/local/bin/redland-config
checking for redland... yes
checking PKG_CFLAGS... -I/usr/local/include  
checking PKG_LIBS... -L/usr/local/lib -L/usr/lib/mysql -L/usr/ssl/lib -lrdf -lmysqlclient -lcrypt -lnsl -lpq -lrasqal -lraptor -lcurl -lssl -lcrypto -ldl -lxml2 -lz -lpthread -lm  
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/include -I/usr/local/include   -I/usr/local/include   -fpic  -g -O2 -Wall -c Rredl.c -o Rredl.o
Rredl.c: In function `get_rdfnode_ref':
Rredl.c:314: warning: `node' might be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib -o Rredland.so Rredl.o -L/usr/local/lib -L/usr/lib/mysql -L/usr/ssl/lib -lrdf -lmysqlclient -lcrypt -lnsl -lpq -lrasqal -lraptor -lcurl -lssl -lcrypto -ldl -lxml2 -lz -lpthread -lm     -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
** inst
** save image
Loading required package: graph
** help
 >>> Building/Updating help pages for package 'Rredland'
     Formats: text html latex example 
  cleanXSDT                         text    html    latex   example
  getProperties                     text    html    latex   example
  gordb                             text    html    latex   example
  makeRedlURI                       text    html    latex   example
  readRDF                           text    html    latex   example
  redlModel-class                   text    html    latex   example
  redlWorld-class                   text    html    latex   example
** building package indices ...
* DONE (Rredland)