CHECK report for Rredland on gladstone

* checking for working latex ... OK * using log directory '/home/biocbuild/1.9d/Rpacks/Rredland.Rcheck' * using R version 2.4.0 alpha (2006-09-10 r39242) * checking for file 'Rredland/DESCRIPTION' ... OK * this is package 'Rredland' version '1.1.3' * 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 ... WARNING Found the following non-empty subdirectories of 'inst' also used by R: libs It is recommended not to interfere with package subdirectories used by R. * checking R files for syntax errors ... OK * checking R files for non-ASCII characters ... 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 ... WARNING Error in .asEnvironmentPackage(where) : Package 'methods' is not loaded Error: unable to load R code in package 'Ruuid' Execution halted A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 ... WARNING Undocumented data sets: EMAPdf gordb All user-level objects in a package should have documentation entries. See the chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C/C++/Fortran sources/headers ... OK * checking for portable compilation flags in Makevars ... WARNING Non-portable flags in variable 'PKG_CFLAGS': -Wall * checking for portable use of $BLAS_LIBS ... OK * creating Rredland-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating Rredland-manual.tex ... OK * checking Rredland-manual.tex ... OK WARNING: There were 4 warnings, see /home/biocbuild/1.9d/Rpacks/Rredland.Rcheck/00check.log for details

* 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/lib64/mysql -L/usr/ssl/lib -lrdf -ldb-4.3 -lmysqlclient -lcrypt -lnsl -lrasqal -lraptor -lcurl -lssl -lcrypto -ldl -lxml2 -lz -lm configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/include -I/usr/local/include -Wall -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c Rredl.c -o Rredl.o Rredl.c: In function 'get_redl_world_uri': Rredl.c:125: warning: pointer targets in assignment differ in signedness Rredl.c: In function 'new_redl_node_from_uri_string': Rredl.c:362: warning: pointer targets in passing argument 2 of 'librdf_new_node_from_uri_string' differ in signedness Rredl.c: In function 'get_rdfnode_ref': Rredl.c:314: warning: 'node' may be used uninitialized in this function gcc -shared -L/usr/local/lib64 -o Rredland.so Rredl.o -L/usr/local/lib -L/usr/lib64/mysql -L/usr/ssl/lib -lrdf -ldb-4.3 -lmysqlclient -lcrypt -lnsl -lrasqal -lraptor -lcurl -lssl -lcrypto -ldl -lxml2 -lz -lm ** R ** data ** inst ** save image Loading required package: graph Loading required package: Ruuid ** help >>> Building/Updating help pages for package 'Rredland' Formats: text html latex example cleanXSDT text html latex example getProperties 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)

Package 169/205	OS	Arch	BUILD	CHECK	BUILD BIN
Rredland 1.1.3 VJ Carey	Linux (SUSE 9.2)	x86_64	OK	WARNINGS
	Linux (SUSE 9.2)	i686	OK	ERROR
	Solaris 2.9	sparc	ERROR	skipped
	Linux (SUSE 10.0)	x86_64	OK	[ WARNINGS ]
	Windows Server 2003	x86_64	OK	WARNINGS	OK
	Windows XP	i686	OK	WARNINGS	skipped
	Mac OS X (10.4.6)	i686	ERROR	skipped

Rredland

1.1.3

Command output