Package: exprDB

Version: 0.3.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check exprDB_0.3.0.tar.gz

RetCode: 1

Time: 74.6 seconds

Status: ERROR

CheckDir: exprDB.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.9d/Rpacks/exprDB.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-06-04 r38279)
* checking for file 'exprDB/DESCRIPTION' ... OK
* this is package 'exprDB' version '0.3.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'exprDB' can be installed ... WARNING
Found the following significant warnings:
  WARNING: use of install.R is no longer supported
* 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 ... WARNING
install.R
These files are deprecated. See manual 'Writing R Extensions'.
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic .exprdb.ptr and siglist ANY
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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
* creating exprDB-Ex.R ... OK
* checking examples ...sh: line 1: 13194 Segmentation fault      '/loc/biocbuild/1.9d/R/bin/R' --vanilla exprDB-Ex.Rout 2>&1
 ERROR
Running examples in exprDB-Ex.R failed.
The error most likely occurred in:

> ### * exprDB-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: exprDB-class
> ### Title: Class exprDB, a BerkeleyDB-based representation for microarray
> ###   data
> ### Aliases: sample.names sample.names<- exprDB exprDB-class $.exprDB
> ###   as.exprDB [,exprDB-method [<-,exprDB-method apply,exprDB-method
> ###   as.exprDB,exprSet-method exprs,exprDB-method exprs<-,exprDB-method
> ###   geneNames,exprDB-method geneNames<-,exprDB-method
> ###   initialize,exprDB-method pData,exprDB-method pData<-,exprDB-method
> ###   phenoData,exprDB-method phenoData<-,exprDB,phenoData-method
> ###   sample.names,exprDB-method sample.names<-,exprDB-method
> ###   sampleNames,exprDB-method se.exprs,exprDB-method show,exprDB-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> require(exprDB)
[1] TRUE
> data <- new('exprDB')

 *** caught segfault ***
address 0xa320a59, cause 'memory not mapped'

Traceback:
 1: .Call("R_EDB_meta_write", x, name, serialize(value, NULL, ascii = TRUE),     PACKAGE = "exprDB")
 2: .exprdb.meta.write(object@x, "phenoData", value)
 3: "phenoData<-"(`*tmp*`, value = list())
 4: "phenoData<-"(`*tmp*`, value = list())
 5: .local(.Object, ...)
 6: initialize(value, ...)
 7: initialize(value, ...)
 8: new("exprDB")
aborting ...

* Installing *source* package 'exprDB' ...
checking for gcc... gcc
checking for C compiler default output... 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
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/include -I/usr/local/include  -Wall  -fpic  -g -O2 -std=gnu99 -Wall -c exprdb_apply.c -o exprdb_apply.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/include -I/usr/local/include  -Wall  -fpic  -g -O2 -std=gnu99 -Wall -c exprdb.c -o exprdb.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/include -I/usr/local/include  -Wall  -fpic  -g -O2 -std=gnu99 -Wall -c exprdb_r.c -o exprdb_r.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/include -I/usr/local/include  -Wall  -fpic  -g -O2 -std=gnu99 -Wall -c exprdb_select.c -o exprdb_select.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/include -I/usr/local/include  -Wall  -fpic  -g -O2 -std=gnu99 -Wall -c express.c -o express.o
express.c: In function `_int_ensure_extents':
express.c:54: warning: unused variable `ret'
express.c: In function `_int_expr':
express.c:70: warning: implicit declaration of function `R_alloc'
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/include -I/usr/local/include  -Wall  -fpic  -g -O2 -std=gnu99 -Wall -c r_col.c -o r_col.o
r_col.c: In function `rcol_assoc':
r_col.c:4: warning: initialization from incompatible pointer type
gcc -shared -L/usr/local/lib -o exprDB.so exprdb_apply.o exprdb.o exprdb_r.o exprdb_select.o express.o r_col.o -L/usr/lib -ldb  
** R
** inst
WARNING: use of install.R is no longer supported
** help
 >>> Building/Updating help pages for package 'exprDB'
     Formats: text html latex example 
  exprDB-class                      text    html    latex   example
  exprdb.ptr-class                  text    html    latex
** building package indices ...
* DONE (exprDB)