BioC 2.1: CHECK report for ACME on wellington

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/ACME.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'ACME/DESCRIPTION' ... OK
* this is package 'ACME' version '1.4.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ACME' 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 ... NOTE
findClosestGene: no visible binding for '<<-' assignment to 'refflat'
findClosestGene: no visible binding for global variable 'refflat'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating ACME-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating ACME-manual.tex ... OK
* checking ACME-manual.tex ... OK

* Installing *source* package 'ACME' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c windowChisq.c -o windowChisq.o
windowChisq.c: In function `windowChisq':
windowChisq.c:58: warning: suggest parentheses around comparison in operand of &
windowChisq.c:63: warning: suggest parentheses around comparison in operand of &
windowChisq.c:21: warning: unused variable `xa'
windowChisq.c: At top level:
windowChisq.c:86: warning: initialization from incompatible pointer type
gcc -std=gnu99 -shared -L/usr/local/lib -o ACME.so windowChisq.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'ACME'
     Formats: text html latex example 
  aGFF-class                        text    html    latex   example
  aGFFCalc-class                    text    html    latex   example
  do.aGFF.calc                      text    html    latex   example
  example.agff                      text    html    latex   example
  findClosestGene                   text    html    latex   example
  findRegions                       text    html    latex   example
  getRefflat                        text    html    latex   example
  read.resultsGFF                   text    html    latex   example
  write.sgr                         text    html    latex   example
** building package indices ...
* DONE (ACME)

Package 3/234	Hostname	OS	Arch	BUILD	CHECK	BUILD BIN
ACME 1.4.0 Sean Davis Last Changed Date: 2007-10-02 17:41:09 -0700 Last Changed Rev: 27709	lamb1	Linux (SUSE 10.1)	x86_64	OK	OK
	wellington	Linux (SUSE 9.2)	i686	OK	[ OK ]
	liverpool	Windows Server 2003 R2 (32-bit)	x64	OK	OK	OK
	pitt	Mac OS X (10.4.10)	i386	OK	OK	OK

Command output