BioC 1.9: CHECK report for bim on churchill

* checking for working latex ... OK
* using log directory '/loc/biocbuild/bbs-1.9/meat/bim.Rcheck'
* using R version 2.4.1 (2006-12-18)
* checking for file 'bim/DESCRIPTION' ... OK
* this is package 'bim' version '1.01-5'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'bim' 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 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 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 for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating bim-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating bim-manual.tex ... OK
* checking bim-manual.tex ... OK

* Installing *source* package 'bim' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c INITVALS.c -o INITVALS.o
INITVALS.c: In function 'printX':
INITVALS.c:166: warning: format '%5.2f' expects type 'double', but argument 3 has type 'int'
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c QTL_MOVE.c -o QTL_MOVE.o
QTL_MOVE.c: In function 'checkIntegrity':
QTL_MOVE.c:157: warning: suggest parentheses around && within ||
QTL_MOVE.c:160: warning: suggest parentheses around && within ||
QTL_MOVE.c:170: warning: format '%d' expects type 'int', but argument 4 has type 'double'
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c R_mcmc.c -o R_mcmc.o
R_mcmc.c: In function 'R_mcmc':
R_mcmc.c:45: warning: unused variable 'new_chrom'
R_mcmc.c:44: warning: unused variable 'new_lambda'
R_mcmc.c: In function 'setupChromosomes':
R_mcmc.c:402: warning: 'mystartptr' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c Utilities.c -o Utilities.o
Utilities.c: In function 'dvector':
Utilities.c:143: warning: unused variable 'ii'
Utilities.c: In function 'ivector':
Utilities.c:153: warning: unused variable 'ii'
Utilities.c: In function 'cvector':
Utilities.c:162: warning: unused variable 'ii'
Utilities.c: In function 'lvector':
Utilities.c:171: warning: unused variable 'ii'
Utilities.c: In function 'cmatrix':
Utilities.c:181: warning: unused variable 'j'
Utilities.c: In function 'imatrix':
Utilities.c:201: warning: unused variable 'j'
Utilities.c: In function 'matrix':
Utilities.c:219: warning: unused variable 'j'
Utilities.c: In function 'smatrix':
Utilities.c:240: warning: unused variable 'j'
Utilities.c: In function 'dmatrix':
Utilities.c:356: warning: unused variable 'j'
Utilities.c: In function 'get_int':
Utilities.c:497: warning: array subscript has type 'char'
Utilities.c: In function 'strupr':
Utilities.c:862: warning: array subscript has type 'char'
Utilities.c: In function 'strlwr':
Utilities.c:874: warning: array subscript has type 'char'
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c accept_birth.c -o accept_birth.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c birth.c -o birth.o
birth.c: In function 'swap_add_dom':
birth.c:585: warning: unused variable 'theparams'
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c com.c -o com.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c death.c -o death.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c mcmc.c -o mcmc.o
mcmc.c: In function 'mcmc':
mcmc.c:40: warning: unused variable 'k'
mcmc.c: In function 'birth_death':
mcmc.c:169: warning: unused variable 'moves'
mcmc.c: In function 'outputResults':
mcmc.c:434: warning: 'H' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c ranlib.c -o ranlib.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_data.c -o read_data.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c update_parms.c -o update_parms.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-1.9/R/include -I/loc/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c update_qtl.c -o update_qtl.o
update_qtl.c: In function 'accept_new_lambda':
update_qtl.c:386: warning: unused variable 'qtlNum'
gcc -std=gnu99 -G -L/usr/local/lib -o bim.so INITVALS.o QTL_MOVE.o R_mcmc.o Utilities.o accept_birth.o birth.o com.o death.o mcmc.o ranlib.o read_data.o update_parms.o update_qtl.o   
** R
** data
** inst
** preparing package for lazy loading
Loading required package: qtl
** help
 >>> Building/Updating help pages for package 'bim'
     Formats: text html latex example 
  Bnapus                            text    html    latex   example
  bim-internal                      text    html    latex
  bim.effects                       text    html    latex   example
  bim.fdr                           text    html    latex   example
  bim.model                         text    html    latex   example
  bim.qtl                           text    html    latex   example
  bmapqtl.options                   text    html    latex   example
  fisch                             text    html    latex   example
  plot.bim                          text    html    latex   example
  plot.bim.diag                     text    html    latex   example
  plot.bim.loci                     text    html    latex   example
  plot.bim.mcmc                     text    html    latex   example
  plot.bim.model                    text    html    latex   example
  read.bim                          text    html    latex   example
  read.bmapqtl                      text    html    latex   example
  run.bmapqtl                       text    html    latex   example
  subset.bim                        text    html    latex   example
  summary.bim                       text    html    latex   example
  vern                              text    html    latex   example
** building package indices ...
* DONE (bim)

Package 27/188	Hostname	OS	Arch	BUILD	CHECK	BUILD BIN
bim 1.01-5 Brian S. Yandell Last Changed Date: 2006-12-01 10:28:44 -0800 Last Changed Rev: 21331	lamb1	Linux (SUSE 10.1)	x86_64	OK	OK
	wellington	Linux (SUSE 9.2)	i686	OK	OK
	churchill	Solaris 2.9	sparc	OK	[ OK ]
	lemming	Windows Server 2003	x86_64	OK	OK	OK

bim

1.01-5

Command output