* checking for file 'bim/DESCRIPTION' ... OK
* preparing 'bim':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* installing the package to re-build vignettes
* Installing *source* package 'bim' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c accept_birth.c -o accept_birth.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c birth.c -o birth.o
birth.c: In function 'swap_add_dom':
birth.c:585: warning: unused variable 'theparams'
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c com.c -o com.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c death.c -o death.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c ranlib.c -o ranlib.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c read_data.c -o read_data.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c update_parms.c -o update_parms.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -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 -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)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'bim_1.6.0.tar.gz'