Package: bim

Version: 1.9.0

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD build bim

RetCode: 1

Time: 18.5 seconds

Status: ERROR

PackageFile: None

* 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 -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c accept_birth.c -o accept_birth.o
In file included from accept_birth.c:13:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from accept_birth.c:13:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c birth.c -o birth.o
In file included from birth.c:13:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from birth.c:13:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
birth.c: In function 'swap_add_dom':
birth.c:585: warning: unused variable 'theparams'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c com.c -o com.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c death.c -o death.o
In file included from death.c:13:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from death.c:13:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c INITVALS.c -o INITVALS.o
In file included from INITVALS.c:13:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from INITVALS.c:13:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c mcmc.c -o mcmc.o
In file included from mcmc.c:17:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from mcmc.c:17:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c QTL_MOVE.c -o QTL_MOVE.o
In file included from QTL_MOVE.c:14:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from QTL_MOVE.c:14:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ranlib.c -o ranlib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_data.c -o read_data.o
In file included from read_data.c:17:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from read_data.c:17:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c R_mcmc.c -o R_mcmc.o
In file included from R_mcmc.c:12:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from R_mcmc.c:12:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c update_parms.c -o update_parms.o
In file included from update_parms.c:12:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from update_parms.c:12:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c update_qtl.c -o update_qtl.o
In file included from update_qtl.c:20:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from revjump.h:22,
                 from update_qtl.c:20:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
update_qtl.c: In function 'accept_new_lambda':
update_qtl.c:386: warning: unused variable 'qtlNum'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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'
gcc -std=gnu99 -shared -L/usr/local/lib64 -o bim.so accept_birth.o birth.o com.o death.o INITVALS.o mcmc.o QTL_MOVE.o ranlib.o read_data.o R_mcmc.o update_parms.o update_qtl.o Utilities.o   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** 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 ... ERROR
Loading required package: qtl

Error: processing vignette 'bim.Rnw' failed with diagnostics:
 chunk 7 
Error in subset.cross(cross, chr) : You must specify either chr or ind.
Execution halted