Package: bim

Version: 1.9.0

Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD build bim

RetCode: 1

Time: 76.0 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 R.css in D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst552876885


---------- Making package bim ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making INITVALS.d from INITVALS.c
making QTL_MOVE.d from QTL_MOVE.c
making R_mcmc.d from R_mcmc.c
making Utilities.d from Utilities.c
making accept_birth.d from accept_birth.c
making birth.d from birth.c
making com.d from com.c
making death.d from death.c
making mcmc.d from mcmc.c
making ranlib.d from ranlib.c
making read_data.d from read_data.c
making update_parms.d from update_parms.c
making update_qtl.d from update_qtl.c
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c INITVALS.c -o INITVALS.o
In file included from INITVALS.c:13:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from revjump.h:22,
                 from INITVALS.c:13:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: warning: this is the location of the previous definition
INITVALS.c: In function `printX':
INITVALS.c:166: warning: double format, different type arg (arg 3)
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -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 revjump.h:22,
                 from QTL_MOVE.c:14:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: 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: int format, double arg (arg 4)
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -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 revjump.h:22,
                 from R_mcmc.c:12:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: warning: this is the location of the previous definition
R_mcmc.c: In function `R_mcmc':
R_mcmc.c:44: warning: unused variable `new_lambda'
R_mcmc.c:45: warning: unused variable `new_chrom'
R_mcmc.c: In function `setupChromosomes':
R_mcmc.c:402: warning: 'mystartptr' might be used uninitialized in this function
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -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 `gamgbh':
Utilities.c:394: warning: 'w' might be used uninitialized in this function
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -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 revjump.h:22,
                 from accept_birth.c:13:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: warning: this is the location of the previous definition
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c birth.c -o birth.o
In file included from birth.c:13:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from revjump.h:22,
                 from birth.c:13:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: warning: this is the location of the previous definition
birth.c: In function `swap_add_dom':
birth.c:585: warning: unused variable `theparams'
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c com.c -o com.o
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c death.c -o death.o
In file included from death.c:13:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from revjump.h:22,
                 from death.c:13:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: warning: this is the location of the previous definition
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c mcmc.c -o mcmc.o
In file included from mcmc.c:17:
revjump.h:111:1: warning: "INFINITY" redefined
In file included from revjump.h:22,
                 from mcmc.c:17:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: 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' might be used uninitialized in this function
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c ranlib.c -o ranlib.o
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -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 revjump.h:22,
                 from read_data.c:17:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: warning: this is the location of the previous definition
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -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 revjump.h:22,
                 from update_parms.c:12:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: warning: this is the location of the previous definition
gcc   -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -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 revjump.h:22,
                 from update_qtl.c:20:
d:/usr/MinGW/bin/../lib/gcc/mingw32/3.4.5/../../../../include/math.h:295:1: 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'
windres -I d:/biocbld/bbs-2.1-bioc/R/include  -i bim_res.rc -o bim_res.o
gcc  -shared -s  -o bim.dll bim.def 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 bim_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'bim'
     Formats: text html latex example chm 
  Bnapus                            text    html    latex   example chm
  bim-internal                      text    html    latex           chm
  bim.effects                       text    html    latex   example chm
  bim.fdr                           text    html    latex   example chm
  bim.model                         text    html    latex   example chm
  bim.qtl                           text    html    latex   example chm
  bmapqtl.options                   text    html    latex   example chm
  fisch                             text    html    latex   example chm
  plot.bim                          text    html    latex   example chm
  plot.bim.diag                     text    html    latex   example chm
  plot.bim.loci                     text    html    latex   example chm
  plot.bim.mcmc                     text    html    latex   example chm
  plot.bim.model                    text    html    latex   example chm
  read.bim                          text    html    latex   example chm
  read.bmapqtl                      text    html    latex   example chm
  run.bmapqtl                       text    html    latex   example chm
  subset.bim                        text    html    latex   example chm
  summary.bim                       text    html    latex   example chm
  vern                              text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling d:\biocbld\bbs-2.1-bioc\meat\bim\chm\bim.chm





Compile time: 0 minutes, 0 seconds

20	Topics

102	Local links

23	Internet links

1	Graphic





Created d:\biocbld\bbs-2.1-bioc\meat\bim\chm\bim.chm, 45,486 bytes

Compression decreased file by 41,070 bytes.

  preparing package bim for lazy loading
Loading required package: qtl
  adding MD5 sums

* 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