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| Package: bim |
| Version: 1.4.0 |
| Command: D:\biocbld\R-2.3.0\bin\R.exe CMD build bim |
| RetCode: 0 |
| Time: 109.5 seconds |
| Status: OK |
| PackageFile: bim_1.4.0.tar.gz |
* 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/work-area/1.8d/tmpdir/Rinst626887881
---------- 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/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: 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/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: 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/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: 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/R-2.3.0/include -Wall -O2 -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/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: warning: this is the location of the previous definition
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: 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/R-2.3.0/include -Wall -O2 -c com.c -o com.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: warning: this is the location of the previous definition
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: 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/R-2.3.0/include -Wall -O2 -c ranlib.c -o ranlib.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: warning: this is the location of the previous definition
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: warning: this is the location of the previous definition
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -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/mingw32/3.4.2/../../../../include/math.h:289:1: 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 --include-dir d:/biocbld/R-2.3.0/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/R-2.3.0/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\work-area\1.8d\madman\Rpacks\bim\chm\bim.chm
Compile time: 0 minutes, 0 seconds
20 Topics
102 Local links
23 Internet links
1 Graphic
Created d:\biocbld\work-area\1.8d\madman\Rpacks\bim\chm\bim.chm, 45,109 bytes
Compression decreased file by 40,231 bytes.
preparing package bim for lazy loading
adding MD5 sums
* 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_1.4.0.tar.gz'