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| Package 28/214 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
bim1.8.2Brian S. YandellLast Changed Date: 2007-04-26 13:06:16 -0700 Last Changed Rev: 24324 | lamb1 | Linux (SUSE 10.1) | x86_64 | [ ERROR ] | skipped | |
| wellington | Linux (SUSE 9.2) | i686 | ERROR | skipped | ||
| lemming | Windows Server 2003 (32-bit) | x64 | ERROR | skipped | skipped |
| Package: bim |
| Version: 1.8.2 |
| Command: /home/biocbuild/bbs-2.0-bioc/R/bin/R CMD build bim |
| RetCode: 1 |
| Time: 21.5 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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c com.c -o com.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c ranlib.c -o ranlib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-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-2.0-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
posterior for number of QTL as %
1 2 3 4 5 6 7 8
22 52 17 6 2 0 0 0
Bayes factor ratios for number of QTL
1 2 3 4 5 6 7 8
1.0 1.6 0.5 0.2 0.1 0.1 0.1 0.2
model posterior above cutoff 1 as %
pattern
2*1 1 3*1 4*1 5*1
52 22 17 6 2
Bayes factor ratios for chromosome pattern
pattern
2*1 1 3*1 4*1 5*1
1.0 1.3 0.2 0.1 0.0
posterior for number of QTL as %
1 2 3 4 5 6 7 8
22 52 17 6 2 0 0 0
Bayes factor ratios for number of QTL
1 2 3 4 5 6 7 8
1.0 1.6 0.5 0.2 0.1 0.1 0.1 0.2
model posterior above cutoff 1 as %
pattern
2*1 1 3*1 4*1 5*1
52 22 17 6 2
Bayes factor ratios for chromosome pattern
pattern
2*1 1 3*1 4*1 5*1
1.0 1.3 0.2 0.1 0.0
Error: processing vignette 'bim.Rnw' failed with diagnostics:
chunk 9
Error in subset.cross(cross, chr) : You must specify either chr or ind.
Execution halted