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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier
Package 30/238HostnameOSArchBUILDCHECKBUILD BIN

bim

1.9.0

Brian S. Yandell
Last Changed Date: 2007-04-24 11:31:42 -0700
Last Changed Rev: 24217
lamb1 Linux (SUSE 10.1) x86_64  ERROR skipped
wellington Linux (SUSE 9.2) i686  ERROR skipped
churchill Solaris 2.9 sparc [ ERROR ]skipped
lemming Windows Server 2003 (32-bit) x64  ERROR skippedskipped
Package: bim
Version: 1.9.0
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build bim
RetCode: 1
Time: 94.2 seconds
Status: ERROR
PackageFile: None

Command output

* 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/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -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 -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -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 -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -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 -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/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'
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 -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c accept_birth.c -o accept_birth.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c birth.c -o birth.o
birth.c: In function 'swap_add_dom':
birth.c:585: warning: unused variable 'theparams'
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/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/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c death.c -o death.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -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 -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/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/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_data.c -o read_data.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c update_parms.c -o update_parms.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -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 -std=gnu99 -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   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: qtl
** help
Note: unmatched right brace in 'read.bim' on or after line 41
 >>> 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