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Command output

* checking for file 'MANOR/DESCRIPTION' ... OK
* preparing 'MANOR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'MANOR' ...
** libs
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function `nem':
Rnem_exe.c:168: warning: 'tmpV' might be used uninitialized in this function
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c exememo.c -o exememo.o
exememo.c: In function `GenAlloc':
exememo.c:39: warning: long int format, size_t arg (arg 5)
exememo.c:39: warning: long int format, size_t arg (arg 6)
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function `CountLinesColumns':
lib_io.c:354: warning: 'mincols' might be used uninitialized in this function
lib_io.c:354: warning: 'maxcols' might be used uninitialized in this function
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c nem_alg.c -o nem_alg.o
nem_alg.c:85:1: warning: "MAXFLOAT" redefined
In file included from nem_alg.c:73:
/usr/local/lib/gcc/sparc-sun-solaris2.9/3.4.2/include/math.h:91:1: warning: this is the location of the previous definition
nem_alg.c: In function `ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' might be used uninitialized in this function
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c nem_hlp.c -o nem_hlp.o
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c nem_mod.c -o nem_mod.o
nem_mod.c:51:1: warning: "MAXFLOAT" redefined
In file included from nem_mod.c:39:
/usr/local/lib/gcc/sparc-sun-solaris2.9/3.4.2/include/math.h:91:1: warning: this is the location of the previous definition
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c nem_nei.c -o nem_nei.o
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c nem_rnd.c -o nem_rnd.o
gcc -I/home/biocbuild/arch/sparc/R-2.3.0/include -I/home/biocbuild/arch/sparc/R-2.3.0/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -Wall -c nem_ver.c -o nem_ver.o
gcc -G -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o   
** R
** data
** inst
** preparing package for lazy loading
Loading required package: GLAD
[1] "Have fun with GLAD"
** help
 >>> Building/Updating help pages for package 'MANOR'
     Formats: text html latex example 
  MANOR-internal                    text    html    latex
  arrayTrend                        text    html    latex   example
  detectSB                          text    html    latex   example
  flag                              text    html    latex   example
  flag.arrayCGH                     text    html    latex   example
  flag.summary                      text    html    latex   example
  flags                             text    html    latex   example
  genome.plot                       text    html    latex   example
  html.report                       text    html    latex   example
  import                            text    html    latex   example
  nem                               text    html    latex   example
  norm.arrayCGH                     text    html    latex   example
  qscore                            text    html    latex   example
  qscore.arrayCGH                   text    html    latex   example
  qscore.summary                    text    html    latex   example
  qscores                           text    html    latex   example
  report.plot                       text    html    latex   example
  sort.arrayCGH                     text    html    latex   example
  spatial                           text    html    latex   example
** building package indices ...
* DONE (MANOR)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'MANOR_1.4.0.tar.gz'