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Package 180/319HostnameOS / ArchBUILDCHECKBUILD BIN
MANOR 1.16.0
Pierre Neuvial
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/MANOR
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386 [ OK ] OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: MANOR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD build MANOR
StartedAt: 2009-10-20 15:30:50 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 15:32:00 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 70.2 seconds
RetCode: 0
Status: OK
PackageFile: MANOR_1.16.0.tar.gz
PackageFileSize: 1.04 MiB

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
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c Rnem_arg.c -o Rnem_arg.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c Rnem_exe.c -o Rnem_exe.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c exememo.c -o exememo.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c lib_io.c -o lib_io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c nem_alg.c -o nem_alg.o
nem_alg.c:85:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:28,
                 from nem_alg.c:73:
/usr/include/architecture/i386/math.h:527:1: warning: this is the location of the previous definition
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c nem_hlp.c -o nem_hlp.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c nem_mod.c -o nem_mod.o
nem_mod.c:51:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:28,
                 from nem_mod.c:39:
/usr/include/architecture/i386/math.h:527:1: warning: this is the location of the previous definition
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c nem_nei.c -o nem_nei.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c nem_rnd.c -o nem_rnd.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c nem_ver.c -o nem_ver.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Rnem_arg.c -o Rnem_arg.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c Rnem_exe.c -o Rnem_exe.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c exememo.c -o exememo.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c lib_io.c -o lib_io.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c nem_alg.c -o nem_alg.o
nem_alg.c:85:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:26,
                 from nem_alg.c:73:
/usr/include/architecture/ppc/math.h:666:1: warning: this is the location of the previous definition
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c nem_hlp.c -o nem_hlp.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c nem_mod.c -o nem_mod.o
nem_mod.c:51:1: warning: "MAXFLOAT" redefined
In file included from /usr/include/math.h:26,
                 from nem_mod.c:39:
/usr/include/architecture/ppc/math.h:666:1: warning: this is the location of the previous definition
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c nem_nei.c -o nem_nei.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c nem_rnd.c -o nem_rnd.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c nem_ver.c -o nem_ver.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
[1] "Have fun with GLAD"
[1] "For smoothing it is possible to use either"
[1] "the AWS algorithm (Polzehl and Spokoiny, 2002)"
[1] "or the HaarSeg algorithm (Ben-Yaacov and Eldar, 2008)"
[1] ""
[1] "If you use the package with AWS, please cite:"
[1] "Hupe et al. (2004) and Polzehl and Spokoiny (2002)"
[1] ""
[1] "If you use the package with HaarSeg, please cite:"
[1] "Hupe et al. (2004) and (Ben-Yaacov and Eldar, 2008)"
** help
*** installing help indices
 >>> 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.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
  import                            text    html    latex   example
  nem                               text    html    latex   example
  norm                              text    html    latex   example
  qscore                            text    html    latex
  qscore.arrayCGH                   text    html    latex   example
  qscore.summary                    text    html    latex   example
  qscores                           text    html    latex   example
  report.plot                       text    html    latex   example
  sort                              text    html    latex   example
  spatial                           text    html    latex   example
  to.flag                           text    html    latex   example
** building package indices ...
* DONE (MANOR)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'MANOR_1.16.0.tar.gz'