INSTALLATION WITH 'R CMD INSTALL --library=MANOR.buildbin-libdir MANOR_1.14.0.tar.gz'
* Installing *source* package 'MANOR' ...
** libs
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c Rnem_arg.c -o Rnem_arg.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c Rnem_exe.c -o Rnem_exe.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c exememo.c -o exememo.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c lib_io.c -o lib_io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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: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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c nem_hlp.c -o nem_hlp.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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: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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c nem_nei.c -o nem_nei.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c nem_rnd.c -o nem_rnd.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
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
Note: ignoring empty \keyword entries in file 'arrayTrend.Rd'
arrayTrend text html latex example
Note: ignoring empty \keyword entries in file 'detectSB.Rd'
detectSB text html latex example
Note: ignoring empty \keyword entries in file 'flag.Rd'
flag text html latex example
Note: ignoring empty \keyword entries in file 'flag.arrayCGH.Rd'
flag.arrayCGH text html latex example
Note: ignoring empty \keyword entries in file 'flag.summary.Rd'
flag.summary text html latex example
flags text html latex example
Note: ignoring empty \keyword entries in file 'genome.plot.Rd'
genome.plot text html latex example
Note: ignoring empty \keyword entries in file 'html.report.Rd'
Note: removing empty section \examples in file 'html.report.Rd'
html.report text html latex
Note: ignoring empty \keyword entries in file 'import.Rd'
import text html latex example
Note: ignoring empty \keyword entries in file 'nem.Rd'
nem text html latex example
Note: ignoring empty \keyword entries in file 'norm.arrayCGH.Rd'
norm.arrayCGH text html latex example
Note: ignoring empty \keyword entries in file 'qscore.Rd'
Note: removing empty section \details in file 'qscore.Rd'
Note: removing empty section \examples in file 'qscore.Rd'
qscore text html latex
Note: ignoring empty \keyword entries in file 'qscore.arrayCGH.Rd'
qscore.arrayCGH text html latex example
Note: ignoring empty \keyword entries in file 'qscore.summary.Rd'
qscore.summary text html latex example
qscores text html latex example
Note: ignoring empty \keyword entries in file 'report.plot.Rd'
report.plot text html latex example
Note: ignoring empty \keyword entries in file 'sort.arrayCGH.Rd'
sort.arrayCGH text html latex example
spatial text html latex example
** building package indices ...
* DONE (MANOR)