MANOR 1.14.0
Pierre Neuvial
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/MANOR | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | 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 (10.5.6) / i386 | [ OK ] | OK | OK |
* 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-4.2 -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 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc-4.2 -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 -Wall -c Rnem_exe.c -o Rnem_exe.o
gcc-4.2 -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 -Wall -c exememo.c -o exememo.o
gcc-4.2 -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 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'maxcols' may be used uninitialized in this function
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc-4.2 -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 -Wall -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:542:1: warning: this is the location of the previous definition
nem_alg.c: In function 'ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' may be used uninitialized in this function
nem_alg.c:1631: note: 'bestbeta' was declared here
gcc-4.2 -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 -Wall -c nem_hlp.c -o nem_hlp.o
gcc-4.2 -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 -Wall -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:542:1: warning: this is the location of the previous definition
gcc-4.2 -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 -Wall -c nem_nei.c -o nem_nei.o
gcc-4.2 -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 -Wall -c nem_rnd.c -o nem_rnd.o
gcc-4.2 -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 -Wall -c nem_ver.c -o nem_ver.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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-4.2 -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 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc-4.2 -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 -Wall -c Rnem_exe.c -o Rnem_exe.o
gcc-4.2 -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 -Wall -c exememo.c -o exememo.o
gcc-4.2 -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 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'maxcols' may be used uninitialized in this function
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc-4.2 -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 -Wall -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:695:1: warning: this is the location of the previous definition
nem_alg.c: In function 'ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' may be used uninitialized in this function
nem_alg.c:1631: note: 'bestbeta' was declared here
gcc-4.2 -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 -Wall -c nem_hlp.c -o nem_hlp.o
gcc-4.2 -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 -Wall -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:695:1: warning: this is the location of the previous definition
gcc-4.2 -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 -Wall -c nem_nei.c -o nem_nei.o
gcc-4.2 -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 -Wall -c nem_rnd.c -o nem_rnd.o
gcc-4.2 -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 -Wall -c nem_ver.c -o nem_ver.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function 'MakeErrinfo':
Rnem_exe.c:216: warning: cast from pointer to integer of different size
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c exememo.c -o exememo.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'maxcols' may be used uninitialized in this function
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -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:695:1: warning: this is the location of the previous definition
nem_alg.c: In function 'ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' may be used uninitialized in this function
nem_alg.c:1631: note: 'bestbeta' was declared here
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_hlp.c -o nem_hlp.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -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:695:1: warning: this is the location of the previous definition
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_nei.c -o nem_nei.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_rnd.c -o nem_rnd.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_ver.c -o nem_ver.o
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function 'MakeErrinfo':
Rnem_exe.c:216: warning: cast from pointer to integer of different size
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c exememo.c -o exememo.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'maxcols' may be used uninitialized in this function
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -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:542:1: warning: this is the location of the previous definition
nem_alg.c: In function 'ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' may be used uninitialized in this function
nem_alg.c:1631: note: 'bestbeta' was declared here
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_hlp.c -o nem_hlp.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -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:542:1: warning: this is the location of the previous definition
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_nei.c -o nem_nei.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_rnd.c -o nem_rnd.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c nem_ver.c -o nem_ver.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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)
* 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_1.14.0.tar.gz'