affy 1.18.2
Rafael A. Irizarry
| Snapshot Date: 2008-08-08 00:12:03 -0700 (Fri, 08 Aug 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/affy | | Last Changed Rev: 32263 / Revision: 33132 | | Last Changed Date: 2008-06-12 13:43:42 -0700 (Thu, 12 Jun 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | 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 ] |
INSTALLATION WITH 'R CMD INSTALL affy_1.18.2.tar.gz'
* Installing to library 'affy.buildbin-libdir'
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -c chipbackground.c -o chipbackground.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -c getall_locations.c -o getall_locations.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -c mas5calls.c -o mas5calls.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -c rma2.c -o rma2.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -march=nocona -c rma_common.c -o rma_common.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -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 affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affyio
Loading required package: preprocessCore
Creating a new generic function for "open" in "affy"
Creating a new generic function for "update" in "affy"
Creating a new generic function for "close" in "affy"
** help
>>> Building/Updating help pages for package 'affy'
Formats: text html latex example
AffyBatch-class text html latex example
AffyRNAdeg text html latex example
MAplot text html latex example
ProbeSet-class text html latex example
ProgressBarText-class text html latex example
SpikeIn text html latex
affy-options text html latex example
affy.scalevalue.exprSet text html latex
affybatch.example text html latex
barplot.ProbeSet text html latex example
bg.adjust text html latex
bgc text html latex example
cdfFromBioC text html latex
cdfenv.example text html latex
cleancdfname text html latex example
debug.affy123 text html latex
expresso text html latex example
expressoWidget text html latex example
fit.li.wong text html latex example
generateExprSet-methods text html latex example
generateExprVal-methods text html latex example
generateExprVal.method.avgdiff text html latex example
generateExprVal.method.playerout text html latex
hlog text html latex
justrma text html latex
list.celfiles text html latex example
loess.normalize text html latex
maffy.normalise text html latex example
maffy.subset text html latex example
mas5 text html latex example
mas5calls text html latex example
merge.AffyBatch text html latex example
multiloess text html latex
mva.pairs text html latex example
normalize-methods text html latex example
normalize text html latex
normalize.constant text html latex
normalize.contrast text html latex
normalize.invariantset text html latex
normalize.loess text html latex example
normalize.qspline text html latex
normalize.quantiles text html latex
normalize.quantiles.robust text html latex
pairs.AffyBatch text html latex
plot.ProbeSet text html latex example
plot.density text html latex example
plotLocation text html latex example
pmcorrect text html latex example
ppsetApply text html latex example
probeMatch-methods text html latex
probeNames-methods text html latex
read.affybatch text html latex example
read.probematrix text html latex
rma text html latex example
setAffyOptions text html latex example
simplemultiLoess text html latex
summary text html latex
tukey.biweight text html latex
whatcdf text html latex
xy2indices text html latex example
** building package indices ...
Loading required package: methods
* DONE (affy)
INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --libs-only affy_1.18.2.tar.gz'
* Installing to library 'affy.buildbin-libdir'
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -c chipbackground.c -o chipbackground.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -c getall_locations.c -o getall_locations.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -c mas5calls.c -o mas5calls.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -c rma2.c -o rma2.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/include" -fPIC -g -O2 -c rma_common.c -o rma_common.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -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 affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
* DONE (affy)