simpleaffy 2.18.0
Crispin Miller
| 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/simpleaffy | | 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 working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/simpleaffy.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.18.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'simpleaffy' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating simpleaffy-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating simpleaffy-manual.tex ... OK
* checking simpleaffy-manual.tex using pdflatex ... OK
* Installing *source* package 'simpleaffy' ...
** 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 simpleaffy.c -o simpleaffy.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 simpleaffy.so simpleaffy.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 simpleaffy.c -o simpleaffy.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 simpleaffy.so simpleaffy.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 simpleaffy.c -o simpleaffy.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 simpleaffy.so simpleaffy.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 simpleaffy.c -o simpleaffy.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 simpleaffy.so simpleaffy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Loading required package: affy
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: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: gcrma
Loading required package: matchprobes
** help
>>> Building/Updating help pages for package 'simpleaffy'
Formats: text html latex example
Note: removing empty section \seealso in file 'PairComp-class.Rd'
PairComp-class text html latex
QCStats-class text html latex
all.present text html latex example
all.present.in.group text html latex example
bg.correct.sa text html latex example
Note: removing empty section \details in file 'call.exprs.Rd'
call.exprs text html latex example
detection.p.val text html latex example
get.annotation text html latex example
Note: removing empty section \seealso in file 'get.array.indices.Rd'
get.array.indices text html latex example
get.array.subset text html latex example
get.array.subset.affy text html latex example
get.fold.change.and.t.test text html latex example
hmap.colors text html latex example
hmap.eset text html latex example
hmap.pc text html latex example
journalpng text html latex example
justMAS text html latex example
pairwise.comparison text html latex example
pairwise.filter text html latex example
plot.pairwise.comparison text html latex example
plot.qc.stats text html latex example
qc text html latex example
qc.affy text html latex example
Note: removing empty section \note in file 'qc.get.alpha1.Rd'
qc.get.alpha1 text html latex example
Note: removing empty section \note in file 'qc.get.array.Rd'
qc.get.array text html latex example
Note: removing empty section \note in file 'qc.get.probes.Rd'
qc.get.probes text html latex example
Note: removing empty section \note in file 'qc.get.ratios.Rd'
qc.get.ratios text html latex example
Note: removing empty section \note in file 'qc.get.spikes.Rd'
qc.get.spikes text html latex example
Note: removing empty section \note in file 'qc.have.params.Rd'
qc.have.params text html latex example
Note: removing empty section \note in file 'qc.ok.Rd'
Note: removing empty section \arguments in file 'qc.ok.Rd'
qc.ok text html latex example
Note: removing empty section \note in file 'qc.read.file.Rd'
qc.read.file text html latex example
qc.stats text html latex example
Note: removing empty section \details in file 'read.affy.Rd'
read.affy text html latex example
Note: removing empty section \details in file 'read.affy.mixed.Rd'
read.affy.mixed text html latex example
Note: removing empty section \note in file 'setQCEnvironment.Rd'
setQCEnvironment text html latex example
Note: removing empty section \value in file 'simpleaffy-deprecated.Rd'
Note: removing empty section \note in file 'simpleaffy-deprecated.Rd'
simpleaffy-deprecated text html latex example
standard.pearson text html latex example
trad.scatter.plot text html latex example
** building package indices ...
* DONE (simpleaffy)