affy 1.16.0
Rafael A. Irizarry
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/affy | | Last Changed Rev: 27709 / Revision: 30966 | | Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007) |
| 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 |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.1-bioc/meat/affy.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.16.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affy' 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 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 ... NOTE
AllButCelsForReadAffy: no visible binding for global variable 'tksn'
cleancdfname: no visible binding for global variable 'mapCdfName'
normalize.AffyBatch.invariantset : do.normalize.Affybatch.invariantset:
no visible global function definition for 'chipNames'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'barplot.ProbeSet':
barplot.ProbeSet
S3 methods shown with full name in documentation object 'merge.AffyBatch':
merge.AffyBatch
S3 methods shown with full name in documentation object 'pairs.AffyBatch':
pairs.AffyBatch
S3 methods shown with full name in documentation object 'plot.ProbeSet':
plot.ProbeSet
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating affy-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.1-bioc/meat/affy.Rcheck/tests'
Running 'affybatch.R'
Running 'bg.correct.R'
Running 'expression.values.R'
Running 'normalize.methods.R'
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.1-bioc/meat/affy.Rcheck/tests'
OK
* checking package vignettes in 'inst/doc' ... OK
* creating affy-manual.tex ... OK
* checking affy-manual.tex ... OK
* 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_background2.o rma_common.o -lz -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** 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 example
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 example
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 example
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 example
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 example
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 ...
* DONE (affy)