affy 1.22.1
Rafael A. Irizarry
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/affy | | Last Changed Rev: 40973 / Revision: 42512 | | Last Changed Date: 2009-08-03 06:33:08 -0700 (Mon, 03 Aug 2009) |
| wilson1 | 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 (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/affy.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.22.1'
* checking package name space information ... OK
* 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 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 ... NOTE
cleancdfname: no visible binding for global variable 'mapCdfName'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... 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 compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'affy' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"e:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"e:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c getall_locations.c -o getall_locations.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"e:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"e:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma2.c -o rma2.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"e:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma_common.c -o rma_common.o
gcc -shared -s -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lRzlib -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** data
** demo
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Creating a new generic function for "open" in "affy"
Creating a new generic function for "close" in "affy"
Creating a new generic function for "colnames" in "affy"
Creating a new generic function for "barplot" in "affy"
** help
*** installing help indices
>>> Building/Updating help pages for package 'affy'
Formats: text html latex example chm
AffyBatch-class text html latex example chm
AffyRNAdeg text html latex example chm
MAplot text html latex example chm
ProbeSet-class text html latex example chm
ProgressBarText-class text html latex example chm
SpikeIn text html latex chm
affy-options text html latex example chm
affy.scalevalue.exprSet text html latex chm
barplot.ProbeSet text html latex example chm
bg.adjust text html latex chm
bgc text html latex example chm
cdfFromBioC text html latex chm
cdfenv.example text html latex chm
cleancdfname text html latex example chm
debug.affy123 text html latex chm
expresso text html latex example chm
expressoWidget text html latex example chm
fit.li.wong text html latex example chm
generateExprSet-methods text html latex example chm
generateExprVal-methods text html latex example chm
generateExprVal.method.avgdiff text html latex example chm
generateExprVal.method.playerout text html latex chm
hlog text html latex chm
justrma text html latex chm
list.celfiles text html latex example chm
loess.normalize text html latex chm
maffy.normalise text html latex example chm
maffy.subset text html latex example chm
mas5 text html latex example chm
mas5calls text html latex example chm
merge.AffyBatch text html latex chm
multiloess text html latex chm
mva.pairs text html latex example chm
normalize-methods text html latex example chm
normalize text html latex chm
normalize.constant text html latex chm
normalize.contrast text html latex chm
normalize.invariantset text html latex chm
normalize.loess text html latex example chm
normalize.qspline text html latex chm
normalize.quantiles text html latex chm
normalize.quantiles.robust text html latex chm
pairs.AffyBatch text html latex chm
plot.ProbeSet text html latex example chm
plot.density text html latex example chm
plotLocation text html latex example chm
pmcorrect text html latex example chm
ppsetApply text html latex example chm
probeMatch-methods text html latex chm
probeNames-methods text html latex chm
read.affybatch text html latex example chm
read.probematrix text html latex chm
rma text html latex example chm
setAffyOptions text html latex example chm
simplemultiLoess text html latex chm
summary text html latex chm
tukey.biweight text html latex chm
whatcdf text html latex chm
xy2indices text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\AFFY~1.RCH\00_PKG~1\affy\chm\affy.chm
Compile time: 0 minutes, 1 second
60 Topics
352 Local links
9 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\AFFY~1.RCH\00_PKG~1\affy\chm\affy.chm, 99,229 bytes
Compression decreased file by 160,069 bytes.
** building package indices ...
** MD5 sums
* DONE (affy)