affy 1.17.3
Rafael A. Irizarry
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy | | Last Changed Rev: 28641 / Revision: 29143 | | Last Changed Date: 2007-11-12 06:00:38 -0800 (Mon, 12 Nov 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | [ WARNINGS ] | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | WARNINGS | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/affy.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.17.3'
* 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’
* checking Rd files ... WARNING
Rd files without 'description':
plot.ProbeSet.Rd
These entries are required in an Rd file.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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-2.2-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-2.2-bioc/meat/affy.Rcheck/tests'
OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affy.tex' ...
Package natbib Warning: Citation `li:wong:2001a' on page 1 undefined on input l
Package natbib Warning: Citation `affy4' on page 1 undefined on input line 50.
Package natbib Warning: Citation `affy5' on page 1 undefined on input line 51.
Package natbib Warning: Citation `li:wong:2001a' on page 1 undefined on input l
Package natbib Warning: Citation `iriz:etal:2003' on page 1 undefined on input
Package natbib Warning: Citation `affy4' on page 1 undefined on input line 57.
Package natbib Warning: Citation `affy5' on page 1 undefined on input line 57.
Package natbib Warning: Citation `gaut:cope:bols:iriz:2003' on page 2 undefined
Package natbib Warning: Citation `iriz:gaut:cope:2003' on page 2 undefined on i
Package natbib Warning: Citation `iriz:etal:2003' on page 4 undefined on input
Package natbib Warning: Citation `iriz:etal:2003' on page 9 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 9 undefined on input
Package natbib Warning: Citation `affy4' on page 13 undefined on input line 771
Package natbib Warning: Citation `bols:etal:2003' on page 19 undefined on input
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affy.tex' ...
Package natbib Warning: Citation `li:wong:2001a' on page 2 undefined on input l
Package natbib Warning: Citation `affy4' on page 2 undefined on input line 50.
Package natbib Warning: Citation `affy5' on page 2 undefined on input line 51.
Package natbib Warning: Citation `li:wong:2001a' on page 2 undefined on input l
Package natbib Warning: Citation `iriz:etal:2003' on page 2 undefined on input
Package natbib Warning: Citation `affy4' on page 2 undefined on input line 57.
Package natbib Warning: Citation `affy5' on page 2 undefined on input line 57.
Package natbib Warning: Citation `gaut:cope:bols:iriz:2003' on page 3 undefined
Package natbib Warning: Citation `iriz:gaut:cope:2003' on page 3 undefined on i
Package natbib Warning: Citation `iriz:etal:2003' on page 4 undefined on input
Package natbib Warning: Citation `iriz:etal:2003' on page 10 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 10 undefined on input
Package natbib Warning: Citation `affy4' on page 14 undefined on input line 771
Package natbib Warning: Citation `bols:etal:2003' on page 20 undefined on input
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affy.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affy.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './builtinMethods.tex' ...
Package natbib Warning: Citation `iriz:etal:2003' on page 1 undefined on input
Package natbib Warning: Citation `affy:tech:2002' on page 2 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 2 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 2 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 3 undefined on input
Package natbib Warning: Citation `Dudoit:2002' on page 3 undefined on input lin
Package natbib Warning: Citation `astr:2003' on page 3 undefined on input line
Package natbib Warning: Citation `li:wong:2001a' on page 3 undefined on input l
Package natbib Warning: Citation `workman:etal:2002' on page 3 undefined on inp
Package natbib Warning: Citation `affy:tech:2002' on page 4 undefined on input
Package natbib Warning: Citation `affy4' on page 4 undefined on input line 138.
Package natbib Warning: Citation `affy4' on page 4 undefined on input line 153.
Package natbib Warning: Citation `li:wong:2001a' on page 4 undefined on input l
Package natbib Warning: Citation `li:wong:2001b' on page 4 undefined on input l
Package natbib Warning: Citation `affy:tech:2002' on page 5 undefined on input
Package natbib Warning: Citation `iriz:etal:2003' on page 5 undefined on input
Package natbib Warning: Citation `tukey:1977' on page 5 undefined on input line
Package natbib Warning: Citation `Lazardis:etal:2002' on page 5 undefined on in
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './builtinMethods.tex' ...
Package natbib Warning: Citation `iriz:etal:2003' on page 2 undefined on input
Package natbib Warning: Citation `affy:tech:2002' on page 2 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 3 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 3 undefined on input
Package natbib Warning: Citation `bols:etal:2003' on page 3 undefined on input
Package natbib Warning: Citation `Dudoit:2002' on page 3 undefined on input lin
Package natbib Warning: Citation `astr:2003' on page 4 undefined on input line
Package natbib Warning: Citation `li:wong:2001a' on page 4 undefined on input l
Package natbib Warning: Citation `workman:etal:2002' on page 4 undefined on inp
Package natbib Warning: Citation `affy:tech:2002' on page 4 undefined on input
Package natbib Warning: Citation `affy4' on page 5 undefined on input line 138.
Package natbib Warning: Citation `affy4' on page 5 undefined on input line 153.
Package natbib Warning: Citation `li:wong:2001a' on page 5 undefined on input l
Package natbib Warning: Citation `li:wong:2001b' on page 5 undefined on input l
Package natbib Warning: Citation `affy:tech:2002' on page 5 undefined on input
Package natbib Warning: Citation `iriz:etal:2003' on page 5 undefined on input
Package natbib Warning: Citation `tukey:1977' on page 6 undefined on input line
Package natbib Warning: Citation `Lazardis:etal:2002' on page 6 undefined on in
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './builtinMethods.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './customMethods.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './customMethods.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './dealing_with_cdfenvs.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './dealing_with_cdfenvs.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './vim.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './vim.tex' ...
* creating affy-manual.tex ... OK
* checking affy-manual.tex ... OK
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/affy.Rcheck/00check.log
for details
/loc/home/biocbuild/bbs-2.2-bioc/meat/affy.Rcheck
* 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-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/home/biocbuild/bbs-2.2-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-2.2-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
Note: removing empty section \details
Note: removing empty section \examples
Note: ignoring empty \keyword entries
Note: removing empty section \examples
Note: removing empty section \examples
Note: ignoring empty \keyword entries
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \examples
>>> 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 ...
* DONE (affy)