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Package 6/354HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.25.2
Rafael A. Irizarry
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy
Last Changed Rev: 42876 / Revision: 43434
Last Changed Date: 2009-11-09 13:04:33 -0800 (Mon, 09 Nov 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 
Package: affy
Version: 1.25.2
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes affy_1.25.2.tar.gz
StartedAt: 2009-12-07 15:17:06 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 15:20:32 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 205.5 seconds
RetCode: 0
Status: OK
CheckDir: affy.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/affy.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-10 r50388)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.25.2'
* 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 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 metadata ... 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

affy.Rcheck/00install.out:

* install options are ' --no-html'

* 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-2.6-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.6-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_common.o -lz -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
** 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 package indices ...
* DONE (affy)