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Package 7/436HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.29.2
Rafael A. Irizarry
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy
Last Changed Rev: 51673 / Revision: 53255
Last Changed Date: 2010-12-26 04:46:49 -0800 (Sun, 26 Dec 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: affy
Version: 1.29.2
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.29.2.tar.gz
StartedAt: 2011-02-24 17:02:37 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 17:06:05 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 207.9 seconds
RetCode: 0
Status:  OK 
CheckDir: affy.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/affy.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.29.2’
* 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 Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: widgetTools
* 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:

* 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-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/affy.Rcheck/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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 ...
** testing if installed package can be loaded

* DONE (affy)

affy.Rcheck/affy-Ex.timings:

nameusersystemelapsed
AffyBatch-class3.0280.0923.192
AffyRNAdeg5.3280.0525.384
MAplot20.881 0.23621.140
ProbeSet-class0.6800.0200.697
ProgressBarText-class 0.836 0.01216.342
affy-options0.0000.0000.001
barplot.ProbeSet0.6930.0200.717
bgc5.7320.1125.853
cleancdfname0.0000.0040.008
expresso25.473 0.09628.180
expressoWidget000
fit.li.wong0.0080.0000.010
generateExprSet-methods0.7130.0000.712
generateExprVal-methods0.7560.0160.769
generateExprVal.method.avgdiff0.6720.0000.676
list.celfiles0.0000.0000.001
maffy.normalise2.9120.0482.960
maffy.subset0.0280.0040.034
mas555.235 0.20456.752
mas5calls2.9320.0085.493
mva.pairs0.1160.0160.130
normalize-methods0.4600.0000.463
normalize.loess0.0360.0000.035
plot.ProbeSet0.0080.0000.005
plot.density1.3490.0201.367
plotLocation2.6040.0842.697
pmcorrect0.6680.0160.691
ppsetApply0.0000.0000.001
read.affybatch2.4720.0442.618
rma3.4120.0363.490
setAffyOptions0.0000.0000.001
xy2indices2.6440.0762.727