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Package 7/419HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.28.1
Rafael A. Irizarry
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/affy
Last Changed Rev: 53881 / Revision: 54588
Last Changed Date: 2011-03-18 13:43:13 -0700 (Fri, 18 Mar 2011)
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 

Summary

Package: affy
Version: 1.28.1
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.28.1.tar.gz
StartedAt: 2011-04-07 04:21:13 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 04:24:33 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 200.1 seconds
RetCode: 0
Status:  OK 
CheckDir: affy.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/affy.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.28.1’
* 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 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) and $(LAPACK_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-2.7-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-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
  '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 ...
** testing if installed package can be loaded

* DONE (affy)

affy.Rcheck/affy-Ex.timings:

nameusersystemelapsed
AffyBatch-class2.7920.0562.845
AffyRNAdeg5.3680.0525.420
MAplot19.437 0.25220.275
ProbeSet-class0.7160.0240.743
ProgressBarText-class 0.808 0.00816.316
affy-options0.0000.0000.001
barplot.ProbeSet0.6800.0120.690
bgc5.5450.0405.595
cleancdfname0.0040.0000.007
expresso24.101 0.10424.274
expressoWidget000
fit.li.wong0.0120.0000.010
generateExprSet-methods0.6320.0040.636
generateExprVal-methods0.7360.0160.749
generateExprVal.method.avgdiff0.6640.0000.663
list.celfiles0.0040.0000.001
maffy.normalise2.8770.0162.893
maffy.subset0.0360.0040.037
mas552.591 0.10452.690
mas5calls2.8480.0242.873
mva.pairs0.1120.0000.116
normalize-methods0.4240.0200.444
normalize.loess0.0360.0040.038
plot.ProbeSet0.0040.0000.005
plot.density1.3440.0121.357
plotLocation2.5320.1162.674
pmcorrect0.6800.0160.693
ppsetApply0.0000.0000.001
read.affybatch2.5810.0482.780
rma3.4000.0243.469
setAffyOptions0.0000.0000.001
xy2indices2.7480.0682.853