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Package 13/467HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.30.0
Rafael A. Irizarry
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/affy
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: affy
Version: 1.30.0
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.30.0.tar.gz
StartedAt: 2011-10-20 11:27:28 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 11:31:09 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 221.1 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 2.13.2 (2011-09-30)
* 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 ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘affy’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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"/loc/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"/loc/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"/loc/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"/loc/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"/loc/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
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-class3.2840.0723.442
AffyRNAdeg5.8640.0365.970
MAplot21.818 0.21622.510
ProbeSet-class0.7440.0200.793
ProgressBarText-class 1.004 0.01216.511
affy-options0.0040.0000.001
barplot.ProbeSet0.7320.0280.783
bgc6.4320.1046.728
cleancdfname0.0160.0000.012
expresso27.678 0.09227.995
expressoWidget0.0000.0000.001
fit.li.wong0.0080.0000.009
generateExprSet-methods0.6600.0280.701
generateExprVal-methods0.7960.0080.809
generateExprVal.method.avgdiff0.7240.0000.725
list.celfiles0.0000.0000.001
maffy.normalise2.8760.0122.937
maffy.subset0.0320.0000.032
mas558.012 0.14058.950
mas5calls2.9880.0283.138
mva.pairs0.1120.0000.130
normalize-methods0.4680.0080.485
normalize.loess0.0320.0000.033
plot.ProbeSet0.0040.0000.006
plot.density1.3720.0321.400
plotLocation2.7240.0842.962
pmcorrect0.6080.0360.643
ppsetApply0.0000.0000.001
read.affybatch2.6720.1282.943
rma3.3330.0163.592
setAffyOptions0.0040.0000.001
xy2indices3.0640.0603.127