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Package 13/462HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.31.1
Rafael A. Irizarry
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy
Last Changed Rev: 55189 / Revision: 55359
Last Changed Date: 2011-04-30 16:17:17 -0700 (Sat, 30 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: affy
Version: 1.31.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affy_1.31.1.tar.gz
StartedAt: 2011-05-09 12:48:00 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:53:01 -0700 (Mon, 09 May 2011)
EllapsedTime: 301.5 seconds
RetCode: 0
Status:  OK 
CheckDir: affy.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/affy.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.31.1’
* 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 installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
* 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 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘affy.pdf’ from 4224Kb to 686Kb
  consider running tools::compactPDF() on these files
* 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
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c chipbackground.c -o chipbackground.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c getall_locations.c -o getall_locations.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c mas5calls.c -o mas5calls.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma2.c -o rma2.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma_common.c -o rma_common.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/affy.Rcheck/affy/libs/i386
** 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 ...
*** tangling vignette sources ...
   ‘affy.Rnw’ 
   ‘builtinMethods.Rnw’ 
   ‘customMethods.Rnw’ 
   ‘vim.Rnw’ 
** testing if installed package can be loaded

* DONE (affy)

affy.Rcheck/affy-Ex.timings:

nameusersystemelapsed
AffyBatch-class3.5580.1384.659
AffyRNAdeg7.0680.2188.176
MAplot23.353 1.65727.140
ProbeSet-class1.4530.0601.526
ProgressBarText-class 1.027 0.02716.599
affy-options0.0010.0000.001
barplot.ProbeSet1.4520.0521.555
bgc6.5610.5847.288
cleancdfname0.0100.0020.013
expresso34.528 1.33336.366
expressoWidget0.0010.0000.001
fit.li.wong0.0140.0010.014
generateExprSet-methods1.3870.0491.447
generateExprVal-methods1.5010.0521.560
generateExprVal.method.avgdiff0.9130.0310.950
list.celfiles0.0010.0010.001
maffy.normalise4.7340.1164.878
maffy.subset0.0520.0050.056
mas576.683 0.73178.918
mas5calls4.2500.2264.510
mva.pairs0.1680.0100.179
normalize-methods0.9960.0321.042
normalize.loess0.0730.0090.082
plot.ProbeSet0.0070.0010.009
plot.density1.8920.2992.210
plotLocation4.1500.4624.722
pmcorrect1.4040.0521.463
ppsetApply0.0030.0000.003
read.affybatch3.2820.5583.906
rma4.8320.1805.045
setAffyOptions0.0000.0000.001
xy2indices4.3950.4754.985