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Package 7/419HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.28.1
Rafael A. Irizarry
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/affy
Last Changed Rev: 53881 / Revision: 54281
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 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: affy
Version: 1.28.1
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affy_1.28.1.tar.gz
StartedAt: 2011-03-31 04:10:32 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 04:15:30 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 297.9 seconds
RetCode: 0
Status:  OK 
CheckDir: affy.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/affy.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘1.28.1’
* 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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c chipbackground.c -o chipbackground.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c getall_locations.c -o getall_locations.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c mas5calls.c -o mas5calls.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c rma2.c -o rma2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c rma_common.c -o rma_common.o
gcc -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-2.7-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
  '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-class3.4770.1393.736
AffyRNAdeg7.1790.2357.809
MAplot23.273 1.66225.457
ProbeSet-class1.4060.0511.474
ProgressBarText-class 1.059 0.03316.590
affy-options0.0010.0010.001
barplot.ProbeSet1.4380.0471.499
bgc6.3070.5736.958
cleancdfname0.0100.0020.013
expresso34.693 1.46337.061
expressoWidget0.0010.0000.001
fit.li.wong0.0150.0010.015
generateExprSet-methods1.3850.0491.453
generateExprVal-methods1.4900.0471.545
generateExprVal.method.avgdiff0.8980.0190.922
list.celfiles0.0010.0000.000
maffy.normalise4.7610.1244.962
maffy.subset0.0520.0050.057
mas577.716 0.87980.358
mas5calls4.1070.2384.380
mva.pairs0.1930.0060.201
normalize-methods0.9960.0361.041
normalize.loess0.0540.0050.059
plot.ProbeSet0.0080.0010.009
plot.density1.7480.2782.049
plotLocation4.0680.4464.661
pmcorrect1.3920.0491.450
ppsetApply0.0020.0000.003
read.affybatch3.3280.6074.205
rma4.9490.2155.299
setAffyOptions0.0000.0000.001
xy2indices4.1700.4405.037