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Package 6/389HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.26.1
Rafael A. Irizarry
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/affy
Last Changed Rev: 46757 / Revision: 49923
Last Changed Date: 2010-05-08 13:59:15 -0700 (Sat, 08 May 2010)
wilson1 Linux (openSUSE 11.1) / 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: 1.26.1
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings affy_1.26.1.tar.gz
StartedAt: 2010-10-04 16:24:35 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 16:28:46 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 250.4 seconds
RetCode: 0
Status:  OK  
CheckDir: affy.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/affy.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.26.1'
* 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 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 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:

* install options are ' --no-html'

* installing *source* package 'affy' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c getall_locations.c -o getall_locations.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lRzlib -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/affy.Rcheck/affy/libs
  ... done
** 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-class2.970.083.35
AffyRNAdeg5.220.055.27
MAplot26.40 0.4727.13
ProbeSet-class0.840.110.95
ProgressBarText-class 0.75 0.0016.47
affy-options000
barplot.ProbeSet0.910.030.94
bgc6.730.066.80
cleancdfname0.020.000.01
expresso25.31 0.2525.68
expressoWidget000
fit.li.wong0.010.000.01
generateExprSet-methods0.830.020.85
generateExprVal-methods0.910.030.94
generateExprVal.method.avgdiff0.680.000.67
list.celfiles000
maffy.normalise3.340.043.38
maffy.subset0.060.010.08
mas553.92 0.1356.16
mas5calls3.270.073.36
mva.pairs0.140.000.14
normalize-methods0.540.020.57
normalize.loess0.060.000.06
plot.ProbeSet000
plot.density1.330.021.34
plotLocation4.580.045.08
pmcorrect0.870.020.89
ppsetApply000
read.affybatch4.140.196.00
rma4.880.014.92
setAffyOptions000
xy2indices4.590.095.02