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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: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings affy_1.28.1.tar.gz
StartedAt: 2011-04-07 08:20:05 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 08:24:25 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 260.0 seconds
RetCode: 0
Status:  OK  
CheckDir: affy.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/affy.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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' ...

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


** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"D:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"D:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c getall_locations.c -o getall_locations.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"D:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c mas5calls.c -o mas5calls.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"D:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rma2.c -o rma2.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"D:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lRzlib -LD:/biocbld/BBS-2˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-bioc/meat/affy.Rcheck/affy/libs/x64
** 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-class2.700.032.74
AffyRNAdeg5.240.045.28
MAplot21.07 0.6021.69
ProbeSet-class0.830.010.84
ProgressBarText-class 0.77 0.0216.50
affy-options000
barplot.ProbeSet0.750.050.80
bgc5.120.115.25
cleancdfname000
expresso24.30 0.3924.74
expressoWidget0.010.000.01
fit.li.wong000
generateExprSet-methods0.780.000.79
generateExprVal-methods0.860.010.87
generateExprVal.method.avgdiff0.560.000.56
list.celfiles000
maffy.normalise2.410.032.44
maffy.subset0.020.020.03
mas554.98 0.1155.10
mas5calls2.770.112.89
mva.pairs0.120.000.12
normalize-methods0.560.000.56
normalize.loess0.040.010.05
plot.ProbeSet000
plot.density1.310.071.38
plotLocation3.450.123.57
pmcorrect0.780.020.80
ppsetApply000
read.affybatch3.810.155.70
rma3.360.023.37
setAffyOptions000
xy2indices3.620.153.79