Package: affy

Version: 1.29.2

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings affy_1.29.2.tar.gz

StartedAt: 2011-02-24 17:51:39 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:55:22 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 223.6 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/affy.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 '1.29.2'
* 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* 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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/BBS-2˜1.8-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˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-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
  '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 ...
** testing if installed package can be loaded

* DONE (affy)

name	user	system	elapsed
AffyBatch-class	2.59	0.08	2.67
AffyRNAdeg	5.58	0.04	5.63
MAplot	22.67	0.64	23.34
ProbeSet-class	0.86	0.03	0.89
ProgressBarText-class	0.78	0.02	16.52
affy-options	0	0	0
barplot.ProbeSet	0.80	0.03	0.82
bgc	5.39	0.28	5.68
cleancdfname	0.01	0.00	0.01
expresso	26.03	0.35	26.38
expressoWidget	0	0	0
fit.li.wong	0.02	0.00	0.01
generateExprSet-methods	0.81	0.03	0.85
generateExprVal-methods	0.89	0.03	0.92
generateExprVal.method.avgdiff	0.60	0.00	0.59
list.celfiles	0	0	0
maffy.normalise	2.65	0.06	2.72
maffy.subset	0.03	0.00	0.03
mas5	58.41	0.11	58.95
mas5calls	2.80	0.02	2.82
mva.pairs	0.11	0.01	0.12
normalize-methods	0.58	0.02	0.60
normalize.loess	0.03	0.00	0.03
plot.ProbeSet	0.01	0.00	0.01
plot.density	1.30	0.06	1.36
plotLocation	3.58	0.16	3.74
pmcorrect	0.75	0.07	0.83
ppsetApply	0	0	0
read.affybatch	3.86	0.29	5.05
rma	3.56	0.01	3.58
setAffyOptions	0	0	0
xy2indices	3.61	0.20	3.83