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

* 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

* 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)

name	user	system	elapsed
AffyBatch-class	2.70	0.03	2.74
AffyRNAdeg	5.24	0.04	5.28
MAplot	21.07	0.60	21.69
ProbeSet-class	0.83	0.01	0.84
ProgressBarText-class	0.77	0.02	16.50
affy-options	0	0	0
barplot.ProbeSet	0.75	0.05	0.80
bgc	5.12	0.11	5.25
cleancdfname	0	0	0
expresso	24.30	0.39	24.74
expressoWidget	0.01	0.00	0.01
fit.li.wong	0	0	0
generateExprSet-methods	0.78	0.00	0.79
generateExprVal-methods	0.86	0.01	0.87
generateExprVal.method.avgdiff	0.56	0.00	0.56
list.celfiles	0	0	0
maffy.normalise	2.41	0.03	2.44
maffy.subset	0.02	0.02	0.03
mas5	54.98	0.11	55.10
mas5calls	2.77	0.11	2.89
mva.pairs	0.12	0.00	0.12
normalize-methods	0.56	0.00	0.56
normalize.loess	0.04	0.01	0.05
plot.ProbeSet	0	0	0
plot.density	1.31	0.07	1.38
plotLocation	3.45	0.12	3.57
pmcorrect	0.78	0.02	0.80
ppsetApply	0	0	0
read.affybatch	3.81	0.15	5.70
rma	3.36	0.02	3.37
setAffyOptions	0	0	0
xy2indices	3.62	0.15	3.79