Package: affy

Version: 1.28.1

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings affy_1.28.1.tar.gz

StartedAt: 2011-03-31 05:01:57 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 05:07:23 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 326.3 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/affy.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-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
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"E:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"E:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c getall_locations.c -o getall_locations.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"E:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"E:/biocbld/BBS-2˜1.7-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include" -DHAVE_ZLIB  -I"E:/biocbld/BBS-2˜1.7-B/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˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/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)

name	user	system	elapsed
AffyBatch-class	3.00	0.11	3.11
AffyRNAdeg	10.58	0.07	10.69
MAplot	46.92	0.46	47.65
ProbeSet-class	1.12	0.06	1.25
ProgressBarText-class	0.72	0.02	16.47
affy-options	0	0	0
barplot.ProbeSet	1.17	0.00	1.19
bgc	9.49	0.20	9.76
cleancdfname	0.00	0.01	0.02
expresso	29.90	0.41	30.48
expressoWidget	0	0	0
fit.li.wong	0	0	0
generateExprSet-methods	1.15	0.02	1.20
generateExprVal-methods	1.19	0.06	1.26
generateExprVal.method.avgdiff	0.80	0.01	0.81
list.celfiles	0	0	0
maffy.normalise	3.94	0.05	4.05
maffy.subset	0.01	0.02	0.03
mas5	72.52	0.12	73.42
mas5calls	3.43	0.03	3.48
mva.pairs	0.27	0.00	0.27
normalize-methods	0.78	0.07	0.84
normalize.loess	0.03	0.01	0.05
plot.ProbeSet	0.02	0.00	0.01
plot.density	1.61	0.05	1.68
plotLocation	17.93	0.15	18.09
pmcorrect	1.22	0.05	1.27
ppsetApply	0	0	0
read.affybatch	4.67	0.13	6.48
rma	5.18	0.01	5.20
setAffyOptions	0	0	0
xy2indices	18.54	0.16	18.72