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

* 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

* 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)

name	user	system	elapsed
AffyBatch-class	2.97	0.08	3.35
AffyRNAdeg	5.22	0.05	5.27
MAplot	26.40	0.47	27.13
ProbeSet-class	0.84	0.11	0.95
ProgressBarText-class	0.75	0.00	16.47
affy-options	0	0	0
barplot.ProbeSet	0.91	0.03	0.94
bgc	6.73	0.06	6.80
cleancdfname	0.02	0.00	0.01
expresso	25.31	0.25	25.68
expressoWidget	0	0	0
fit.li.wong	0.01	0.00	0.01
generateExprSet-methods	0.83	0.02	0.85
generateExprVal-methods	0.91	0.03	0.94
generateExprVal.method.avgdiff	0.68	0.00	0.67
list.celfiles	0	0	0
maffy.normalise	3.34	0.04	3.38
maffy.subset	0.06	0.01	0.08
mas5	53.92	0.13	56.16
mas5calls	3.27	0.07	3.36
mva.pairs	0.14	0.00	0.14
normalize-methods	0.54	0.02	0.57
normalize.loess	0.06	0.00	0.06
plot.ProbeSet	0	0	0
plot.density	1.33	0.02	1.34
plotLocation	4.58	0.04	5.08
pmcorrect	0.87	0.02	0.89
ppsetApply	0	0	0
read.affybatch	4.14	0.19	6.00
rma	4.88	0.01	4.92
setAffyOptions	0	0	0
xy2indices	4.59	0.09	5.02