Package: affy

Version: 1.31.1

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings affy_1.31.1.tar.gz

StartedAt: 2011-05-09 14:13:34 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:19:31 -0700 (Mon, 09 May 2011)

EllapsedTime: 357.6 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/affy.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '1.31.1'
* 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 installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/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˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c mas5calls.c -o mas5calls.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rma2.c -o rma2.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/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˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-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 ...
*** tangling vignette sources ...
   'affy.Rnw' 
   'builtinMethods.Rnw' 
   'customMethods.Rnw' 
   'vim.Rnw' 
** testing if installed package can be loaded

* DONE (affy)

name	user	system	elapsed
AffyBatch-class	3.31	0.08	5.24
AffyRNAdeg	5.89	0.08	7.24
MAplot	25.00	0.62	27.61
ProbeSet-class	0.84	0.07	0.91
ProgressBarText-class	0.83	0.01	16.89
affy-options	0	0	0
barplot.ProbeSet	0.79	0.05	0.84
bgc	5.93	0.14	6.34
cleancdfname	0.01	0.00	0.02
expresso	27.97	0.39	30.25
expressoWidget	0	0	0
fit.li.wong	0	0	0
generateExprSet-methods	0.75	0.03	0.78
generateExprVal-methods	0.85	0.02	3.14
generateExprVal.method.avgdiff	0.67	0.00	1.07
list.celfiles	0	0	0
maffy.normalise	2.65	0.01	2.72
maffy.subset	0.08	0.00	0.08
mas5	61.37	0.21	70.89
mas5calls	2.96	0.21	3.37
mva.pairs	0.13	0.00	0.13
normalize-methods	0.56	0.02	0.57
normalize.loess	0.05	0.00	0.05
plot.ProbeSet	0.01	0.00	0.02
plot.density	1.25	0.12	1.46
plotLocation	3.99	0.19	4.36
pmcorrect	0.81	0.00	1.16
ppsetApply	0	0	0
read.affybatch	3.83	0.21	5.41
rma	3.20	0.06	3.32
setAffyOptions	0	0	0
xy2indices	3.53	0.17	3.72