Package: affy

Version: 1.30.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch affy_1.30.0.tar.gz

StartedAt: 2011-10-20 12:42:29 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 12:46:09 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 220.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affy.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/affy.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.30.0'
* checking package namespace 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 ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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' ... WARNING
Package vignette(s) without corresponding PDF:
   affy.Rnw
   builtinMethods.Rnw
   customMethods.Rnw
   vim.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/affy.Rcheck/00check.log'
for details

* 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-2.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.8-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˜1.8-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.8-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˜1.8-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
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	2.81	0.01	3.33
AffyRNAdeg	5.00	0.06	5.12
MAplot	22.75	0.50	23.39
ProbeSet-class	0.82	0.02	0.83
ProgressBarText-class	0.75	0.02	16.48
affy-options	0	0	0
barplot.ProbeSet	0.79	0.01	0.82
bgc	5.33	0.17	5.50
cleancdfname	0.02	0.00	0.01
expresso	25.96	0.35	26.36
expressoWidget	0	0	0
fit.li.wong	0.02	0.00	0.02
generateExprSet-methods	0.77	0.00	0.76
generateExprVal-methods	0.87	0.01	0.89
generateExprVal.method.avgdiff	0.56	0.00	0.57
list.celfiles	0	0	0
maffy.normalise	2.64	0.02	2.67
maffy.subset	0.02	0.01	0.04
mas5	56.67	0.19	56.92
mas5calls	2.92	0.11	3.03
mva.pairs	0.12	0.00	0.13
normalize-methods	0.58	0.03	0.61
normalize.loess	0.05	0.02	0.06
plot.ProbeSet	0	0	0
plot.density	1.45	0.06	1.52
plotLocation	3.30	0.20	4.23
pmcorrect	0.81	0.02	0.91
ppsetApply	0	0	0
read.affybatch	4.08	0.23	6.39
rma	3.36	0.02	3.39
setAffyOptions	0	0	0
xy2indices	4.63	0.12	4.91