Package: sva

Version: 3.0.2

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch sva_3.0.2.tar.gz

StartedAt: 2012-01-09 05:59:53 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 06:00:54 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 61.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sva.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/sva.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sva/DESCRIPTION' ... OK
* this is package 'sva' version '3.0.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'sva' 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'sva':
sva
  Code: function(dat, mod, mod0 = NULL, n.sv = NULL, method = c("irw",
                 "two-step"), vfilter = NULL, B = 5, numSVmethod =
                 "be")
  Docs: function(dat, mod, mod0 = NULL, n.sv = NULL, method = c("irw",
                 "two-step"), vfilter = NULL, B = 5)
  Argument names in code not in docs:
    numSVmethod

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.9-bioc/meat/sva.Rcheck/00check.log'
for details

* installing *source* package 'sva' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c sva.c -o sva.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o sva.dll tmp.def sva.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/sva.Rcheck/sva/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'sva.Rnw' 
** testing if installed package can be loaded

* DONE (sva)

name	user	system	elapsed
ComBat	0	0	0
f.pvalue	0	0	0
fsva	0	0	0
irwsva.build	0	0	0
num.sv	0	0	0
sva	0	0	0
twostepsva.build	0	0	0