Package: affyPara

Version: 1.19.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings affyPara_1.19.2.tar.gz

StartedAt: 2013-03-24 23:51:13 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:53:22 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 129.6 seconds

RetCode: 0

Status:  OK

CheckDir: affyPara.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/affyPara.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.19.2’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘affyPara’ can be installed ... [9s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following directories should probably not be installed:
  ‘fig’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [19s/20s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mergeSplitObjects 10.78  0.332  11.436
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/affyPara.Rcheck/00check.log’
for details.

* installing *source* package ‘affyPara’ ...
** R
** inst
** preparing package for lazy loading
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘affyPara.Rnw’ 
   ‘vsnStudy.Rnw’ 
** testing if installed package can be loaded
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
* DONE (affyPara)

name	user	system	elapsed
MAplotPara	0.032	0.000	0.032
bgcPara	0.024	0.008	0.033
boxplotPara	0.016	0.020	0.035
computeExprSetPara	0.016	0.012	0.028
distributeFiles	0.016	0.008	0.024
mergeSplitObjects	10.780	0.332	11.436
normalizeAffyBatchConstantPara	0.012	0.000	0.009
normalizeAffyBatchInvariantsetPara	0.012	0.000	0.011
normalizeAffyBatchLoessPara	0.012	0.000	0.011
normalizeAffyBatchLoessParaIter	0.052	0.000	0.053
normalizeAffyBatchQuantilesPara	0.012	0.000	0.012
preproPara	0.048	0.000	0.050
qa	0.008	0.000	0.008
readAffybatchPara	0.008	0.000	0.009
removeDistributedFiles	0.036	0.000	0.039
rmaPara	0.008	0.000	0.009
snowReplace	0.044	0.000	0.042
split	3.157	0.032	3.202
vsnPara	0.008	0.000	0.014