BioC 2.12: CHECK report for AgiMicroRna on george2

Package: AgiMicroRna

Version: 2.10.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings AgiMicroRna_2.10.0.tar.gz

StartedAt: 2013-10-09 00:02:16 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:17:27 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 910.3 seconds

RetCode: 0

Status:  OK

CheckDir: AgiMicroRna.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/AgiMicroRna.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.10.0’
* 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 ‘AgiMicroRna’ can be installed ... [65s/68s] 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("rma_c_complete_copy", ..., PACKAGE = "affy")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
HeatMapMicroRna: warning in heatmap.2(DD.s, labCol = samples, labRow =
  names, scale = "none", col = rbg, margin = c(10, 10), tracecol =
  "cyan"): partial argument match of 'margin' to 'margins'
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [341s/346s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
rmaMicroRna 270.885  1.156 276.148
mvaMicroRna  19.969  0.108  20.379
* 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/AgiMicroRna.Rcheck/00check.log’
for details.

* installing *source* package ‘AgiMicroRna’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AgiMicroRna)

name	user	system	elapsed
HeatMapMicroRna	0.916	0.188	1.143
PCAplotMicroRna	0.172	0.012	0.184
RleMicroRna	4.317	0.092	4.492
basicLimma	0.028	0.008	0.037
boxplotMicroRna	1.364	0.028	1.429
cvArray	0.016	0.000	0.016
filterMicroRna	3.712	0.028	3.776
getDecideTests	0.016	0.000	0.015
hierclusMicroRna	0.020	0.012	0.031
mvaBASIC	2.840	0.056	2.901
mvaMicroRna	19.969	0.108	20.379
plotDensityMicroRna	0.340	0.020	0.408
pvalHistogram	1.136	0.000	1.137
qcPlots	0.012	0.000	0.014
readMicroRnaAFE	0.004	0.000	0.004
rmaMicroRna	270.885	1.156	276.148
significantMicroRna	0.944	0.016	0.962
tgsMicroRna	2.921	0.036	2.989
tgsNormalization	0.008	0.000	0.008
uRNAList	0.008	0.000	0.006
writeEset	0.020	0.000	0.023