Package: Agi4x44PreProcess

Version: 1.18.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings Agi4x44PreProcess_1.18.0.tar.gz

StartedAt: 2013-03-24 23:08:06 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:10:40 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 153.7 seconds

RetCode: 0

Status:  OK

CheckDir: Agi4x44PreProcess.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Agi4x44PreProcess.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Agi4x44PreProcess/DESCRIPTION’ ... OK
* this is package ‘Agi4x44PreProcess’ version ‘1.18.0’
* 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 whether package ‘Agi4x44PreProcess’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* checking R code for possible problems ... NOTE
HeatMap: 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'
filter.probes: warning in .packages(all = TRUE): partial argument match
  of 'all' to 'all.available'
genes.rpt.agi: warning in ensembl.htmlpage(PROBE_ID, probe.chr,
  filename, annotation.package, title, table.head = head, table.center
  = TRUE, other = list(unlist(GENE_ID), unlist(gene.sym),
  unlist(probe.chr))): partial argument match of 'other' to
  'othernames'
write.eset: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
* 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
genes.rpt.agi 5.028  0.064   5.441
* 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 was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Agi4x44PreProcess.Rcheck/00check.log’
for details.

* installing *source* package ‘Agi4x44PreProcess’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Agi4x44PreProcess.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded

* DONE (Agi4x44PreProcess)

name	user	system	elapsed
Agi4x44PreProcess-package	0	0	0
BGandNorm	0	0	0
BoxPlot	0	0	0
CV.rep.probes	0	0	0
HeatMap	0	0	0
MVAplotMED	0	0	0
MVAplotMEDctrl	2.372	0.052	2.538
PCAplot	0	0	0
RLE	0	0	0
boxplotNegCtrl	0	0	0
build.eset	0	0	0
build.mappings	0	0	0
dd	0.000	0.000	0.001
ensembl.htmlpage	0	0	0
filter.NonUnifOL	0	0	0
filter.PopnOL	0	0	0
filter.control	0	0	0
filter.isfound	0.000	0.000	0.001
filter.probes	0.000	0.000	0.001
filter.saturated	0	0	0
filter.wellaboveBG	0	0	0
filter.wellaboveNEG	0	0	0
genes.rpt.agi	5.028	0.064	5.441
gsea.files	0	0	0
hierclus	0	0	0
plotDensity	0	0	0
read.AgilentFE	0.180	0.012	0.218
read.targets	0.004	0.000	0.034
summarize.probe	0	0	0
targets	0	0	0
write.eset	0	0	0