BioC 2.12: CHECK report for Agi4x44PreProcess on petty

Package: Agi4x44PreProcess

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Agi4x44PreProcess_1.20.0.tar.gz

StartedAt: 2013-10-08 21:31:44 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:35:36 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 232.7 seconds

RetCode: 0

Status:  OK

CheckDir: Agi4x44PreProcess.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Agi4x44PreProcess.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Agi4x44PreProcess/DESCRIPTION' ... OK
* this is package 'Agi4x44PreProcess' version '1.20.0'
* 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 'Agi4x44PreProcess' can be installed ... [20s/22s] 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 ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
genes.rpt.agi 5.71  0.256   6.039
* 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
  '/Users/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (Agi4x44PreProcess)

name	user	system	elapsed
Agi4x44PreProcess-package	0.255	0.011	0.266
BGandNorm	0.006	0.001	0.008
BoxPlot	0.008	0.001	0.010
CV.rep.probes	0.010	0.001	0.011
HeatMap	0.010	0.001	0.012
MVAplotMED	0.009	0.001	0.009
MVAplotMEDctrl	3.490	0.114	3.639
PCAplot	0.028	0.003	0.032
RLE	0.020	0.001	0.021
boxplotNegCtrl	0.011	0.001	0.012
build.eset	0.021	0.003	0.023
build.mappings	0.019	0.002	0.021
dd	0.018	0.001	0.019
ensembl.htmlpage	0.031	0.001	0.033
filter.NonUnifOL	0.026	0.002	0.027
filter.PopnOL	0.020	0.002	0.022
filter.control	0.019	0.002	0.021
filter.isfound	0.024	0.002	0.026
filter.probes	0.040	0.003	0.043
filter.saturated	0.029	0.003	0.031
filter.wellaboveBG	0.022	0.002	0.022
filter.wellaboveNEG	0.022	0.003	0.024
genes.rpt.agi	5.710	0.256	6.039
gsea.files	0.022	0.006	0.028
hierclus	0.022	0.005	0.027
plotDensity	0.002	0.003	0.005
read.AgilentFE	0.348	0.026	0.376
read.targets	0.005	0.004	0.009
summarize.probe	0.019	0.003	0.024
targets	0.002	0.003	0.006
write.eset	0.021	0.006	0.026