BioC experimental data: CHECK report for Hiiragi2013 on perceval

Package: Hiiragi2013

Version: 0.99.14

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Hiiragi2013_0.99.14.tar.gz

StartedAt: 2014-04-04 11:10:31 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 11:17:51 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 439.3 seconds

RetCode: 0

Status:  OK

CheckDir: Hiiragi2013.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/Hiiragi2013.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Hiiragi2013’ version ‘0.99.14’
* 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 ‘Hiiragi2013’ can be installed ... [20s/22s] OK
* checking installed package size ... NOTE
  installed size is 139.3Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
    doc     2.9Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘affy’ ‘Biobase’ ‘boot’ ‘clue’ ‘cluster’ ‘genefilter’ ‘geneplotter’
  ‘gplots’ ‘gtools’ ‘KEGGREST’ ‘lattice’ ‘latticeExtra’ ‘MASS’
  ‘mouse4302.db’ ‘RColorBrewer’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [50s/51s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
a       17.991  0.976  19.153
MDSplot  5.687  0.247   5.986
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/Hiiragi2013.Rcheck/00check.log’
for details.

* installing *source* package ‘Hiiragi2013’ ...
** 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 (Hiiragi2013)

name	user	system	elapsed
MDSplot	5.687	0.247	5.986
a	17.991	0.976	19.153
getDifferentialExpressedGenes	4.299	0.491	4.790
myHeatmap	3.715	0.422	4.146
myHeatmap2	0.006	0.007	0.013
pamCluster	3.039	0.190	3.272
plotProjection	0.002	0.004	0.005
x	2.911	0.311	3.310
xq	0.024	0.029	0.156
xql	0.012	0.028	0.075