BioC experimental data: CHECK report for Hiiragi2013 on zin2

Package: Hiiragi2013

Version: 1.4.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Hiiragi2013_1.4.0.tar.gz

StartedAt: 2015-10-07 10:06:58 -0700 (Wed, 07 Oct 2015)

EndedAt: 2015-10-07 10:11:01 -0700 (Wed, 07 Oct 2015)

EllapsedTime: 243.0 seconds

RetCode: 0

Status:  OK

CheckDir: Hiiragi2013.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Hiiragi2013_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-data-experiment/meat/Hiiragi2013.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘affy’ ‘Biobase’ ‘boot’ ‘clue’ ‘cluster’ ‘genefilter’ ‘geneplotter’
  ‘gplots’ ‘gtools’ ‘KEGGREST’ ‘MASS’ ‘mouse4302.db’ ‘RColorBrewer’
  ‘xtable’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [9s/17s] OK
* checking installed package size ... NOTE
  installed size is 139.2Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
    doc     2.8Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘KEGGREST’ ‘affy’ ‘boot’ ‘clue’ ‘geneplotter’ ‘gtools’ ‘mouse4302.db’
  ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... [35s/50s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
a       13.049  0.181  20.141
MDSplot  3.941  0.019   6.442
* 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-data-experiment/meat/Hiiragi2013.Rcheck/00check.log’
for details.

* installing *source* package ‘Hiiragi2013’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Hiiragi2013)

name	user	system	elapsed
MDSplot	3.941	0.019	6.442
a	13.049	0.181	20.141
getDifferentialExpressedGenes	3.351	0.090	3.781
myHeatmap	3.706	0.066	4.644
myHeatmap2	0.002	0.000	0.001
pamCluster	3.132	0.007	3.533
plotProjection	0	0	0
x	3.056	0.008	3.917
xq	0.015	0.000	0.014
xql	0.007	0.000	0.019