Package: Hiiragi2013

Version: 1.14.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Hiiragi2013_1.14.1.tar.gz

StartedAt: 2018-04-12 10:07:58 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:10:53 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 175.2 seconds

RetCode: 0

Status:  OK

CheckDir: Hiiragi2013.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Hiiragi2013_1.14.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/Hiiragi2013.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.14.1’
* 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 ... 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 ... NOTE
MDSplot: no visible global function definition for ‘dist’
MDSplot: no visible global function definition for ‘par’
MDSplot: no visible global function definition for ‘plot’
MDSplot: no visible global function definition for ‘points’
MDSplot: no visible global function definition for ‘grey’
MDSplot: no visible global function definition for ‘text’
getDifferentialExpressedGenes: no visible global function definition
  for ‘quantile’
getDifferentialExpressedGenes: no visible global function definition
  for ‘p.adjust’
myHeatmap: no visible global function definition for ‘as.dendrogram’
myHeatmap: no visible global function definition for ‘hclust’
myHeatmap: no visible global function definition for ‘dist’
myHeatmap: no visible global function definition for ‘order.dendrogram’
myHeatmap2: no visible global function definition for
  ‘colorRampPalette’
ordermat : <anonymous>: no visible global function definition for
  ‘order.dendrogram’
ordermat : <anonymous>: no visible global function definition for
  ‘as.dendrogram’
ordermat : <anonymous>: no visible global function definition for
  ‘hclust’
ordermat : <anonymous>: no visible global function definition for
  ‘dist’
pamCluster: no visible global function definition for ‘dist’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dist grey hclust order.dendrogram
  p.adjust par plot points quantile text
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "par", "plot", "points", "text")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "p.adjust", "quantile")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
    user system elapsed
a 12.688   0.38  13.103
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-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	4.484	0.072	4.569
a	12.688	0.380	13.103
getDifferentialExpressedGenes	3.488	0.136	3.632
myHeatmap	3.340	0.072	3.412
myHeatmap2	0.004	0.000	0.003
pamCluster	2.700	0.068	2.769
plotProjection	0.000	0.000	0.001
x	2.536	0.044	2.584
xq	0.020	0.004	0.023
xql	0.008	0.000	0.005