Package: pmm

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pmm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pmm_1.16.0.tar.gz

StartedAt: 2019-10-16 05:38:40 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:41:02 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 142.4 seconds

RetCode: 0

Status:  OK

CheckDir: pmm.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pmm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pmm_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pmm.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pmm’ version ‘1.16.0’
* 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 ‘pmm’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hitheatmap: no visible global function definition for ‘na.omit’
hitheatmap: no visible global function definition for ‘par’
hitheatmap: no visible global function definition for ‘colorRamp’
hitheatmap: no visible global function definition for ‘rgb’
hitheatmap: no visible global function definition for ‘plot’
hitheatmap: no visible global function definition for ‘polygon’
hitheatmap: no visible global function definition for ‘points’
hitheatmap: no visible global function definition for ‘text’
hitheatmap: no visible global function definition for
  ‘colorRampPalette’
hitheatmap : color.bar: no visible global function definition for
  ‘axis’
hitheatmap : color.bar: no visible global function definition for
  ‘rect’
hitheatmap: no visible global function definition for ‘axis’
local.fdr: no visible global function definition for ‘hist’
local.fdr: no visible global function definition for ‘glm’
local.fdr: no visible global function definition for ‘quantile’
local.fdr: no visible global function definition for ‘qnorm’
local.fdr: no visible global function definition for ‘median’
local.fdr: no visible global function definition for ‘dnorm’
local.fdr: no visible global function definition for ‘approx’
mle.fct: no visible global function definition for ‘pnorm’
mle.fct: no visible global function definition for ‘dnorm’
pmm: no visible global function definition for ‘reshape’
pmm: no visible global function definition for ‘na.omit’
sharedness: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  approx axis colorRamp colorRampPalette dnorm glm hist median na.omit
  par plot pnorm points polygon qnorm quantile rect reshape rgb text
Consider adding
  importFrom("grDevices", "colorRamp", "colorRampPalette", "rgb")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon", "rect", "text")
  importFrom("stats", "approx", "dnorm", "glm", "median", "na.omit",
             "pnorm", "qnorm", "quantile", "reshape")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
pmm        31.317  1.702  33.029
hitheatmap 17.061  1.010  18.074
sharedness 15.757  0.891  16.654
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/pmm.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pmm
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pmm’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pmm)

name	user	system	elapsed
hitheatmap	17.061	1.010	18.074
kinome	0.064	0.010	0.074
pmm	31.317	1.702	33.029
sharedness	15.757	0.891	16.654