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CHECK report for pmm on malbec1

This page was generated on 2021-05-06 12:28:37 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the pmm package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1362/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pmm 1.22.0  (landing page)
Anna Drewek
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/pmm
Branch: RELEASE_3_12
Last Commit: 526ba35
Last Changed Date: 2020-10-27 11:04:06 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: pmm
Version: 1.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pmm.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pmm_1.22.0.tar.gz
StartedAt: 2021-05-06 04:36:19 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:38:08 -0400 (Thu, 06 May 2021)
EllapsedTime: 109.7 seconds
RetCode: 0
Status:   OK  
CheckDir: pmm.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pmm.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pmm_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/pmm.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 ‘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 pnorm points polygon qnorm quantile rect reshape rgb text
Consider adding
  importFrom("grDevices", "colorRamp", "colorRampPalette", "rgb")
  importFrom("graphics", "axis", "hist", "par", "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
pmm        29.420  0.024  29.472
hitheatmap 15.364  0.040  15.439
sharedness 14.412  0.012  14.447
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/pmm.Rcheck/00check.log’
for details.



Installation output

pmm.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL pmm
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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)

Tests output


Example timings

pmm.Rcheck/pmm-Ex.timings

nameusersystemelapsed
hitheatmap15.364 0.04015.439
kinome0.0600.0040.066
pmm29.420 0.02429.472
sharedness14.412 0.01214.447