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CHECK report for iPAC on malbec1

This page was generated on 2019-04-16 11:49:40 -0400 (Tue, 16 Apr 2019).

Package 789/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iPAC 1.26.0
Gregory Ryslik
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/iPAC
Branch: RELEASE_3_8
Last Commit: bebe766
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iPAC
Version: 1.26.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:iPAC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings iPAC_1.26.0.tar.gz
StartedAt: 2019-04-16 00:51:54 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:55:45 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 231.0 seconds
RetCode: 0
Status:  OK 
CheckDir: iPAC.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:iPAC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings iPAC_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/iPAC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iPAC’ version ‘1.26.0’
* 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 ‘iPAC’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biostrings’ ‘gdata’ ‘multtest’ ‘scatterplot3d’
  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
Plot.Protein.Linear: no visible global function definition for
  ‘heat.colors’
Plot.Protein.Linear: no visible global function definition for ‘gray’
Plot.Protein.Linear: no visible global function definition for
  ‘topo.colors’
Plot.Protein.Linear: no visible global function definition for
  ‘cm.colors’
Plot.Protein.Linear: no visible global function definition for ‘par’
Plot.Protein.Linear: no visible global function definition for ‘plot’
Plot.Protein.Linear: no visible global function definition for ‘rect’
Plot.Protein.Linear: no visible global function definition for ‘text’
SetTextContrastColor: no visible global function definition for
  ‘col2rgb’
calcorder: no visible global function definition for ‘dist’
calcorder: no visible global function definition for ‘cmdscale’
difforder0: no visible global function definition for ‘pbinom’
difforder0: no visible global function definition for ‘dmultinom’
difforder1: no visible global function definition for ‘dmultinom’
get.AlignedPositions: no visible global function definition for
  ‘PhredQuality’
get.AlignedPositions: no visible global function definition for
  ‘pairwiseAlignment’
get.AlignedPositions: no visible global function definition for ‘start’
nmc: no visible global function definition for ‘pbeta’
nmc: no visible global function definition for ‘mt.rawp2adjp’
plotLinear: no visible global function definition for ‘pdf’
plotLinear: no visible global function definition for ‘scatterplot3d’
plotLinear: no visible global function definition for ‘dev.off’
plotLinear: no visible global function definition for ‘dev.copy2pdf’
plotMDS: no visible global function definition for ‘pdf’
plotMDS: no visible global function definition for ‘scatterplot3d’
plotMDS: no visible global function definition for ‘dev.off’
plotMDS: no visible global function definition for ‘dev.copy2pdf’
Undefined global functions or variables:
  PhredQuality cm.colors cmdscale col2rgb dev.copy2pdf dev.off dist
  dmultinom gray heat.colors mt.rawp2adjp pairwiseAlignment par pbeta
  pbinom pdf plot rect scatterplot3d start text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "col2rgb", "dev.copy2pdf",
             "dev.off", "gray", "heat.colors", "pdf", "topo.colors")
  importFrom("graphics", "par", "plot", "rect", "text")
  importFrom("stats", "cmdscale", "dist", "dmultinom", "pbeta", "pbinom",
             "start")
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 or elapsed time > 5s
                user system elapsed
ClusterFind   89.620  0.096  90.859
get.Positions 22.324  0.128  25.677
nmc           20.512  0.004  20.530
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/iPAC.Rcheck/00check.log’
for details.



Installation output

iPAC.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL iPAC
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘iPAC’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iPAC)

Tests output


Example timings

iPAC.Rcheck/iPAC-Ex.timings

nameusersystemelapsed
ClusterFind89.620 0.09690.859
KRAS.Mutations0.0080.0000.006
PIK3CA.Mutations0.0160.0200.033
Plot.Protein.Linear2.1720.0683.162
get.AASeq0.1000.0080.756
get.AlignedPositions2.5280.0123.544
get.Positions22.324 0.12825.677
get.Remapped.Order2.3120.0283.366
get.SingleLetterCode0.0000.0000.001
iPAC-package0.0000.0000.001
nmc20.512 0.00420.530