Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:12 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for iPAC on machv2


To the developers/maintainers of the iPAC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iPAC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 950/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iPAC 1.38.0  (landing page)
Gregory Ryslik
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/iPAC
git_branch: RELEASE_3_14
git_last_commit: e34e9ed
git_last_commit_date: 2021-10-26 12:03:56 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: iPAC
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iPAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iPAC_1.38.0.tar.gz
StartedAt: 2022-04-12 14:33:21 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 14:40:53 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 452.0 seconds
RetCode: 0
Status:   OK  
CheckDir: iPAC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iPAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iPAC_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/iPAC.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.38.0’
* 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
Package in Depends field not imported from: ‘gdata’
  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 ‘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’
nmc: no visible global function definition for ‘pbeta’
plotLinear: no visible global function definition for ‘pdf’
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 ‘dev.off’
plotMDS: no visible global function definition for ‘dev.copy2pdf’
Undefined global functions or variables:
  cm.colors cmdscale col2rgb dev.copy2pdf dev.off dist dmultinom gray
  heat.colors par pbeta pbinom pdf rect text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "col2rgb", "dev.copy2pdf",
             "dev.off", "gray", "heat.colors", "pdf", "topo.colors")
  importFrom("graphics", "par", "rect", "text")
  importFrom("stats", "cmdscale", "dist", "dmultinom", "pbeta", "pbinom")
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 (user + system) or elapsed time > 5s
                 user system elapsed
ClusterFind   199.248  1.159 201.583
nmc            43.284  0.110  43.440
get.Positions  26.161  4.973  34.813
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/iPAC.Rcheck/00check.log’
for details.



Installation output

iPAC.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iPAC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘iPAC’ ...
** using staged installation
** 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 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 (iPAC)

Tests output


Example timings

iPAC.Rcheck/iPAC-Ex.timings

nameusersystemelapsed
ClusterFind199.248 1.159201.583
KRAS.Mutations0.0080.0200.029
PIK3CA.Mutations0.0280.0860.116
Plot.Protein.Linear3.2740.4984.925
get.AASeq0.0230.0040.654
get.AlignedPositions2.9900.2744.603
get.Positions26.161 4.97334.813
get.Remapped.Order2.5890.2883.949
get.SingleLetterCode0.0000.0000.001
iPAC-package0.0000.0010.001
nmc43.284 0.11043.440