Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:40 -0400 (Fri, 15 Oct 2021).

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? here 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 939/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iPAC 1.36.0  (landing page)
Gregory Ryslik
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/iPAC
git_branch: RELEASE_3_13
git_last_commit: c449c77
git_last_commit_date: 2021-05-19 11:53:11 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iPAC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iPAC_1.36.0.tar.gz
StartedAt: 2021-10-14 20:15:49 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:22:13 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 384.2 seconds
RetCode: 0
Status:   OK  
CheckDir: iPAC.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iPAC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iPAC_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/iPAC.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.36.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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         163.459  0.899 165.569
nmc                  38.130  0.103  38.255
get.Positions        23.103  4.309  32.406
Plot.Protein.Linear   3.729  0.499   5.165
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/iPAC.Rcheck/00check.log’
for details.



Installation output

iPAC.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL iPAC
###
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* 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
ClusterFind163.459 0.899165.569
KRAS.Mutations0.0070.0190.027
PIK3CA.Mutations0.0270.0840.111
Plot.Protein.Linear3.7290.4995.165
get.AASeq0.0180.0060.629
get.AlignedPositions2.5420.2253.941
get.Positions23.103 4.30932.406
get.Remapped.Order2.1840.2213.325
get.SingleLetterCode0.0000.0010.002
iPAC-package0.0000.0010.001
nmc38.130 0.10338.255