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CHECK report for tracktables on merida1

This page was generated on 2021-05-06 12:37:14 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the tracktables package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1883/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tracktables 1.24.0  (landing page)
Tom Carroll
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/tracktables
Branch: RELEASE_3_12
Last Commit: 26c4770
Last Changed Date: 2020-10-27 11:00:33 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: tracktables
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tracktables.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tracktables_1.24.0.tar.gz
StartedAt: 2021-05-06 06:58:35 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:00:39 -0400 (Thu, 06 May 2021)
EllapsedTime: 124.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: tracktables.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tracktables.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tracktables_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/tracktables.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tracktables/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tracktables’ version ‘1.24.0’
* 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 ‘tracktables’ 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 ... WARNING
'library' or 'require' call not declared from: ‘ore’
'library' or 'require' call to ‘ore’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetGRanges: no visible global function definition for ‘read.delim’
MakeIGVSampleMetadata: no visible global function definition for
  ‘write.table’
MakeIGVSession: no visible global function definition for ‘col2rgb’
MakeIGVSessionXML: no visible global function definition for ‘col2rgb’
maketracktable: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb read.delim write.table
Consider adding
  importFrom("grDevices", "col2rgb")
  importFrom("utils", "read.delim", "write.table")
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
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/tracktables.Rcheck/00check.log’
for details.



Installation output

tracktables.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tracktables
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘tracktables’ ...
** 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 (tracktables)

Tests output


Example timings

tracktables.Rcheck/tracktables-Ex.timings

nameusersystemelapsed
MakeIGVSampleMetadata0.0200.0030.023
MakeIGVSession0.0490.0060.055
MakeIGVSessionXML0.0350.0030.038
igvParam0.0440.0040.049
makebedtable0.1240.0070.133
maketracktable0.1970.0150.237