Package: tracktables

Version: 1.17.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:tracktables.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings tracktables_1.17.0.tar.gz

StartedAt: 2019-04-09 04:06:33 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:08:18 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 105.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: tracktables.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:tracktables.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings tracktables_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/tracktables.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.17.0’
* 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/tracktables.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL tracktables
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

name	user	system	elapsed
MakeIGVSampleMetadata	0.027	0.000	0.028
MakeIGVSession	0.062	0.000	0.062
MakeIGVSessionXML	0.044	0.000	0.045
igvParam	0.056	0.000	0.056
makebedtable	0.134	0.000	0.169
maketracktable	0.187	0.000	0.186