Package: Ularcirc

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Ularcirc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Ularcirc_1.1.2.tar.gz

StartedAt: 2019-04-09 04:17:38 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:21:49 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 251.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Ularcirc.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Ularcirc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Ularcirc_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Ularcirc.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ularcirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ularcirc’ version ‘1.1.2’
* package encoding: UTF-8
* 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 ‘Ularcirc’ 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
Namespaces in Imports field not imported from:
  ‘DT’ ‘GenomeInfoDb’ ‘GenomeInfoDbData’ ‘GenomicFeatures’ ‘Sushi’
  ‘data.table’ ‘ggplot2’ ‘ggrepel’ ‘gsubfn’ ‘httpuv’ ‘mirbase.db’
  ‘moments’ ‘shinyFiles’ ‘yaml’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘genes’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘GRanges’
BSJ_to_circRNA_sequence: no visible binding for global variable
  ‘strand’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘findOverlaps’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘invertStrand’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘subjectHits’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘select’
BSJ_to_circRNA_sequence: no visible binding for global variable
  ‘GeneList’
BSJ_to_circRNA_sequence: no visible binding for global variable
  ‘GeneName’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘as.data.table’
BSJ_to_circRNA_sequence: no visible binding for global variable ‘start’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘getSeq’
BSJ_to_circRNA_sequence: no visible global function definition for
  ‘DNAString’
Undefined global functions or variables:
  DNAString GRanges GeneList GeneName as.data.table findOverlaps genes
  getSeq invertStrand select start strand subjectHits
Consider adding
  importFrom("stats", "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 ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
'library' or 'require' call not declared from: ‘BiocManager’
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
Compatible_Annotation_DBs 172.852 22.919 215.068
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Ularcirc.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Ularcirc
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Ularcirc’ ...
** R
** 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 (Ularcirc)

name	user	system	elapsed
Compatible_Annotation_DBs	172.852	22.919	215.068
Ularcirc	0	0	0