Package: TFutils

Version: 1.3.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFutils_1.3.4.tar.gz

StartedAt: 2019-04-09 04:05:38 -0400 (Tue, 09 Apr 2019)

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

EllapsedTime: 251.7 seconds

RetCode: 0

Status:  OK

CheckDir: TFutils.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFutils_1.3.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.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 ‘TFutils/DESCRIPTION’ ... OK
* this is package ‘TFutils’ version ‘1.3.4’
* 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 ‘TFutils’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
directHitsInCISBP: no visible binding for global variable
  ‘DISEASE.TRAIT’
directHitsInCISBP: no visible binding for global variable ‘MAPPED_GENE’
directHitsInCISBP: no visible binding for global variable ‘cisbpTFcat’
directHitsInCISBP: no visible binding for global variable ‘HGNC’
directHitsInCISBP: no visible binding for global variable ‘Family_Name’
setupHIZE: no visible global function definition for ‘read.delim’
topTraitsOfTargets: no visible global function definition for
  ‘geneIdType’
topTraitsOfTargets: no visible global function definition for
  ‘mapIdentifiers’
topTraitsOfTargets: no visible global function definition for
  ‘SymbolIdentifier’
topTraitsOfTargets: no visible global function definition for ‘geneIds’
topTraitsOfTargets: no visible global function definition for ‘mcols’
topTraitsOfTargets: no visible binding for global variable
  ‘DISEASE.TRAIT’
Undefined global functions or variables:
  DISEASE.TRAIT Family_Name HGNC MAPPED_GENE SymbolIdentifier
  cisbpTFcat geneIdType geneIds mapIdentifiers mcols read.delim
Consider adding
  importFrom("utils", "read.delim")
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 ... NOTE
  Note: found 62 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
topTraitsOfTargets 10.738  0.444  11.301
genemodForGviz      6.826  0.305   7.262
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.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 TFutils
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘TFutils’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (TFutils)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TFutils)
> 
> test_check("TFutils")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 5 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
 15.443   0.780  16.364 

name	user	system	elapsed
HGNCmap	0.001	0.000	0.000
TFCatalog	1.758	0.096	1.872
TFtargs	0.000	0.000	0.001
URL_s3_tf	0.001	0.000	0.001
cisbpTFcat	0.045	0.005	0.049
directHitsInCISBP	0.627	0.005	0.633
encode690	0.049	0.001	0.054
fimo16	4.247	0.160	4.453
fimoMap	0.001	0.000	0.002
genemodForGviz	6.826	0.305	7.262
genemodelDF	0.139	0.018	0.160
grabTab	0.405	0.047	0.457
gwascat_hg19_chr17	0.041	0.005	0.046
hocomoco.mono	0.005	0.001	0.006
hocomoco.mono.sep2018	0.005	0.001	0.006
importFIMO	0.032	0.005	0.037
importFIMO_local_split	0.020	0.004	0.025
metadata_tf	0.024	0.006	0.031
named_tf	0.015	0.011	0.026
tfhash	1.452	0.432	1.904
tftColl	0.158	0.013	0.174
tftCollMap	0.002	0.000	0.002
topTraitsOfTargets	10.738	0.444	11.301