Package: TFutils

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2020-04-15 06:07:24 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:12:46 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 321.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TFutils.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:TFutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFutils_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/TFutils.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      3.5Mb
    lambert   1.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rsamtools’
A package should be listed in only one of these fields.
* 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
'::' or ':::' imports not declared from:
  'BiocFileCache' 'DT' 'httr' 'readxl' 'rjson'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
browse_lambert_gwaslinks: no visible global function definition for
  ‘read.csv’
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’
fimo_granges: no visible global function definition for ‘rowRanges<-’
fimo_granges : proctext: no visible global function definition for
  ‘read.delim’
fimo_granges: no visible global function definition for ‘reduceByRange’
fimo_granges : <anonymous>: no visible global function definition for
  ‘seqinfo<-’
retrieve_lambert_main: no visible global function definition for
  ‘bfcadd’
setupHIZE: no visible global function definition for ‘read.delim’
tffamCirc.prep: no visible binding for global variable ‘TF family’
tffamCirc.prep: no visible binding for global variable ‘TFfamily’
tffamCirc.prep: no visible binding for global variable ‘Transcription
  factor’
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 TF family TFfamily
  Transcription factor bfcadd cisbpTFcat mcols read.csv read.delim
  reduceByRange rowRanges<- seqinfo<-
Consider adding
  importFrom("base", "factor")
  importFrom("stats", "family")
  importFrom("utils", "read.csv", "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
tffamCirc.plot     29.417  0.405  30.085
tffamCirc.prep     16.894  0.072  17.131
topTraitsOfTargets 10.074  0.412  10.575
fimo16              8.591  0.412   9.082
genemodForGviz      7.007  0.285   7.344
get_rslocs_38       0.535  0.018  10.707
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-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’ ...
** using staged installation
** 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 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 (TFutils)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
 17.315   0.881  18.338 

name	user	system	elapsed
HGNCmap	0	0	0
TFCatalog	0.214	0.019	0.234
TFtargs	0	0	0
URL_s3_tf	0.001	0.000	0.001
anchor_pmids	0.007	0.000	0.007
browse_lambert_gwaslinks	0.000	0.000	0.001
browse_lambert_main	0	0	0
cisbpTFcat	0.051	0.005	0.055
cisbpTFcat_2.0	0.041	0.002	0.045
defaultCircosParms	0.011	0.001	0.012
demo_fimo_granges	0.018	0.000	0.019
directHitsInCISBP	0.115	0.003	0.119
encode690	0.046	0.001	0.047
fimo16	8.591	0.412	9.082
fimoMap	0.003	0.000	0.003
fimo_granges	0.001	0.000	0.002
genemodForGviz	7.007	0.285	7.344
genemodelDF	0.142	0.013	0.155
get_rslocs_38	0.535	0.018	10.707
grabTab	0.432	0.050	0.488
gwascat_hg19_chr17	0.062	0.006	0.068
hocomoco.mono	0.005	0.000	0.005
hocomoco.mono.sep2018	0.006	0.001	0.008
importFIMO	0.055	0.008	0.063
importFIMO_local_split	0.023	0.007	0.030
lambert_snps	0.337	0.021	0.359
metadata_tf	0.020	0.005	0.027
named_tf	0.019	0.013	0.032
retrieve_lambert_main	0	0	0
seqinfo_hg19_chr17	0.005	0.001	0.005
tffamCirc.plot	29.417	0.405	30.085
tffamCirc.prep	16.894	0.072	17.131
tfhash	1.571	0.433	2.017
tftColl	0.246	0.006	0.252
tftCollMap	0.001	0.001	0.001
topTraitsOfTargets	10.074	0.412	10.575