Package: TFutils

Version: 1.7.0

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_1.7.0.tar.gz

StartedAt: 2020-01-16 09:26:15 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:33:38 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 443.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TFutils.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TFutils.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.7.0’
* 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  5.4Mb
  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 (user + system) or elapsed time > 5s
                     user system elapsed
tffamCirc.plot     37.786  0.612  38.554
tffamCirc.prep     20.570  0.076  20.647
topTraitsOfTargets 15.437  0.863  16.299
fimo16             12.597  0.929  13.528
genemodForGviz      9.611  0.785  10.513
* 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-3.11-bioc/meat/TFutils.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFutils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 
 23.526   2.066  25.538 

name	user	system	elapsed
HGNCmap	0.001	0.000	0.001
TFCatalog	0.407	0.035	0.443
TFtargs	0.000	0.000	0.001
URL_s3_tf	0.000	0.000	0.001
anchor_pmids	0.010	0.001	0.011
browse_lambert_gwaslinks	0.001	0.000	0.001
browse_lambert_main	0	0	0
cisbpTFcat	0.039	0.010	0.048
cisbpTFcat_2.0	0.054	0.003	0.057
defaultCircosParms	0.011	0.002	0.013
demo_fimo_granges	0.022	0.000	0.022
directHitsInCISBP	0.130	0.005	0.135
encode690	0.207	0.002	0.209
fimo16	12.597	0.929	13.528
fimoMap	0.004	0.000	0.004
fimo_granges	0.002	0.000	0.002
genemodForGviz	9.611	0.785	10.513
genemodelDF	0.207	0.001	0.208
get_rslocs_38	0.657	0.023	3.686
grabTab	0.561	0.035	0.596
gwascat_hg19_chr17	0.106	0.015	0.122
hocomoco.mono	0.010	0.002	0.012
hocomoco.mono.sep2018	0.009	0.002	0.011
importFIMO	0.090	0.016	0.107
importFIMO_local_split	0.029	0.011	0.042
lambert_snps	0.373	0.048	0.421
metadata_tf	0.028	0.015	0.044
named_tf	0.025	0.026	0.051
retrieve_lambert_main	0.000	0.000	0.001
seqinfo_hg19_chr17	0.005	0.002	0.007
tffamCirc.plot	37.786	0.612	38.554
tffamCirc.prep	20.570	0.076	20.647
tfhash	1.710	0.880	2.595
tftColl	0.470	0.015	0.485
tftCollMap	0.002	0.001	0.003
topTraitsOfTargets	15.437	0.863	16.299