Package: TFutils

Version: 1.6.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TFutils_1.6.0.tar.gz

StartedAt: 2020-04-15 05:40:00 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:44:51 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 291.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TFutils.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TFutils_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/TFutils.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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  5.4Mb
  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 or elapsed time > 5s
                     user system elapsed
tffamCirc.plot     25.668  0.236  26.043
tffamCirc.prep     15.148  0.012  15.196
topTraitsOfTargets  9.368  0.076   9.465
fimo16              8.804  0.368   9.248
genemodForGviz      7.368  0.132   7.813
get_rslocs_38       0.168  0.008   5.315
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/TFutils.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TFutils
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-pc-linux-gnu (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 
 17.364   0.588  18.063 

name	user	system	elapsed
HGNCmap	0.000	0.000	0.001
TFCatalog	0.672	0.008	0.681
TFtargs	0	0	0
URL_s3_tf	0.000	0.000	0.001
anchor_pmids	0.008	0.000	0.007
browse_lambert_gwaslinks	0	0	0
browse_lambert_main	0	0	0
cisbpTFcat	0.056	0.004	0.063
cisbpTFcat_2.0	0.068	0.004	0.074
defaultCircosParms	0.012	0.000	0.012
demo_fimo_granges	0.02	0.00	0.02
directHitsInCISBP	0.116	0.004	0.121
encode690	0.060	0.000	0.059
fimo16	8.804	0.368	9.248
fimoMap	0.004	0.000	0.003
fimo_granges	0.004	0.000	0.001
genemodForGviz	7.368	0.132	7.813
genemodelDF	0.144	0.008	0.179
get_rslocs_38	0.168	0.008	5.315
grabTab	0.340	0.028	0.367
gwascat_hg19_chr17	0.068	0.000	0.067
hocomoco.mono	0.004	0.000	0.005
hocomoco.mono.sep2018	0.008	0.000	0.005
importFIMO	0.040	0.008	0.061
importFIMO_local_split	0.020	0.000	0.032
lambert_snps	0.304	0.016	0.320
metadata_tf	0.016	0.000	0.019
named_tf	0.004	0.008	0.013
retrieve_lambert_main	0	0	0
seqinfo_hg19_chr17	0.004	0.000	0.004
tffamCirc.plot	25.668	0.236	26.043
tffamCirc.prep	15.148	0.012	15.196
tfhash	0.552	0.200	0.754
tftColl	0.308	0.000	0.311
tftCollMap	0.004	0.000	0.001
topTraitsOfTargets	9.368	0.076	9.465