Package: TFutils

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-10-16 07:21:32 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:25:09 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 216.9 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: in method for ‘importFIMO’ with signature ‘"TabixFile","GRanges"’: no definition for classes “TabixFile”, “GRanges”
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck/00install.out’ for details.
* 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 13.199  0.848  14.051
fimo16             12.590  0.862  13.457
genemodForGviz      8.964  0.732   9.801
TFCatalog           5.685  0.500   6.187
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-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/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
Warning: in method for ‘importFIMO’ with signature ‘"TabixFile","GRanges"’: no definition for classes “TabixFile”, “GRanges”
** 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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 
 21.692   1.784  23.579 

name	user	system	elapsed
HGNCmap	0.000	0.000	0.001
TFCatalog	5.685	0.500	6.187
TFtargs	0.001	0.000	0.001
URL_s3_tf	0.001	0.001	0.001
cisbpTFcat	0.063	0.013	0.076
directHitsInCISBP	1.075	0.073	1.149
encode690	0.039	0.001	0.041
fimo16	12.590	0.862	13.457
fimoMap	0.003	0.001	0.004
genemodForGviz	8.964	0.732	9.801
genemodelDF	0.188	0.011	0.199
grabTab	0.648	0.098	0.746
gwascat_hg19_chr17	0.066	0.011	0.076
hocomoco.mono	0.006	0.001	0.007
hocomoco.mono.sep2018	0.009	0.001	0.010
importFIMO	0.058	0.009	0.070
importFIMO_local_split	0.025	0.007	0.035
metadata_tf	0.032	0.017	0.049
named_tf	0.024	0.024	0.049
tfhash	1.850	0.981	2.831
tftColl	0.226	0.030	0.256
tftCollMap	0.002	0.000	0.002
topTraitsOfTargets	13.199	0.848	14.051