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CHECK report for TFutils on merida1

This page was generated on 2021-05-06 12:37:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the TFutils package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1854/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFutils 1.10.1  (landing page)
Shweta Gopaulakrishnan
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/TFutils
Branch: RELEASE_3_12
Last Commit: 268035b
Last Changed Date: 2020-11-04 10:41:48 -0400 (Wed, 04 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: TFutils
Version: 1.10.1
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_1.10.1.tar.gz
StartedAt: 2021-05-06 06:51:17 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:56:56 -0400 (Thu, 06 May 2021)
EllapsedTime: 338.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TFutils.Rcheck
Warnings: 0

Command output

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### 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_1.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/TFutils.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TFutils/DESCRIPTION’ ... OK
* this is package ‘TFutils’ version ‘1.10.1’
* 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  5.9Mb
  sub-directories of 1Mb or more:
    data      4.0Mb
    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 ... OK
* 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<-’
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 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     28.769  0.211  29.016
tffamCirc.prep     19.159  0.267  19.446
fimo16              9.024  0.304  10.722
topTraitsOfTargets  8.506  0.216   8.734
genemodForGviz      6.653  0.235   6.916
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/TFutils.Rcheck/00check.log’
for details.



Installation output

TFutils.Rcheck/00install.out

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###
### 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)

Tests output

TFutils.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> 
> proc.time()
   user  system elapsed 
 17.688   0.739  19.716 

Example timings

TFutils.Rcheck/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap0.0000.0000.001
TFCatalog0.2400.0180.259
TFtargs0.0000.0010.000
URL_s3_tf0.0010.0000.001
anchor_pmids0.0050.0000.007
browse_lambert_gwaslinks000
browse_lambert_main000
cisbpTFcat0.0570.0040.061
cisbpTFcat_2.00.0490.0050.054
defaultCircosParms0.0080.0020.011
demo_fimo_granges0.0210.0000.021
directHitsInCISBP0.1340.0060.140
encode6900.0590.0020.061
fimo16 9.024 0.30410.722
fimoMap0.0020.0010.003
fimo_granges0.0010.0010.001
genemodForGviz6.6530.2356.916
genemodelDF0.1310.0110.144
get_rslocs_380.0000.0000.001
grabTab0.420.040.46
gwascat_hg19_chr170.0690.0060.075
hocomoco.mono0.0080.0020.009
hocomoco.mono.sep20180.0080.0020.010
importFIMO0.0620.0070.069
importFIMO_local_split0.0150.0060.022
lambert_snps0.2440.0150.260
metadata_tf0.0180.0100.028
named_tf0.0140.0240.040
retrieve_lambert_main000
seqinfo_hg19_chr170.0050.0010.006
tffamCirc.plot28.769 0.21129.016
tffamCirc.prep19.159 0.26719.446
tfhash0.9620.6961.678
tftColl0.1790.0010.180
tftCollMap0.0020.0000.002
topTraitsOfTargets8.5060.2168.734