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CHECK report for TFutils on malbec2

This page was generated on 2019-10-16 12:14:02 -0400 (Wed, 16 Oct 2019).

Package 1643/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFutils 1.4.0
Shweta Gopaulakrishnan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/TFutils
Branch: RELEASE_3_9
Last Commit: a2f8f46
Last Changed Date: 2019-05-02 11:54:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: TFutils
Version: 1.4.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TFutils_1.4.0.tar.gz
StartedAt: 2019-10-16 05:25:37 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:28:07 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 149.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: TFutils.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TFutils_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 ‘/home/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 11.130  0.068  11.198
genemodForGviz      7.380  0.139   7.888
fimo16              7.102  0.255   7.374
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck/00check.log’
for details.



Installation output

TFutils.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TFutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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
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)

Tests output

TFutils.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
 14.572   0.486  15.046 

Example timings

TFutils.Rcheck/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog3.3380.1193.458
TFtargs0.0010.0010.000
URL_s3_tf0.0000.0000.001
cisbpTFcat0.0330.0000.034
directHitsInCISBP0.8170.0240.842
encode6900.0300.0000.031
fimo167.1020.2557.374
fimoMap0.0020.0000.001
genemodForGviz7.3800.1397.888
genemodelDF0.1190.0000.120
grabTab0.4500.0240.473
gwascat_hg19_chr170.080.000.08
hocomoco.mono0.0060.0000.006
hocomoco.mono.sep20180.0030.0040.006
importFIMO0.0390.0040.069
importFIMO_local_split0.0150.0040.021
metadata_tf0.0190.0000.019
named_tf0.0110.0040.016
tfhash0.9210.2321.153
tftColl0.2080.0120.220
tftCollMap0.0020.0000.001
topTraitsOfTargets11.130 0.06811.198