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This page was generated on 2023-04-12 11:05:55 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TFutils on palomino4


To the developers/maintainers of the TFutils package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFutils.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2042/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFutils 1.18.0  (landing page)
Vincent Carey
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/TFutils
git_branch: RELEASE_3_16
git_last_commit: fa5538c
git_last_commit_date: 2022-11-01 11:17:33 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TFutils
Version: 1.18.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFutils.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings TFutils_1.18.0.tar.gz
StartedAt: 2023-04-11 06:44:34 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 06:49:08 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 274.1 seconds
RetCode: 0
Status:   OK  
CheckDir: TFutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFutils.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings TFutils_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/TFutils.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TFutils/DESCRIPTION' ... OK
* this is package 'TFutils' version '1.18.0'
* 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 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 ... 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
fimo_granges : proctext: warning in read.delim(con, h = FALSE,
  stringsAsFactors = FALSE, sep = "\t"): partial argument match of 'h'
  to 'header'
setupHIZE: warning in read.delim(txtfn, sep = "\t", skip = 3, h =
  FALSE, stringsAsFactors = FALSE): partial argument match of 'h' to
  'header'
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: no visible global function definition for 'reduceByRange'
fimo_granges : <anonymous>: no visible global function definition for
  'seqinfo<-'
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 reduceByRange rowRanges<-
  seqinfo<-
Consider adding
  importFrom("base", "factor")
  importFrom("stats", "family")
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 LazyData ... OK
* 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     23.26   0.44   23.79
tffamCirc.prep     13.38   0.04   13.44
topTraitsOfTargets  8.33   0.27    8.59
fimo16              7.36   0.48    7.85
genemodForGviz      6.11   0.29    6.47
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/TFutils.Rcheck/00check.log'
for details.



Installation output

TFutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL TFutils
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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)

Tests output

TFutils.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  14.00    1.01   15.00 

Example timings

TFutils.Rcheck/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog0.160.050.21
TFtargs000
URL_s3_tf000
anchor_pmids000
browse_gotf_main000
browse_humantfs_main000
browse_lambert_gwaslinks000
browse_lambert_main000
cisbpTFcat0.070.000.06
cisbpTFcat_2.00.030.000.03
defaultCircosParms0.010.000.02
demo_fimo_granges0.000.020.01
directHitsInCISBP0.660.000.66
encode6900.030.000.03
fimo167.360.487.85
fimoMap000
fimo_granges000
genemodForGviz6.110.296.47
genemodelDF0.080.000.08
get_rslocs_38000
grabTab0.170.000.17
gwascat_hg19_chr170.050.000.05
hocomoco.mono000
hocomoco.mono.sep2018000
importFIMO0.040.000.04
importFIMO_local_split0.020.000.02
lambert_snps0.190.020.20
metadata_tf0.010.000.02
named_tf0.030.000.03
retrieve_gotf_main000
retrieve_humantfs_main000
retrieve_lambert_main000
seqinfo_hg19_chr170.020.000.01
tffamCirc.plot23.26 0.4423.79
tffamCirc.prep13.38 0.0413.44
tfhash0.70.31.0
tftColl0.20.00.2
tftCollMap0.020.000.02
topTraitsOfTargets8.330.278.59