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This page was generated on 2022-01-21 11:06:49 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 nebbiolo1


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? here 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 1941/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFutils 1.15.1  (landing page)
Vincent Carey
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/TFutils
git_branch: master
git_last_commit: 6dccfdd
git_last_commit_date: 2021-11-21 01:00:28 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Rsamtools' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TFutils
Version: 1.15.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TFutils_1.15.1.tar.gz
StartedAt: 2022-01-20 21:19:57 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 21:23:47 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 230.1 seconds
RetCode: 0
Status:   OK  
CheckDir: TFutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TFutils_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TFutils.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.15.1’
* 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  5.4Mb
  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     13.753  0.144  13.897
topTraitsOfTargets  8.108  0.099   8.209
fimo16              7.134  0.404   7.540
tffamCirc.prep      6.618  0.020   6.637
genemodForGviz      5.547  0.301   5.874
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/TFutils.Rcheck/00check.log’
for details.



Installation output

TFutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TFutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> 
> proc.time()
   user  system elapsed 
 13.802   0.790  14.574 

Example timings

TFutils.Rcheck/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog0.3550.0240.380
TFtargs000
URL_s3_tf000
anchor_pmids0.0070.0000.006
browse_gotf_main000
browse_humantfs_main000
browse_lambert_gwaslinks000
browse_lambert_main0.0000.0000.001
cisbpTFcat0.0330.0070.040
cisbpTFcat_2.00.6870.2840.971
defaultCircosParms0.0080.0000.008
demo_fimo_granges0.0070.0000.007
directHitsInCISBP0.1360.0000.136
encode6900.0300.0040.034
fimo167.1340.4047.540
fimoMap0.0000.0010.002
fimo_granges0.0000.0010.001
genemodForGviz5.5470.3015.874
genemodelDF0.0800.0000.079
get_rslocs_38000
grabTab0.1650.0040.169
gwascat_hg19_chr170.0390.0040.042
hocomoco.mono0.0040.0000.004
hocomoco.mono.sep20180.0000.0050.004
importFIMO0.0310.0030.034
importFIMO_local_split0.0060.0080.015
lambert_snps0.2090.0200.228
metadata_tf0.0070.0120.019
named_tf0.0030.0200.024
retrieve_gotf_main0.0000.0000.001
retrieve_humantfs_main0.0000.0010.000
retrieve_lambert_main000
seqinfo_hg19_chr170.0020.0020.003
tffamCirc.plot13.753 0.14413.897
tffamCirc.prep6.6180.0206.637
tfhash0.4160.8441.260
tftColl0.1870.0000.187
tftCollMap0.0010.0000.001
topTraitsOfTargets8.1080.0998.209