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This page was generated on 2021-12-04 12:32:23 -0500 (Sat, 04 Dec 2021).

CHECK results for TCseq on nebbiolo1

To the developers/maintainers of the TCseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCseq.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 1925/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCseq 1.19.0  (landing page)
Mengjun Wu
Snapshot Date: 2021-12-03 13:55:11 -0500 (Fri, 03 Dec 2021)
git_url: https://git.bioconductor.org/packages/TCseq
git_branch: master
git_last_commit: 29167cf
git_last_commit_date: 2021-10-26 12:32:20 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TCseq
Version: 1.19.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TCseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TCseq_1.19.0.tar.gz
StartedAt: 2021-12-03 21:24:52 -0500 (Fri, 03 Dec 2021)
EndedAt: 2021-12-03 21:27:43 -0500 (Fri, 03 Dec 2021)
EllapsedTime: 171.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TCseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TCseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TCseq_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TCseq.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCseq’ version ‘1.19.0’
* 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 ‘TCseq’ can be installed ... OK
* 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
DBresult: no visible global function definition for ‘as’
DBresult.cluster: no visible global function definition for ‘as’
TCA: no visible global function definition for ‘is’
TCA: no visible global function definition for ‘as’
TCAFromSummarizedExperiment: no visible global function definition for
  ‘is’
TCAFromSummarizedExperiment: no visible global function definition for
  ‘as’
countReads: no visible global function definition for
  ‘createAnnotationFile’
countReads: no visible global function definition for ‘featureCounts’
timeclustplot: no visible binding for global variable ‘group’
timecourseTable: no visible global function definition for ‘as’
Undefined global functions or variables:
  as createAnnotationFile featureCounts group is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/TCseq.Rcheck/00check.log’
for details.



Installation output

TCseq.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘TCseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (TCseq)

Tests output

TCseq.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-10 r81171) -- "Unsuffered Consequences"
Copyright (C) 2021 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(TCseq)
> 
> test_check("TCseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  7.832   0.305   8.123 

Example timings

TCseq.Rcheck/TCseq-Ex.timings

nameusersystemelapsed
DBanalysis0.6690.0120.680
DBresult1.6960.0121.709
TCA0.0070.0000.007
TCA.accessors0.0450.0640.108
counts0.0490.0040.053
countsTable0.0010.0000.001
experiment0.0000.0010.001
experiment_BAMfile0.0000.0010.001
genomicIntervals0.0010.0000.000
peakreference0.0080.0000.008
tca_ATAC0.0010.0000.001
timeclustplot1.4170.0601.476
timecourseTable0.6360.0320.668