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This page was generated on 2023-01-30 11:09:05 -0500 (Mon, 30 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4510
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4288
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4317
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 SpectralTAD on lconway


To the developers/maintainers of the SpectralTAD package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpectralTAD.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 1935/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpectralTAD 1.14.0  (landing page)
Kellen Cresswell
Snapshot Date: 2023-01-29 14:00:05 -0500 (Sun, 29 Jan 2023)
git_url: https://git.bioconductor.org/packages/SpectralTAD
git_branch: RELEASE_3_16
git_last_commit: 8970942
git_last_commit_date: 2022-11-01 11:19:18 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
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: SpectralTAD
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpectralTAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpectralTAD_1.14.0.tar.gz
StartedAt: 2023-01-29 23:13:06 -0500 (Sun, 29 Jan 2023)
EndedAt: 2023-01-29 23:15:32 -0500 (Sun, 29 Jan 2023)
EllapsedTime: 145.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SpectralTAD.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpectralTAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpectralTAD_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SpectralTAD.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpectralTAD/DESCRIPTION’ ... OK
* this is package ‘SpectralTAD’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpectralTAD’ 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
.windowedSpec: no visible binding for global variable ‘Group’
.windowedSpec: no visible binding for global variable ‘group_place’
.windowedSpec: no visible binding for global variable ‘ID’
.windowedSpec: no visible binding for global variable ‘Sil_Score’
SpectralTAD: no visible binding for global variable ‘end’
Undefined global functions or variables:
  Group ID Sil_Score end group_place
Consider adding
  importFrom("stats", "end")
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
SpectralTAD     11.282  0.544  11.886
SpectralTAD_Par  2.367  0.092   8.126
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/SpectralTAD.Rcheck/00check.log’
for details.



Installation output

SpectralTAD.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpectralTAD
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘SpectralTAD’ ...
** using staged installation
** R
** data
** 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 (SpectralTAD)

Tests output

SpectralTAD.Rcheck/tests/testthat.Rout


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 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(SpectralTAD)
> 
> test_check("SpectralTAD")
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 1 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 14.843   0.819  15.731 

Example timings

SpectralTAD.Rcheck/SpectralTAD-Ex.timings

nameusersystemelapsed
SpectralTAD11.282 0.54411.886
SpectralTAD_Par2.3670.0928.126