Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2023-01-30 11:06:07 -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 TADCompare on nebbiolo2


To the developers/maintainers of the TADCompare package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TADCompare.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 2017/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TADCompare 1.8.0  (landing page)
Kellen Cresswell
Snapshot Date: 2023-01-29 14:00:05 -0500 (Sun, 29 Jan 2023)
git_url: https://git.bioconductor.org/packages/TADCompare
git_branch: RELEASE_3_16
git_last_commit: ca77240
git_last_commit_date: 2022-11-01 11:22:10 -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: TADCompare
Version: 1.8.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TADCompare.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings TADCompare_1.8.0.tar.gz
StartedAt: 2023-01-30 00:21:45 -0500 (Mon, 30 Jan 2023)
EndedAt: 2023-01-30 00:27:08 -0500 (Mon, 30 Jan 2023)
EllapsedTime: 323.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TADCompare.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TADCompare.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings TADCompare_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TADCompare.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TADCompare/DESCRIPTION’ ... OK
* this is package ‘TADCompare’ version ‘1.8.0’
* 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 ‘TADCompare’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘cluster’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Make_Triangles: no visible binding for global variable ‘start’
.Make_Triangles: no visible binding for global variable ‘end’
.Make_Triangles: no visible global function definition for ‘na.omit’
.Make_Triangles: no visible binding for global variable
  ‘boundary_start’
.Make_Triangles: no visible binding for global variable ‘orig_regx’
.Make_Triangles: no visible binding for global variable ‘start1’
.Make_Triangles: no visible binding for global variable ‘boundary_end’
ConsensusTADs : <anonymous>: no visible binding for global variable
  ‘Coordinate’
ConsensusTADs: no visible binding for global variable ‘Sample’
ConsensusTADs: no visible binding for global variable ‘Boundary’
ConsensusTADs: no visible binding for global variable ‘Diff_Score’
ConsensusTADs: no visible global function definition for ‘sd’
ConsensusTADs: no visible binding for global variable ‘Differential’
ConsensusTADs: no visible binding for global variable ‘Coordinate’
ConsensusTADs: no visible binding for global variable ‘TAD_Score’
ConsensusTADs: no visible binding for global variable ‘.’
ConsensusTADs: no visible binding for global variable ‘median’
DiffPlot: no visible binding for global variable ‘Type’
DiffPlot: no visible binding for global variable ‘Differential’
DiffPlot: no visible binding for global variable ‘Boundary’
DiffPlot: no visible binding for global variable ‘Enriched_In’
DiffPlot: no visible global function definition for ‘na.omit’
DiffPlot: no visible binding for global variable ‘boundary_start’
DiffPlot: no visible binding for global variable ‘orig_regx’
DiffPlot: no visible binding for global variable ‘start1’
DiffPlot: no visible binding for global variable ‘boundary_end’
DiffPlot: no visible binding for global variable ‘start2’
DiffPlot: no visible binding for global variable ‘TAD_Score1’
DiffPlot: no visible binding for global variable ‘TAD_Score2’
DiffPlot: no visible binding for global variable ‘Gap_Score’
DiffPlot: no visible binding for global variable ‘variable’
DiffPlot: no visible binding for global variable ‘value’
DiffPlot: no visible binding for global variable ‘line_spot’
DiffPlot: no visible global function definition for ‘complete.cases’
DiffPlot: no visible binding for global variable ‘.’
DiffPlot: no visible binding for global variable ‘x’
DiffPlot: no visible binding for global variable ‘y’
DiffPlot: no visible binding for global variable ‘orig_regy’
TADCompare: no visible global function definition for ‘sd’
TADCompare: no visible binding for global variable ‘Boundary’
TADCompare: no visible binding for global variable ‘Gap_Score’
TADCompare: no visible binding for global variable ‘Differential’
TADCompare: no visible binding for global variable ‘Bound_Dist’
TADCompare: no visible binding for global variable ‘Enriched_In’
TADCompare: no visible binding for global variable ‘Type’
TADCompare: no visible binding for global variable ‘Count’
TimeCompare : <anonymous>: no visible binding for global variable
  ‘Coordinate’
TimeCompare: no visible binding for global variable ‘Sample’
TimeCompare: no visible binding for global variable ‘Groups’
TimeCompare: no visible binding for global variable ‘Coordinate’
TimeCompare: no visible binding for global variable ‘Boundary’
TimeCompare: no visible global function definition for ‘median’
TimeCompare: no visible binding for global variable ‘Diff_Score’
TimeCompare: no visible global function definition for ‘sd’
TimeCompare: no visible binding for global variable ‘Differential’
TimeCompare: no visible binding for global variable ‘TAD_Score’
TimeCompare: no visible binding for global variable ‘.’
TimeCompare: no visible binding for global variable ‘median’
TimeCompare: no visible binding for global variable ‘Sample 1’
TimeCompare: no visible binding for global variable ‘Consensus_Score’
TimeCompare: no visible binding for global variable ‘Category’
TimeCompare: no visible binding for global variable ‘Count’
Undefined global functions or variables:
  . Bound_Dist Boundary Category Consensus_Score Coordinate Count
  Diff_Score Differential Enriched_In Gap_Score Groups Sample Sample 1
  TAD_Score TAD_Score1 TAD_Score2 Type boundary_end boundary_start
  complete.cases end line_spot median na.omit orig_regx orig_regy sd
  start start1 start2 value variable x y
Consider adding
  importFrom("stats", "complete.cases", "end", "median", "na.omit", "sd",
             "start")
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Input_Data.Rmd’ using ‘UTF-8’... OK
  ‘Ontology_Analysis.Rmd’ using ‘UTF-8’... OK
  ‘TADCompare.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Input_Data.Rmd’ using rmarkdown
--- finished re-building ‘Input_Data.Rmd’

--- re-building ‘Ontology_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Ontology_Analysis.Rmd’

--- re-building ‘TADCompare.Rmd’ using rmarkdown
Quitting from lines 96-103 (TADCompare.Rmd) 
Error: processing vignette 'TADCompare.Rmd' failed with diagnostics:
`x` must be a vector, not `NULL`.
--- failed re-building ‘TADCompare.Rmd’

SUMMARY: processing the following file failed:
  ‘TADCompare.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/TADCompare.Rcheck/00check.log’
for details.


Installation output

TADCompare.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TADCompare
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘TADCompare’ ...
** 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 (TADCompare)

Tests output


Example timings

TADCompare.Rcheck/TADCompare-Ex.timings

nameusersystemelapsed
ConsensusTADs1.9670.0962.063
DiffPlot1.2050.0601.266
TADCompare0.2380.0040.242
TimeCompare1.2860.0881.373