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This page was generated on 2024-03-04 11:40:03 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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

Package 2085/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TADCompare 1.13.1  (landing page)
Mikhail Dozmorov
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/TADCompare
git_branch: devel
git_last_commit: 031908c
git_last_commit_date: 2024-02-28 09:23:29 -0500 (Wed, 28 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for TADCompare on merida1


To the developers/maintainers of the TADCompare package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TADCompare
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TADCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TADCompare_1.13.1.tar.gz
StartedAt: 2024-03-02 11:35:10 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 11:41:51 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 401.0 seconds
RetCode: 0
Status:   OK  
CheckDir: TADCompare.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TADCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TADCompare_1.13.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TADCompare.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TADCompare/DESCRIPTION’ ... OK
* this is package ‘TADCompare’ version ‘1.13.1’
* 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 ‘TADCompare’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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
.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 ... 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-3.19-bioc/meat/TADCompare.Rcheck/00check.log’
for details.



Installation output

TADCompare.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
ConsensusTADs1.7030.1432.203
DiffPlot3.7680.2064.593
TADCompare0.3190.0110.380
TimeCompare1.5760.0761.880