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This page was generated on 2024-07-09 17:43 -0400 (Tue, 09 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4709
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1600/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preciseTAD 1.14.0  (landing page)
Mikhail Dozmorov
Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024)
git_url: https://git.bioconductor.org/packages/preciseTAD
git_branch: RELEASE_3_19
git_last_commit: f8f7c6f
git_last_commit_date: 2024-04-30 11:27:10 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for preciseTAD on kjohnson1

To the developers/maintainers of the preciseTAD package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preciseTAD.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: preciseTAD
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preciseTAD_1.14.0.tar.gz
StartedAt: 2024-07-09 05:14:06 -0400 (Tue, 09 Jul 2024)
EndedAt: 2024-07-09 05:28:07 -0400 (Tue, 09 Jul 2024)
EllapsedTime: 841.6 seconds
RetCode: 0
Status:   OK  
CheckDir: preciseTAD.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preciseTAD_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/preciseTAD.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘preciseTAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘preciseTAD’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘preciseTAD’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* checking code 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
preciseTAD      82.891  3.238  86.228
TADrandomForest 33.905  0.963  34.872
TADrfe          19.632  0.623  20.264
createTADdata    5.051  0.165   5.218
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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/preciseTAD.Rcheck/00check.log’
for details.


Installation output

preciseTAD.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘preciseTAD’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (preciseTAD)

Tests output

preciseTAD.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(preciseTAD)

> 
> test_check("preciseTAD")
+ Fold1: mtry= 2, ntree=500, nodesize=1 
- Fold1: mtry= 2, ntree=500, nodesize=1 
+ Fold1: mtry= 5, ntree=500, nodesize=1 
- Fold1: mtry= 5, ntree=500, nodesize=1 
+ Fold1: mtry= 8, ntree=500, nodesize=1 
- Fold1: mtry= 8, ntree=500, nodesize=1 
+ Fold1: mtry=10, ntree=500, nodesize=1 
- Fold1: mtry=10, ntree=500, nodesize=1 
+ Fold1: mtry=13, ntree=500, nodesize=1 
- Fold1: mtry=13, ntree=500, nodesize=1 
+ Fold1: mtry=16, ntree=500, nodesize=1 
- Fold1: mtry=16, ntree=500, nodesize=1 
+ Fold1: mtry=18, ntree=500, nodesize=1 
- Fold1: mtry=18, ntree=500, nodesize=1 
+ Fold1: mtry=21, ntree=500, nodesize=1 
- Fold1: mtry=21, ntree=500, nodesize=1 
+ Fold1: mtry=24, ntree=500, nodesize=1 
- Fold1: mtry=24, ntree=500, nodesize=1 
+ Fold1: mtry=26, ntree=500, nodesize=1 
- Fold1: mtry=26, ntree=500, nodesize=1 
+ Fold2: mtry= 2, ntree=500, nodesize=1 
- Fold2: mtry= 2, ntree=500, nodesize=1 
+ Fold2: mtry= 5, ntree=500, nodesize=1 
- Fold2: mtry= 5, ntree=500, nodesize=1 
+ Fold2: mtry= 8, ntree=500, nodesize=1 
- Fold2: mtry= 8, ntree=500, nodesize=1 
+ Fold2: mtry=10, ntree=500, nodesize=1 
- Fold2: mtry=10, ntree=500, nodesize=1 
+ Fold2: mtry=13, ntree=500, nodesize=1 
- Fold2: mtry=13, ntree=500, nodesize=1 
+ Fold2: mtry=16, ntree=500, nodesize=1 
- Fold2: mtry=16, ntree=500, nodesize=1 
+ Fold2: mtry=18, ntree=500, nodesize=1 
- Fold2: mtry=18, ntree=500, nodesize=1 
+ Fold2: mtry=21, ntree=500, nodesize=1 
- Fold2: mtry=21, ntree=500, nodesize=1 
+ Fold2: mtry=24, ntree=500, nodesize=1 
- Fold2: mtry=24, ntree=500, nodesize=1 
+ Fold2: mtry=26, ntree=500, nodesize=1 
- Fold2: mtry=26, ntree=500, nodesize=1 
+ Fold3: mtry= 2, ntree=500, nodesize=1 
- Fold3: mtry= 2, ntree=500, nodesize=1 
+ Fold3: mtry= 5, ntree=500, nodesize=1 
- Fold3: mtry= 5, ntree=500, nodesize=1 
+ Fold3: mtry= 8, ntree=500, nodesize=1 
- Fold3: mtry= 8, ntree=500, nodesize=1 
+ Fold3: mtry=10, ntree=500, nodesize=1 
- Fold3: mtry=10, ntree=500, nodesize=1 
+ Fold3: mtry=13, ntree=500, nodesize=1 
- Fold3: mtry=13, ntree=500, nodesize=1 
+ Fold3: mtry=16, ntree=500, nodesize=1 
- Fold3: mtry=16, ntree=500, nodesize=1 
+ Fold3: mtry=18, ntree=500, nodesize=1 
- Fold3: mtry=18, ntree=500, nodesize=1 
+ Fold3: mtry=21, ntree=500, nodesize=1 
- Fold3: mtry=21, ntree=500, nodesize=1 
+ Fold3: mtry=24, ntree=500, nodesize=1 
- Fold3: mtry=24, ntree=500, nodesize=1 
+ Fold3: mtry=26, ntree=500, nodesize=1 
- Fold3: mtry=26, ntree=500, nodesize=1 
Aggregating results
Selecting tuning parameters
Fitting mtry = 2, ntree = 500, nodesize = 1 on full training set
+(rfe) fit Fold1 size: 26 
-(rfe) fit Fold1 size: 26 
+(rfe) imp Fold1 
-(rfe) imp Fold1 
+(rfe) fit Fold1 size: 16 
-(rfe) fit Fold1 size: 16 
+(rfe) fit Fold1 size:  8 
-(rfe) fit Fold1 size:  8 
+(rfe) fit Fold1 size:  4 
-(rfe) fit Fold1 size:  4 
+(rfe) fit Fold1 size:  2 
-(rfe) fit Fold1 size:  2 
+(rfe) fit Fold2 size: 26 
-(rfe) fit Fold2 size: 26 
+(rfe) imp Fold2 
-(rfe) imp Fold2 
+(rfe) fit Fold2 size: 16 
-(rfe) fit Fold2 size: 16 
+(rfe) fit Fold2 size:  8 
-(rfe) fit Fold2 size:  8 
+(rfe) fit Fold2 size:  4 
-(rfe) fit Fold2 size:  4 
+(rfe) fit Fold2 size:  2 
-(rfe) fit Fold2 size:  2 
+(rfe) fit Fold3 size: 26 
-(rfe) fit Fold3 size: 26 
+(rfe) imp Fold3 
-(rfe) imp Fold3 
+(rfe) fit Fold3 size: 16 
-(rfe) fit Fold3 size: 16 
+(rfe) fit Fold3 size:  8 
-(rfe) fit Fold3 size:  8 
+(rfe) fit Fold3 size:  4 
-(rfe) fit Fold3 size:  4 
+(rfe) fit Fold3 size:  2 
-(rfe) fit Fold3 size:  2 
+(rfe) fit Fold4 size: 26 
-(rfe) fit Fold4 size: 26 
+(rfe) imp Fold4 
-(rfe) imp Fold4 
+(rfe) fit Fold4 size: 16 
-(rfe) fit Fold4 size: 16 
+(rfe) fit Fold4 size:  8 
-(rfe) fit Fold4 size:  8 
+(rfe) fit Fold4 size:  4 
-(rfe) fit Fold4 size:  4 
+(rfe) fit Fold4 size:  2 
-(rfe) fit Fold4 size:  2 
+(rfe) fit Fold5 size: 26 
-(rfe) fit Fold5 size: 26 
+(rfe) imp Fold5 
-(rfe) imp Fold5 
+(rfe) fit Fold5 size: 16 
-(rfe) fit Fold5 size: 16 
+(rfe) fit Fold5 size:  8 
-(rfe) fit Fold5 size:  8 
+(rfe) fit Fold5 size:  4 
-(rfe) fit Fold5 size:  4 
+(rfe) fit Fold5 size:  2 
-(rfe) fit Fold5 size:  2 
+ Fold1: mtry=2, ntree=500, nodesize=1 
- Fold1: mtry=2, ntree=500, nodesize=1 
+ Fold2: mtry=2, ntree=500, nodesize=1 
- Fold2: mtry=2, ntree=500, nodesize=1 
+ Fold3: mtry=2, ntree=500, nodesize=1 
- Fold3: mtry=2, ntree=500, nodesize=1 
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=3 and eps=10000"
[1] "    preciseTAD identified 13 PTBRs"
[1] "    Establishing PTBPs"
[1] "        Cluster 1 out of 13"
[1] "        Cluster 2 out of 13"
[1] "        Cluster 3 out of 13"
[1] "        Cluster 4 out of 13"
[1] "        Cluster 5 out of 13"
[1] "        Cluster 6 out of 13"
[1] "        Cluster 7 out of 13"
[1] "        Cluster 8 out of 13"
[1] "        Cluster 9 out of 13"
[1] "        Cluster 10 out of 13"
[1] "        Cluster 11 out of 13"
[1] "        Cluster 12 out of 13"
[1] "        Cluster 13 out of 13"
[1] "Optimal combination of MinPts and eps is = (3, 10000)"
[1] "preciseTAD identified a total of 12897 base pairs whose predictive probability was equal to or exceeded a threshold of 1"
[1] "Initializing DBSCAN for MinPts = 3 and eps = 10000"
[1] "preciseTAD identified 13 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 13"
[1] "Cluster 2 out of 13"
[1] "Cluster 3 out of 13"
[1] "Cluster 4 out of 13"
[1] "Cluster 5 out of 13"
[1] "Cluster 6 out of 13"
[1] "Cluster 7 out of 13"
[1] "Cluster 8 out of 13"
[1] "Cluster 9 out of 13"
[1] "Cluster 10 out of 13"
[1] "Cluster 11 out of 13"
[1] "Cluster 12 out of 13"
[1] "Cluster 13 out of 13"
+ Fold1: mtry=2, ntree=500, nodesize=1 
- Fold1: mtry=2, ntree=500, nodesize=1 
+ Fold2: mtry=2, ntree=500, nodesize=1 
- Fold2: mtry=2, ntree=500, nodesize=1 
+ Fold3: mtry=2, ntree=500, nodesize=1 
- Fold3: mtry=2, ntree=500, nodesize=1 
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=1000 and eps=5000"
[1] "    preciseTAD identified 14 PTBRs"
[1] "    Establishing PTBPs"
[1] "        Cluster 1 out of 14"
[1] "        Cluster 2 out of 14"
[1] "        Cluster 3 out of 14"
[1] "        Cluster 4 out of 14"
[1] "        Cluster 5 out of 14"
[1] "        Cluster 6 out of 14"
[1] "        Cluster 7 out of 14"
[1] "        Cluster 8 out of 14"
[1] "        Cluster 9 out of 14"
[1] "        Cluster 10 out of 14"
[1] "        Cluster 11 out of 14"
[1] "        Cluster 12 out of 14"
[1] "        Cluster 13 out of 14"
[1] "        Cluster 14 out of 14"
[1] "Optimal combination of MinPts and eps is = (1000, 5000)"
[1] "preciseTAD identified a total of 59929 base pairs whose predictive probability was equal to or exceeded a threshold of 0.99"
[1] "Initializing DBSCAN for MinPts = 1000 and eps = 5000"
[1] "preciseTAD identified 14 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 14"
[1] "Cluster 2 out of 14"
[1] "Cluster 3 out of 14"
[1] "Cluster 4 out of 14"
[1] "Cluster 5 out of 14"
[1] "Cluster 6 out of 14"
[1] "Cluster 7 out of 14"
[1] "Cluster 8 out of 14"
[1] "Cluster 9 out of 14"
[1] "Cluster 10 out of 14"
[1] "Cluster 11 out of 14"
[1] "Cluster 12 out of 14"
[1] "Cluster 13 out of 14"
[1] "Cluster 14 out of 14"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
268.522  13.789 365.757 

Example timings

preciseTAD.Rcheck/preciseTAD-Ex.timings

nameusersystemelapsed
TADrandomForest33.905 0.96334.872
TADrfe19.632 0.62320.264
bedToGRangesList0.1920.0030.197
createTADdata5.0510.1655.218
extractBoundaries1.9190.0451.964
preciseTAD82.891 3.23886.228