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This page was generated on 2022-04-13 12:08:33 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 preciseTAD on machv2


To the developers/maintainers of the preciseTAD package:
- Please 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 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 1450/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preciseTAD 1.4.0  (landing page)
Mikhail Dozmorov
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/preciseTAD
git_branch: RELEASE_3_14
git_last_commit: 676dd8e
git_last_commit_date: 2021-10-26 13:02:48 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: preciseTAD
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2022-04-12 16:55:41 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:11:46 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 964.7 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/preciseTAD.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘preciseTAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘preciseTAD’ version ‘1.4.0’
* 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 ... OK
* 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 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 ... 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        88.993  3.073  92.178
TADrandomForest   38.869  1.242  40.148
TADrfe            19.920  0.604  20.538
createTADdata     10.718  0.113  10.840
extractBoundaries  4.991  0.010   5.004
* 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
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
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(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 
294.856  12.479 398.737 

Example timings

preciseTAD.Rcheck/preciseTAD-Ex.timings

nameusersystemelapsed
TADrandomForest38.869 1.24240.148
TADrfe19.920 0.60420.538
bedToGRangesList0.3850.0030.389
createTADdata10.718 0.11310.840
extractBoundaries4.9910.0105.004
preciseTAD88.993 3.07392.178