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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/FindIT2.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ 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 ‘FindIT2’ 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 ... 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 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
findIT_regionRP     11.829  0.153  13.458
calcRP_region        9.695  0.204  10.538
plot_peakGeneCor     7.502  0.158   8.055
calcRP_coverage      6.420  0.557   7.346
calcRP_TFHit         6.499  0.296   7.431
enhancerPromoterCor  5.429  0.108   6.304
peakGeneCor          5.305  0.206   5.881
integrate_ChIP_RNA   4.990  0.082   6.016
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘FindIT2’ ...
** 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 (FindIT2)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(FindIT2)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) {
+     stop("unable to load TxDb.Athaliana.BioMart.plantsmart28")
+ }
Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28
> 
> test_check("FindIT2")
>> preparing gene features information...		2024-03-28 02:58:12
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:58:15
>> preparing weight info...		2024-03-28 02:58:15
>> loading E50h_sampleChr5.bw info...		2024-03-28 02:58:15
------------
>> extracting and calcluating Chr5 signal...		2024-03-28 02:58:15
>> dealing with Chr5 left gene signal...		2024-03-28 02:58:21
>> norming Chr5RP accoring to the whole Chr RP...		2024-03-28 02:58:21
>> merging all Chr RP together...		2024-03-28 02:58:21
>> done		2024-03-28 02:58:21
>> checking seqlevels match...		2024-03-28 02:58:21
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-03-28 02:58:21
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:58:23
>> finding overlap peak in gene scan region...		2024-03-28 02:58:23
>> dealing with left peak not your gene scan region...		2024-03-28 02:58:23
>> merging two set peaks...		2024-03-28 02:58:24
>> calculating distance and dealing with gene strand...		2024-03-28 02:58:24
>> merging all info together ...		2024-03-28 02:58:24
>> done		2024-03-28 02:58:24
>> calculating peakCenter to TSS using peak-gene pair...		2024-03-28 02:58:24
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-03-28 02:58:26
>> calculating RP using centerToTSS and peak score2024-03-28 02:58:26
>> merging all info together		2024-03-28 02:58:31
>> done		2024-03-28 02:58:33
>> calculating peakCenter to TSS using peak-gene pair...		2024-03-28 02:58:33
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-03-28 02:58:35
>> calculating RP using centerToTSS and peak score2024-03-28 02:58:35
>> merging all info together		2024-03-28 02:58:40
>> done		2024-03-28 02:58:41
>> checking seqlevels match...		2024-03-28 02:58:42
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-03-28 02:58:42
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:58:43
>> finding overlap peak in gene scan region...		2024-03-28 02:58:43
>> dealing with left peak not your gene scan region...		2024-03-28 02:58:43
>> merging two set peaks...		2024-03-28 02:58:44
>> calculating distance and dealing with gene strand...		2024-03-28 02:58:44
>> merging all info together ...		2024-03-28 02:58:44
>> done		2024-03-28 02:58:44
>> calculating peakCenter to TSS using peak-gene pair...		2024-03-28 02:58:44
>> calculating RP using centerToTSS and TF hit		2024-03-28 02:58:46
>> merging all info together		2024-03-28 02:58:46
>> done		2024-03-28 02:58:46
>> calculating peakCenter to TSS using peak-gene pair...		2024-03-28 02:58:46
>> calculating RP using centerToTSS and TF hit		2024-03-28 02:58:47
>> merging all info together		2024-03-28 02:58:48
>> done		2024-03-28 02:58:48
>> checking seqlevels match...		2024-03-28 02:58:50
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-03-28 02:58:50
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:58:52
>> finding overlap peak in gene scan region...		2024-03-28 02:58:52
>> dealing with left peak not your gene scan region...		2024-03-28 02:58:52
>> merging two set peaks...		2024-03-28 02:58:53
>> calculating distance and dealing with gene strand...		2024-03-28 02:58:53
>> merging all info together ...		2024-03-28 02:58:53
>> done		2024-03-28 02:58:53
>> calculating peakCenter to TSS using peak-gene pair...		2024-03-28 02:58:53
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-03-28 02:58:55
>> calculating RP using centerToTSS and peak score2024-03-28 02:58:55
>> merging all info together		2024-03-28 02:58:59
>> done		2024-03-28 02:59:00
>> extracting RP info from regionRP...		2024-03-28 02:59:01
>> dealing with TF_GR_databse...		2024-03-28 02:59:01
>> calculating percent and p-value...		2024-03-28 02:59:01
>> dealing withE5_0h_R1...		2024-03-28 02:59:01
>> dealing withE5_0h_R2...		2024-03-28 02:59:02
>> dealing withE5_4h_R1...		2024-03-28 02:59:02
>> dealing withE5_4h_R2...		2024-03-28 02:59:02
>> dealing withE5_8h_R1...		2024-03-28 02:59:02
>> dealing withE5_8h_R2...		2024-03-28 02:59:02
>> dealing withE5_16h_R1...		2024-03-28 02:59:02
>> dealing withE5_16h_R2...		2024-03-28 02:59:02
>> dealing withE5_24h_R1...		2024-03-28 02:59:02
>> dealing withE5_24h_R2...		2024-03-28 02:59:02
>> dealing withE5_48h_R1...		2024-03-28 02:59:02
>> dealing withE5_48h_R2...		2024-03-28 02:59:02
>> dealing withE5_48h_R3...		2024-03-28 02:59:03
>> dealing withE5_72h_R1...		2024-03-28 02:59:03
>> dealing withE5_72h_R2...		2024-03-28 02:59:03
>> dealing withE5_72h_R3...		2024-03-28 02:59:03
>> merging all info together...		2024-03-28 02:59:03
>> done		2024-03-28 02:59:03
>> preparing gene features information...		2024-03-28 02:59:04
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:59:05
>> calculating p-value for each TF, which may be time consuming...		2024-03-28 02:59:05
>> merging all info together...		2024-03-28 02:59:05
>> done		2024-03-28 02:59:05
>> dealing with TF_GR_database...		2024-03-28 02:59:06
>> calculating coef and converting into z-score using INT...		2024-03-28 02:59:06
>> dealing with E5_0h_R1...		2024-03-28 02:59:06
>> dealing with E5_0h_R2...		2024-03-28 02:59:07
>> dealing with E5_4h_R1...		2024-03-28 02:59:07
>> dealing with E5_4h_R2...		2024-03-28 02:59:07
>> dealing with E5_8h_R1...		2024-03-28 02:59:07
>> dealing with E5_8h_R2...		2024-03-28 02:59:07
>> dealing with E5_16h_R1...		2024-03-28 02:59:07
>> dealing with E5_16h_R2...		2024-03-28 02:59:08
>> dealing with E5_24h_R1...		2024-03-28 02:59:08
>> dealing with E5_24h_R2...		2024-03-28 02:59:08
>> dealing with E5_48h_R1...		2024-03-28 02:59:08
>> dealing with E5_48h_R2...		2024-03-28 02:59:08
>> dealing with E5_48h_R3...		2024-03-28 02:59:08
>> dealing with E5_72h_R1...		2024-03-28 02:59:08
>> dealing with E5_72h_R2...		2024-03-28 02:59:09
>> dealing with E5_72h_R3...		2024-03-28 02:59:09
>> merging all info together...		2024-03-28 02:59:09
>> done		2024-03-28 02:59:09
>> checking seqlevels match...		2024-03-28 02:59:10
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-03-28 02:59:10
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:59:11
>> finding overlap peak in gene scan region...		2024-03-28 02:59:11
>> dealing with left peak not your gene scan region...		2024-03-28 02:59:11
>> merging two set peaks...		2024-03-28 02:59:12
>> calculating distance and dealing with gene strand...		2024-03-28 02:59:12
>> merging all info together ...		2024-03-28 02:59:12
>> done		2024-03-28 02:59:12
>> calculating peakCenter to TSS using peak-gene pair...		2024-03-28 02:59:12
>> calculating RP using centerToTSS and TF hit		2024-03-28 02:59:13
>> merging all info together		2024-03-28 02:59:13
>> done		2024-03-28 02:59:13
>> checking seqlevels match...		2024-03-28 02:59:14
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-03-28 02:59:14
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-03-28 02:59:21
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-03-28 02:59:21
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-03-28 02:59:21
>> finding nearest gene and calculating distance...		2024-03-28 02:59:22
>> dealing with gene strand ...		2024-03-28 02:59:23
>> merging all info together ...		2024-03-28 02:59:23
>> done		2024-03-28 02:59:23
>> checking seqlevels match...		2024-03-28 02:59:23
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-03-28 02:59:23
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-03-28 02:59:23
>> finding nearest gene and calculating distance...		2024-03-28 02:59:25
>> dealing with gene strand ...		2024-03-28 02:59:25
>> merging all info together ...		2024-03-28 02:59:25
>> done		2024-03-28 02:59:25
>> checking seqlevels match...		2024-03-28 02:59:26
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-03-28 02:59:27
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-03-28 02:59:27
>> finding nearest gene and calculating distance...		2024-03-28 02:59:28
>> dealing with gene strand ...		2024-03-28 02:59:29
>> merging all info together ...		2024-03-28 02:59:29
>> done		2024-03-28 02:59:29
>> checking seqlevels match...		2024-03-28 02:59:30
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-03-28 02:59:30
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-03-28 02:59:31
>> finding nearest gene and calculating distance...		2024-03-28 02:59:32
>> dealing with gene strand ...		2024-03-28 02:59:32
>> merging all info together ...		2024-03-28 02:59:32
>> done		2024-03-28 02:59:32
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-03-28 02:59:34
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-03-28 02:59:34
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-03-28 02:59:34
>> finding nearest gene and calculating distance...		2024-03-28 02:59:35
>> dealing with gene strand ...		2024-03-28 02:59:36
>> merging all info together ...		2024-03-28 02:59:36
>> done		2024-03-28 02:59:36
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-03-28 02:59:38
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-03-28 02:59:39
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:59:41
>> checking seqlevels match...		2024-03-28 02:59:42
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:59:44
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-03-28 02:59:47
>> merging all info together...		2024-03-28 02:59:47
>> done		2024-03-28 02:59:47
>> checking seqlevels match...		2024-03-28 02:59:47
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene...		2024-03-28 02:59:48
>> checking seqlevels match...		2024-03-28 02:59:48
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:59:49
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-03-28 02:59:50
>> checking seqlevels match...		2024-03-28 02:59:50
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:59:51
>> calculating cor and pvalue, which may be time consuming...		2024-03-28 02:59:52
>> merging all info together...		2024-03-28 02:59:52
>> done		2024-03-28 02:59:52
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-03-28 02:59:52
>> merging all info together...		2024-03-28 02:59:52
>> done		2024-03-28 02:59:53
>> checking seqlevels match...		2024-03-28 02:59:53
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-03-28 02:59:53
>> some scan range may cross Chr bound, trimming...		2024-03-28 02:59:54
>> finding overlap peak in gene scan region...		2024-03-28 02:59:54
>> dealing with left peak not your gene scan region...		2024-03-28 02:59:54
>> merging two set peaks...		2024-03-28 02:59:55
>> calculating distance and dealing with gene strand...		2024-03-28 02:59:55
>> merging all info together ...		2024-03-28 02:59:55
>> done		2024-03-28 02:59:55
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-03-28 02:59:58
>> merging all info together...		2024-03-28 02:59:58
>> done		2024-03-28 02:59:58
>> checking seqlevels match...		2024-03-28 02:59:58
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene...		2024-03-28 02:59:58
>> checking seqlevels match...		2024-03-28 02:59:58
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-03-28 03:00:00
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-03-28 03:00:00
>> checking seqlevels match...		2024-03-28 03:00:00
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-03-28 03:00:03
>> calculating cor and pvalue, which may be time consuming...		2024-03-28 03:00:03
>> merging all info together...		2024-03-28 03:00:04
>> done		2024-03-28 03:00:04
Joining with `by = join_by(feature_id)`
Joining with `by = join_by(feature_id)`
`geom_smooth()` using formula = 'y ~ x'
Joining with `by = join_by(feature_id)`
Joining with `by = join_by(feature_id)`
`geom_smooth()` using formula = 'y ~ x'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
127.785   3.602 139.853