##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FindIT2_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 loading without being on the library search path ... 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 6.063  0.152   6.215
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘FindIT2’ ...
** this is package ‘FindIT2’ version ‘1.17.0’
** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
> 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...		2026-02-12 23:53:06
>> some scan range may cross Chr bound, trimming...		2026-02-12 23:53:08
>> preparing weight info...		2026-02-12 23:53:08
>> loading E50h_sampleChr5.bw info...		2026-02-12 23:53:08
------------
>> extracting and calcluating Chr5 signal...		2026-02-12 23:53:08
>> dealing with Chr5 left gene signal...		2026-02-12 23:53:11
>> norming Chr5RP accoring to the whole Chr RP...		2026-02-12 23:53:11
>> merging all Chr RP together...		2026-02-12 23:53:11
>> done		2026-02-12 23:53:11
>> checking seqlevels match...		2026-02-12 23:53:11
>> 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...		2026-02-12 23:53:11
>> some scan range may cross Chr bound, trimming...		2026-02-12 23:53:12
>> finding overlap peak in gene scan region...		2026-02-12 23:53:12
>> dealing with left peak not your gene scan region...		2026-02-12 23:53:12
>> merging two set peaks...		2026-02-12 23:53:12
>> calculating distance and dealing with gene strand...		2026-02-12 23:53:12
>> merging all info together ...		2026-02-12 23:53:12
>> done		2026-02-12 23:53:12
>> calculating peakCenter to TSS using peak-gene pair...		2026-02-12 23:53:12
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2026-02-12 23:53:13
>> calculating RP using centerToTSS and peak score2026-02-12 23:53:13
>> merging all info together		2026-02-12 23:53:15
>> done		2026-02-12 23:53:16
>> calculating peakCenter to TSS using peak-gene pair...		2026-02-12 23:53:16
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2026-02-12 23:53:17
>> calculating RP using centerToTSS and peak score2026-02-12 23:53:17
>> merging all info together		2026-02-12 23:53:20
>> done		2026-02-12 23:53:20
>> checking seqlevels match...		2026-02-12 23:53:21
>> 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...		2026-02-12 23:53:21
>> some scan range may cross Chr bound, trimming...		2026-02-12 23:53:21
>> finding overlap peak in gene scan region...		2026-02-12 23:53:21
>> dealing with left peak not your gene scan region...		2026-02-12 23:53:21
>> merging two set peaks...		2026-02-12 23:53:22
>> calculating distance and dealing with gene strand...		2026-02-12 23:53:22
>> merging all info together ...		2026-02-12 23:53:22
>> done		2026-02-12 23:53:22
>> calculating peakCenter to TSS using peak-gene pair...		2026-02-12 23:53:22
>> calculating RP using centerToTSS and TF hit		2026-02-12 23:53:23
>> merging all info together		2026-02-12 23:53:23
>> done		2026-02-12 23:53:23
>> calculating peakCenter to TSS using peak-gene pair...		2026-02-12 23:53:23
>> calculating RP using centerToTSS and TF hit		2026-02-12 23:53:24
>> merging all info together		2026-02-12 23:53:24
>> done		2026-02-12 23:53:24
>> checking seqlevels match...		2026-02-12 23:53:25
>> 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...		2026-02-12 23:53:25
>> some scan range may cross Chr bound, trimming...		2026-02-12 23:53:25
>> finding overlap peak in gene scan region...		2026-02-12 23:53:25
>> dealing with left peak not your gene scan region...		2026-02-12 23:53:26
>> merging two set peaks...		2026-02-12 23:53:26
>> calculating distance and dealing with gene strand...		2026-02-12 23:53:26
>> merging all info together ...		2026-02-12 23:53:26
>> done		2026-02-12 23:53:26
>> calculating peakCenter to TSS using peak-gene pair...		2026-02-12 23:53:26
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2026-02-12 23:53:26
>> calculating RP using centerToTSS and peak score2026-02-12 23:53:26
>> merging all info together		2026-02-12 23:53:28
>> done		2026-02-12 23:53:29
>> extracting RP info from regionRP...		2026-02-12 23:53:29
>> dealing with TF_GR_databse...		2026-02-12 23:53:29
>> calculating percent and p-value...		2026-02-12 23:53:29
>> dealing withE5_0h_R1...		2026-02-12 23:53:29
>> dealing withE5_0h_R2...		2026-02-12 23:53:30
>> dealing withE5_4h_R1...		2026-02-12 23:53:30
>> dealing withE5_4h_R2...		2026-02-12 23:53:30
>> dealing withE5_8h_R1...		2026-02-12 23:53:30
>> dealing withE5_8h_R2...		2026-02-12 23:53:30
>> dealing withE5_16h_R1...		2026-02-12 23:53:30
>> dealing withE5_16h_R2...		2026-02-12 23:53:30
>> dealing withE5_24h_R1...		2026-02-12 23:53:30
>> dealing withE5_24h_R2...		2026-02-12 23:53:30
>> dealing withE5_48h_R1...		2026-02-12 23:53:30
>> dealing withE5_48h_R2...		2026-02-12 23:53:30
>> dealing withE5_48h_R3...		2026-02-12 23:53:30
>> dealing withE5_72h_R1...		2026-02-12 23:53:30
>> dealing withE5_72h_R2...		2026-02-12 23:53:30
>> dealing withE5_72h_R3...		2026-02-12 23:53:30
>> merging all info together...		2026-02-12 23:53:30
>> done		2026-02-12 23:53:30
>> preparing gene features information...		2026-02-12 23:53:30
>> some scan range may cross Chr bound, trimming...		2026-02-12 23:53:31
>> calculating p-value for each TF, which may be time consuming...		2026-02-12 23:53:31
>> merging all info together...		2026-02-12 23:53:31
>> done		2026-02-12 23:53:31
>> dealing with TF_GR_database...		2026-02-12 23:53:31
>> calculating coef and converting into z-score using INT...		2026-02-12 23:53:31
>> dealing with E5_0h_R1...		2026-02-12 23:53:31
>> dealing with E5_0h_R2...		2026-02-12 23:53:32
>> dealing with E5_4h_R1...		2026-02-12 23:53:32
>> dealing with E5_4h_R2...		2026-02-12 23:53:32
>> dealing with E5_8h_R1...		2026-02-12 23:53:32
>> dealing with E5_8h_R2...		2026-02-12 23:53:32
>> dealing with E5_16h_R1...		2026-02-12 23:53:32
>> dealing with E5_16h_R2...		2026-02-12 23:53:32
>> dealing with E5_24h_R1...		2026-02-12 23:53:32
>> dealing with E5_24h_R2...		2026-02-12 23:53:32
>> dealing with E5_48h_R1...		2026-02-12 23:53:32
>> dealing with E5_48h_R2...		2026-02-12 23:53:32
>> dealing with E5_48h_R3...		2026-02-12 23:53:32
>> dealing with E5_72h_R1...		2026-02-12 23:53:32
>> dealing with E5_72h_R2...		2026-02-12 23:53:32
>> dealing with E5_72h_R3...		2026-02-12 23:53:32
>> merging all info together...		2026-02-12 23:53:33
>> done		2026-02-12 23:53:33
>> checking seqlevels match...		2026-02-12 23:53:33
>> 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...		2026-02-12 23:53:33
>> some scan range may cross Chr bound, trimming...		2026-02-12 23:53:34
>> finding overlap peak in gene scan region...		2026-02-12 23:53:34
>> dealing with left peak not your gene scan region...		2026-02-12 23:53:34
>> merging two set peaks...		2026-02-12 23:53:34
>> calculating distance and dealing with gene strand...		2026-02-12 23:53:34
>> merging all info together ...		2026-02-12 23:53:34
>> done		2026-02-12 23:53:34
>> calculating peakCenter to TSS using peak-gene pair...		2026-02-12 23:53:34
>> calculating RP using centerToTSS and TF hit		2026-02-12 23:53:34
>> merging all info together		2026-02-12 23:53:34
>> done		2026-02-12 23:53:35
>> checking seqlevels match...		2026-02-12 23:53:35
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2026-02-12 23:53:35
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2026-02-12 23:53:38
>> 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...		2026-02-12 23:53:38
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2026-02-12 23:53:38
>> finding nearest gene and calculating distance...		2026-02-12 23:53:38
>> dealing with gene strand ...		2026-02-12 23:53:39
>> merging all info together ...		2026-02-12 23:53:39
>> done		2026-02-12 23:53:39
>> checking seqlevels match...		2026-02-12 23:53:39
>> 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
>> checking seqlevels match...		2026-02-12 23:53:39
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2026-02-12 23:53:39
>> finding nearest gene and calculating distance...		2026-02-12 23:53:39
>> dealing with gene strand ...		2026-02-12 23:53:40
>> merging all info together ...		2026-02-12 23:53:40
>> done		2026-02-12 23:53:40
>> checking seqlevels match...		2026-02-12 23:53:40
>> 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...		2026-02-12 23:53:40
>> 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...		2026-02-12 23:53:40
>> finding nearest gene and calculating distance...		2026-02-12 23:53:41
>> dealing with gene strand ...		2026-02-12 23:53:41
>> merging all info together ...		2026-02-12 23:53:41
>> done		2026-02-12 23:53:41
>> checking seqlevels match...		2026-02-12 23:53:42
>> 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
>> checking seqlevels match...		2026-02-12 23:53:42
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2026-02-12 23:53:42
>> finding nearest gene and calculating distance...		2026-02-12 23:53:43
>> dealing with gene strand ...		2026-02-12 23:53:43
>> merging all info together ...		2026-02-12 23:53:43
>> done		2026-02-12 23:53:43
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2026-02-12 23:53:44
>> 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...		2026-02-12 23:53:44
>> 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...		2026-02-12 23:53:44
>> finding nearest gene and calculating distance...		2026-02-12 23:53:44
>> dealing with gene strand ...		2026-02-12 23:53:45
>> merging all info together ...		2026-02-12 23:53:45
>> done		2026-02-12 23:53:45
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2026-02-12 23:53:45
>> 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...		2026-02-12 23:53:46
>> 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...		2026-02-12 23:53:48
>> checking seqlevels match...		2026-02-12 23:53:49
>> 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...		2026-02-12 23:53:49
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2026-02-12 23:53:51
>> merging all info together...		2026-02-12 23:53:51
>> done		2026-02-12 23:53:51
>> checking seqlevels match...		2026-02-12 23:53:51
>> 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...		2026-02-12 23:53:51
>> checking seqlevels match...		2026-02-12 23:53:51
>> 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...		2026-02-12 23:53:51
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2026-02-12 23:53:52
>> checking seqlevels match...		2026-02-12 23:53:52
>> 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...		2026-02-12 23:53:52
>> calculating cor and pvalue, which may be time consuming...		2026-02-12 23:53:52
>> merging all info together...		2026-02-12 23:53:53
>> done		2026-02-12 23:53:53
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2026-02-12 23:53:53
>> merging all info together...		2026-02-12 23:53:53
>> done		2026-02-12 23:53:53
>> checking seqlevels match...		2026-02-12 23:53:53
>> 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...		2026-02-12 23:53:53
>> some scan range may cross Chr bound, trimming...		2026-02-12 23:53:54
>> finding overlap peak in gene scan region...		2026-02-12 23:53:54
>> dealing with left peak not your gene scan region...		2026-02-12 23:53:54
>> merging two set peaks...		2026-02-12 23:53:54
>> calculating distance and dealing with gene strand...		2026-02-12 23:53:54
>> merging all info together ...		2026-02-12 23:53:54
>> done		2026-02-12 23:53:54
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2026-02-12 23:53:55
>> merging all info together...		2026-02-12 23:53:55
>> done		2026-02-12 23:53:55
>> checking seqlevels match...		2026-02-12 23:53:55
>> 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...		2026-02-12 23:53:55
>> checking seqlevels match...		2026-02-12 23:53:55
>> 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...		2026-02-12 23:53:56
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2026-02-12 23:53:56
>> checking seqlevels match...		2026-02-12 23:53:56
>> 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...		2026-02-12 23:53:57
>> calculating cor and pvalue, which may be time consuming...		2026-02-12 23:53:57
>> merging all info together...		2026-02-12 23:53:57
>> done		2026-02-12 23:53:57
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 
 61.632   2.088  63.716