Build/check report for BioC 3.22 - CHECK results for FindIT2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4892
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CHECK results for FindIT2 on nebbiolo2

To the developers/maintainers of the FindIT2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindIT2.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: FindIT2

Version: 1.16.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings FindIT2_1.16.0.tar.gz

StartedAt: 2026-03-09 23:29:38 -0400 (Mon, 09 Mar 2026)

EndedAt: 2026-03-09 23:36:37 -0400 (Mon, 09 Mar 2026)

EllapsedTime: 418.5 seconds

RetCode: 0

Status: OK

CheckDir: FindIT2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings FindIT2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FindIT2.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.16.0’
* 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 5.451  0.025   5.475
calcRP_region   5.333  0.069   5.402
* 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

Installation output

FindIT2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘FindIT2’ ...
** this is package ‘FindIT2’ version ‘1.16.0’
** 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)

Tests output

FindIT2.Rcheck/tests/testthat.Rout


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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...		2026-03-09 23:34:44
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:34:46
>> preparing weight info...		2026-03-09 23:34:46
>> loading E50h_sampleChr5.bw info...		2026-03-09 23:34:46
------------
>> extracting and calcluating Chr5 signal...		2026-03-09 23:34:46
>> dealing with Chr5 left gene signal...		2026-03-09 23:34:49
>> norming Chr5RP accoring to the whole Chr RP...		2026-03-09 23:34:49
>> merging all Chr RP together...		2026-03-09 23:34:49
>> done		2026-03-09 23:34:49
>> checking seqlevels match...		2026-03-09 23:34:49
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2026-03-09 23:34:49
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:34:50
>> finding overlap peak in gene scan region...		2026-03-09 23:34:50
>> dealing with left peak not your gene scan region...		2026-03-09 23:34:50
>> merging two set peaks...		2026-03-09 23:34:50
>> calculating distance and dealing with gene strand...		2026-03-09 23:34:50
>> merging all info together ...		2026-03-09 23:34:50
>> done		2026-03-09 23:34:50
>> calculating peakCenter to TSS using peak-gene pair...		2026-03-09 23:34:50
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2026-03-09 23:34:51
>> calculating RP using centerToTSS and peak score2026-03-09 23:34:51
>> merging all info together		2026-03-09 23:34:53
>> done		2026-03-09 23:34:54
>> calculating peakCenter to TSS using peak-gene pair...		2026-03-09 23:34:54
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2026-03-09 23:34:55
>> calculating RP using centerToTSS and peak score2026-03-09 23:34:55
>> merging all info together		2026-03-09 23:34:57
>> done		2026-03-09 23:34:58
>> checking seqlevels match...		2026-03-09 23:34:58
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2026-03-09 23:34:58
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:34:59
>> finding overlap peak in gene scan region...		2026-03-09 23:34:59
>> dealing with left peak not your gene scan region...		2026-03-09 23:34:59
>> merging two set peaks...		2026-03-09 23:34:59
>> calculating distance and dealing with gene strand...		2026-03-09 23:34:59
>> merging all info together ...		2026-03-09 23:34:59
>> done		2026-03-09 23:34:59
>> calculating peakCenter to TSS using peak-gene pair...		2026-03-09 23:34:59
>> calculating RP using centerToTSS and TF hit		2026-03-09 23:35:00
>> merging all info together		2026-03-09 23:35:00
>> done		2026-03-09 23:35:00
>> calculating peakCenter to TSS using peak-gene pair...		2026-03-09 23:35:00
>> calculating RP using centerToTSS and TF hit		2026-03-09 23:35:00
>> merging all info together		2026-03-09 23:35:00
>> done		2026-03-09 23:35:00
>> checking seqlevels match...		2026-03-09 23:35:01
>> 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...		2026-03-09 23:35:01
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:35:03
>> finding overlap peak in gene scan region...		2026-03-09 23:35:03
>> dealing with left peak not your gene scan region...		2026-03-09 23:35:03
>> merging two set peaks...		2026-03-09 23:35:03
>> calculating distance and dealing with gene strand...		2026-03-09 23:35:03
>> merging all info together ...		2026-03-09 23:35:03
>> done		2026-03-09 23:35:03
>> calculating peakCenter to TSS using peak-gene pair...		2026-03-09 23:35:03
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2026-03-09 23:35:04
>> calculating RP using centerToTSS and peak score2026-03-09 23:35:04
>> merging all info together		2026-03-09 23:35:06
>> done		2026-03-09 23:35:06
>> extracting RP info from regionRP...		2026-03-09 23:35:06
>> dealing with TF_GR_databse...		2026-03-09 23:35:07
>> calculating percent and p-value...		2026-03-09 23:35:07
>> dealing withE5_0h_R1...		2026-03-09 23:35:07
>> dealing withE5_0h_R2...		2026-03-09 23:35:07
>> dealing withE5_4h_R1...		2026-03-09 23:35:07
>> dealing withE5_4h_R2...		2026-03-09 23:35:07
>> dealing withE5_8h_R1...		2026-03-09 23:35:07
>> dealing withE5_8h_R2...		2026-03-09 23:35:07
>> dealing withE5_16h_R1...		2026-03-09 23:35:07
>> dealing withE5_16h_R2...		2026-03-09 23:35:07
>> dealing withE5_24h_R1...		2026-03-09 23:35:07
>> dealing withE5_24h_R2...		2026-03-09 23:35:07
>> dealing withE5_48h_R1...		2026-03-09 23:35:07
>> dealing withE5_48h_R2...		2026-03-09 23:35:07
>> dealing withE5_48h_R3...		2026-03-09 23:35:07
>> dealing withE5_72h_R1...		2026-03-09 23:35:07
>> dealing withE5_72h_R2...		2026-03-09 23:35:07
>> dealing withE5_72h_R3...		2026-03-09 23:35:07
>> merging all info together...		2026-03-09 23:35:07
>> done		2026-03-09 23:35:07
>> preparing gene features information...		2026-03-09 23:35:07
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:35:08
>> calculating p-value for each TF, which may be time consuming...		2026-03-09 23:35:08
>> merging all info together...		2026-03-09 23:35:08
>> done		2026-03-09 23:35:08
>> dealing with TF_GR_database...		2026-03-09 23:35:08
>> calculating coef and converting into z-score using INT...		2026-03-09 23:35:08
>> dealing with E5_0h_R1...		2026-03-09 23:35:08
>> dealing with E5_0h_R2...		2026-03-09 23:35:09
>> dealing with E5_4h_R1...		2026-03-09 23:35:09
>> dealing with E5_4h_R2...		2026-03-09 23:35:09
>> dealing with E5_8h_R1...		2026-03-09 23:35:09
>> dealing with E5_8h_R2...		2026-03-09 23:35:09
>> dealing with E5_16h_R1...		2026-03-09 23:35:09
>> dealing with E5_16h_R2...		2026-03-09 23:35:09
>> dealing with E5_24h_R1...		2026-03-09 23:35:09
>> dealing with E5_24h_R2...		2026-03-09 23:35:09
>> dealing with E5_48h_R1...		2026-03-09 23:35:09
>> dealing with E5_48h_R2...		2026-03-09 23:35:09
>> dealing with E5_48h_R3...		2026-03-09 23:35:09
>> dealing with E5_72h_R1...		2026-03-09 23:35:09
>> dealing with E5_72h_R2...		2026-03-09 23:35:09
>> dealing with E5_72h_R3...		2026-03-09 23:35:09
>> merging all info together...		2026-03-09 23:35:10
>> done		2026-03-09 23:35:10
>> checking seqlevels match...		2026-03-09 23:35:10
>> 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...		2026-03-09 23:35:10
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:35:10
>> finding overlap peak in gene scan region...		2026-03-09 23:35:10
>> dealing with left peak not your gene scan region...		2026-03-09 23:35:10
>> merging two set peaks...		2026-03-09 23:35:11
>> calculating distance and dealing with gene strand...		2026-03-09 23:35:11
>> merging all info together ...		2026-03-09 23:35:11
>> done		2026-03-09 23:35:11
>> calculating peakCenter to TSS using peak-gene pair...		2026-03-09 23:35:11
>> calculating RP using centerToTSS and TF hit		2026-03-09 23:35:11
>> merging all info together		2026-03-09 23:35:11
>> done		2026-03-09 23:35:11
>> checking seqlevels match...		2026-03-09 23:35:12
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2026-03-09 23:35:12
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2026-03-09 23:35:14
>> 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...		2026-03-09 23:35:15
>> 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...		2026-03-09 23:35:15
>> finding nearest gene and calculating distance...		2026-03-09 23:35:15
>> dealing with gene strand ...		2026-03-09 23:35:15
>> merging all info together ...		2026-03-09 23:35:15
>> done		2026-03-09 23:35:15
>> checking seqlevels match...		2026-03-09 23:35:15
>> 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...		2026-03-09 23:35:15
>> 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...		2026-03-09 23:35:15
>> finding nearest gene and calculating distance...		2026-03-09 23:35:16
>> dealing with gene strand ...		2026-03-09 23:35:16
>> merging all info together ...		2026-03-09 23:35:16
>> done		2026-03-09 23:35:16
>> checking seqlevels match...		2026-03-09 23:35:17
>> 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...		2026-03-09 23:35:17
>> 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...		2026-03-09 23:35:17
>> finding nearest gene and calculating distance...		2026-03-09 23:35:17
>> dealing with gene strand ...		2026-03-09 23:35:18
>> merging all info together ...		2026-03-09 23:35:18
>> done		2026-03-09 23:35:18
>> checking seqlevels match...		2026-03-09 23:35:18
>> 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...		2026-03-09 23:35:18
>> 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...		2026-03-09 23:35:18
>> finding nearest gene and calculating distance...		2026-03-09 23:35:19
>> dealing with gene strand ...		2026-03-09 23:35:19
>> merging all info together ...		2026-03-09 23:35:19
>> done		2026-03-09 23:35:19
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2026-03-09 23:35:20
>> 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...		2026-03-09 23:35:20
>> 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...		2026-03-09 23:35:20
>> finding nearest gene and calculating distance...		2026-03-09 23:35:21
>> dealing with gene strand ...		2026-03-09 23:35:21
>> merging all info together ...		2026-03-09 23:35:21
>> done		2026-03-09 23:35:21
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2026-03-09 23:35:21
>> 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...		2026-03-09 23:35:22
>> 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...		2026-03-09 23:35:23
>> checking seqlevels match...		2026-03-09 23:35:24
>> 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...		2026-03-09 23:35:24
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2026-03-09 23:35:25
>> merging all info together...		2026-03-09 23:35:25
>> done		2026-03-09 23:35:26
>> checking seqlevels match...		2026-03-09 23:35:26
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2026-03-09 23:35:26
>> checking seqlevels match...		2026-03-09 23:35:26
>> 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
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:35:26
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2026-03-09 23:35:27
>> checking seqlevels match...		2026-03-09 23:35:27
>> 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
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:35:27
>> calculating cor and pvalue, which may be time consuming...		2026-03-09 23:35:27
>> merging all info together...		2026-03-09 23:35:28
>> done		2026-03-09 23:35:28
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2026-03-09 23:35:28
>> merging all info together...		2026-03-09 23:35:28
>> done		2026-03-09 23:35:28
>> checking seqlevels match...		2026-03-09 23:35:28
>> 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...		2026-03-09 23:35:28
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:35:29
>> finding overlap peak in gene scan region...		2026-03-09 23:35:29
>> dealing with left peak not your gene scan region...		2026-03-09 23:35:29
>> merging two set peaks...		2026-03-09 23:35:29
>> calculating distance and dealing with gene strand...		2026-03-09 23:35:29
>> merging all info together ...		2026-03-09 23:35:29
>> done		2026-03-09 23:35:29
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2026-03-09 23:35:30
>> merging all info together...		2026-03-09 23:35:30
>> done		2026-03-09 23:35:30
>> checking seqlevels match...		2026-03-09 23:35:30
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2026-03-09 23:35:30
>> checking seqlevels match...		2026-03-09 23:35:30
>> 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
>> some scan range may cross Chr bound, trimming...		2026-03-09 23:35:31
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2026-03-09 23:35:31
>> checking seqlevels match...		2026-03-09 23:35:31
>> 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...		2026-03-09 23:35:32
>> calculating cor and pvalue, which may be time consuming...		2026-03-09 23:35:32
>> merging all info together...		2026-03-09 23:35:32
>> done		2026-03-09 23:35:32
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 
 58.813   1.907  60.715

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

name	user	system	elapsed
TF_target_database	0	0	0
calcRP_TFHit	3.383	0.182	3.627
calcRP_coverage	2.623	0.164	2.788
calcRP_region	5.333	0.069	5.402
enhancerPromoterCor	2.401	0.032	2.433
findIT_MARA	0.396	0.015	0.411
findIT_TFHit	0.839	0.009	0.848
findIT_TTPair	0.074	0.000	0.074
findIT_enrichFisher	0.163	0.000	0.164
findIT_enrichWilcox	0.17	0.00	0.17
findIT_regionRP	5.451	0.025	5.475
getAssocPairNumber	1.030	0.031	1.060
integrate_ChIP_RNA	1.945	0.019	1.964
integrate_replicates	0.002	0.000	0.002
jaccard_findIT_TTpair	0.088	0.003	0.090
jaccard_findIT_enrichFisher	0.188	0.000	0.188
loadPeakFile	0.056	0.004	0.060
mm_geneBound	1.114	0.065	1.180
mm_geneScan	1.062	0.008	1.070
mm_nearestGene	0.974	0.003	0.976
peakGeneCor	2.040	0.026	2.065
plot_annoDistance	1.522	0.004	1.526
plot_peakGeneAlias_summary	1.251	0.007	1.258
plot_peakGeneCor	3.625	0.192	3.817
test_geneSet	0	0	0