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HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
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Package 730/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.15.1  (landing page)
Guandong Shang
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: devel
git_last_commit: 82d0b10
git_last_commit_date: 2025-07-22 19:49:08 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for FindIT2 on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: FindIT2
Version: 1.15.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FindIT2_1.15.1.tar.gz
StartedAt: 2025-10-03 07:09:56 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 07:17:16 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 440.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FindIT2_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FindIT2.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.15.1’
* 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 7.485  0.056   7.561
calcRP_region   6.723  0.064   6.805
calcRP_coverage 6.161  0.124   6.303
* 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: OK


Installation output

FindIT2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘FindIT2’ ...
** this is package ‘FindIT2’ version ‘1.15.1’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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...		2025-10-03 07:16:05
>> some scan range may cross Chr bound, trimming...		2025-10-03 07:16:06
>> preparing weight info...		2025-10-03 07:16:06
>> loading E50h_sampleChr5.bw info...		2025-10-03 07:16:06
------------
>> extracting and calcluating Chr5 signal...		2025-10-03 07:16:06
>> dealing with Chr5 left gene signal...		2025-10-03 07:16:12
>> norming Chr5RP accoring to the whole Chr RP...		2025-10-03 07:16:13
>> merging all Chr RP together...		2025-10-03 07:16:13
>> done		2025-10-03 07:16:13
>> checking seqlevels match...		2025-10-03 07:16:13
>> 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...		2025-10-03 07:16:13
>> some scan range may cross Chr bound, trimming...		2025-10-03 07:16:14
>> finding overlap peak in gene scan region...		2025-10-03 07:16:14
>> dealing with left peak not your gene scan region...		2025-10-03 07:16:14
>> merging two set peaks...		2025-10-03 07:16:14
>> calculating distance and dealing with gene strand...		2025-10-03 07:16:14
>> merging all info together ...		2025-10-03 07:16:14
>> done		2025-10-03 07:16:14
>> calculating peakCenter to TSS using peak-gene pair...		2025-10-03 07:16:14
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-10-03 07:16:15
>> calculating RP using centerToTSS and peak score2025-10-03 07:16:15
>> merging all info together		2025-10-03 07:16:18
>> done		2025-10-03 07:16:19
>> calculating peakCenter to TSS using peak-gene pair...		2025-10-03 07:16:19
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-10-03 07:16:20
>> calculating RP using centerToTSS and peak score2025-10-03 07:16:20
>> merging all info together		2025-10-03 07:16:23
>> done		2025-10-03 07:16:24
>> checking seqlevels match...		2025-10-03 07:16:24
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2025-10-03 07:16:24
>> some scan range may cross Chr bound, trimming...		2025-10-03 07:16:26
>> finding overlap peak in gene scan region...		2025-10-03 07:16:26
>> dealing with left peak not your gene scan region...		2025-10-03 07:16:26
>> merging two set peaks...		2025-10-03 07:16:26
>> calculating distance and dealing with gene strand...		2025-10-03 07:16:26
>> merging all info together ...		2025-10-03 07:16:26
>> done		2025-10-03 07:16:26
>> calculating peakCenter to TSS using peak-gene pair...		2025-10-03 07:16:26
>> calculating RP using centerToTSS and TF hit		2025-10-03 07:16:27
>> merging all info together		2025-10-03 07:16:27
>> done		2025-10-03 07:16:27
>> calculating peakCenter to TSS using peak-gene pair...		2025-10-03 07:16:27
>> calculating RP using centerToTSS and TF hit		2025-10-03 07:16:28
>> merging all info together		2025-10-03 07:16:28
>> done		2025-10-03 07:16:28
>> checking seqlevels match...		2025-10-03 07:16:29
>> 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...		2025-10-03 07:16:29
>> some scan range may cross Chr bound, trimming...		2025-10-03 07:16:30
>> finding overlap peak in gene scan region...		2025-10-03 07:16:30
>> dealing with left peak not your gene scan region...		2025-10-03 07:16:30
>> merging two set peaks...		2025-10-03 07:16:30
>> calculating distance and dealing with gene strand...		2025-10-03 07:16:30
>> merging all info together ...		2025-10-03 07:16:30
>> done		2025-10-03 07:16:30
>> calculating peakCenter to TSS using peak-gene pair...		2025-10-03 07:16:30
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-10-03 07:16:31
>> calculating RP using centerToTSS and peak score2025-10-03 07:16:31
>> merging all info together		2025-10-03 07:16:34
>> done		2025-10-03 07:16:34
>> extracting RP info from regionRP...		2025-10-03 07:16:35
>> dealing with TF_GR_databse...		2025-10-03 07:16:35
>> calculating percent and p-value...		2025-10-03 07:16:35
>> dealing withE5_0h_R1...		2025-10-03 07:16:35
>> dealing withE5_0h_R2...		2025-10-03 07:16:35
>> dealing withE5_4h_R1...		2025-10-03 07:16:35
>> dealing withE5_4h_R2...		2025-10-03 07:16:35
>> dealing withE5_8h_R1...		2025-10-03 07:16:35
>> dealing withE5_8h_R2...		2025-10-03 07:16:35
>> dealing withE5_16h_R1...		2025-10-03 07:16:35
>> dealing withE5_16h_R2...		2025-10-03 07:16:35
>> dealing withE5_24h_R1...		2025-10-03 07:16:35
>> dealing withE5_24h_R2...		2025-10-03 07:16:35
>> dealing withE5_48h_R1...		2025-10-03 07:16:35
>> dealing withE5_48h_R2...		2025-10-03 07:16:36
>> dealing withE5_48h_R3...		2025-10-03 07:16:36
>> dealing withE5_72h_R1...		2025-10-03 07:16:36
>> dealing withE5_72h_R2...		2025-10-03 07:16:36
>> dealing withE5_72h_R3...		2025-10-03 07:16:36
>> merging all info together...		2025-10-03 07:16:36
>> done		2025-10-03 07:16:36
>> preparing gene features information...		2025-10-03 07:16:36
>> some scan range may cross Chr bound, trimming...		2025-10-03 07:16:37
>> calculating p-value for each TF, which may be time consuming...		2025-10-03 07:16:37
>> merging all info together...		2025-10-03 07:16:37
>> done		2025-10-03 07:16:37
>> dealing with TF_GR_database...		2025-10-03 07:16:37
>> calculating coef and converting into z-score using INT...		2025-10-03 07:16:38
>> dealing with E5_0h_R1...		2025-10-03 07:16:38
>> dealing with E5_0h_R2...		2025-10-03 07:16:38
>> dealing with E5_4h_R1...		2025-10-03 07:16:38
>> dealing with E5_4h_R2...		2025-10-03 07:16:38
>> dealing with E5_8h_R1...		2025-10-03 07:16:38
>> dealing with E5_8h_R2...		2025-10-03 07:16:38
>> dealing with E5_16h_R1...		2025-10-03 07:16:38
>> dealing with E5_16h_R2...		2025-10-03 07:16:38
>> dealing with E5_24h_R1...		2025-10-03 07:16:38
>> dealing with E5_24h_R2...		2025-10-03 07:16:38
>> dealing with E5_48h_R1...		2025-10-03 07:16:39
>> dealing with E5_48h_R2...		2025-10-03 07:16:39
>> dealing with E5_48h_R3...		2025-10-03 07:16:39
>> dealing with E5_72h_R1...		2025-10-03 07:16:39
>> dealing with E5_72h_R2...		2025-10-03 07:16:39
>> dealing with E5_72h_R3...		2025-10-03 07:16:39
>> merging all info together...		2025-10-03 07:16:39
>> done		2025-10-03 07:16:39
>> checking seqlevels match...		2025-10-03 07:16:40
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2025-10-03 07:16:40
>> some scan range may cross Chr bound, trimming...		2025-10-03 07:16:40
>> finding overlap peak in gene scan region...		2025-10-03 07:16:40
>> dealing with left peak not your gene scan region...		2025-10-03 07:16:40
>> merging two set peaks...		2025-10-03 07:16:41
>> calculating distance and dealing with gene strand...		2025-10-03 07:16:41
>> merging all info together ...		2025-10-03 07:16:41
>> done		2025-10-03 07:16:41
>> calculating peakCenter to TSS using peak-gene pair...		2025-10-03 07:16:41
>> calculating RP using centerToTSS and TF hit		2025-10-03 07:16:42
>> merging all info together		2025-10-03 07:16:42
>> done		2025-10-03 07:16:42
>> checking seqlevels match...		2025-10-03 07:16:42
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2025-10-03 07:16:42
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2025-10-03 07:16:46
>> 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
>> checking seqlevels match...		2025-10-03 07:16:46
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2025-10-03 07:16:46
>> finding nearest gene and calculating distance...		2025-10-03 07:16:47
>> dealing with gene strand ...		2025-10-03 07:16:47
>> merging all info together ...		2025-10-03 07:16:47
>> done		2025-10-03 07:16:47
>> checking seqlevels match...		2025-10-03 07:16:47
>> 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
>> checking seqlevels match...		2025-10-03 07:16:47
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2025-10-03 07:16:47
>> finding nearest gene and calculating distance...		2025-10-03 07:16:48
>> dealing with gene strand ...		2025-10-03 07:16:48
>> merging all info together ...		2025-10-03 07:16:48
>> done		2025-10-03 07:16:48
>> checking seqlevels match...		2025-10-03 07:16:49
>> 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
>> checking seqlevels match...		2025-10-03 07:16:49
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2025-10-03 07:16:49
>> finding nearest gene and calculating distance...		2025-10-03 07:16:50
>> dealing with gene strand ...		2025-10-03 07:16:51
>> merging all info together ...		2025-10-03 07:16:51
>> done		2025-10-03 07:16:51
>> checking seqlevels match...		2025-10-03 07:16:52
>> 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
>> checking seqlevels match...		2025-10-03 07:16:52
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2025-10-03 07:16:52
>> finding nearest gene and calculating distance...		2025-10-03 07:16:53
>> dealing with gene strand ...		2025-10-03 07:16:53
>> merging all info together ...		2025-10-03 07:16:53
>> done		2025-10-03 07:16:53
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2025-10-03 07:16:54
>> 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...		2025-10-03 07:16:54
>> 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...		2025-10-03 07:16:54
>> finding nearest gene and calculating distance...		2025-10-03 07:16:55
>> dealing with gene strand ...		2025-10-03 07:16:55
>> merging all info together ...		2025-10-03 07:16:55
>> done		2025-10-03 07:16:55
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2025-10-03 07:16:56
>> 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
>> checking seqlevels match...		2025-10-03 07:16:57
>> 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...		2025-10-03 07:16:58
>> checking seqlevels match...		2025-10-03 07:16:59
>> 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...		2025-10-03 07:17:00
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-10-03 07:17:02
>> merging all info together...		2025-10-03 07:17:02
>> done		2025-10-03 07:17:02
>> checking seqlevels match...		2025-10-03 07:17:02
>> 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...		2025-10-03 07:17:02
>> checking seqlevels match...		2025-10-03 07:17:02
>> 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...		2025-10-03 07:17:03
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2025-10-03 07:17:03
>> checking seqlevels match...		2025-10-03 07:17:03
>> 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...		2025-10-03 07:17:04
>> calculating cor and pvalue, which may be time consuming...		2025-10-03 07:17:04
>> merging all info together...		2025-10-03 07:17:05
>> done		2025-10-03 07:17:05
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-10-03 07:17:05
>> merging all info together...		2025-10-03 07:17:05
>> done		2025-10-03 07:17:05
>> checking seqlevels match...		2025-10-03 07:17:05
>> 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...		2025-10-03 07:17:05
>> some scan range may cross Chr bound, trimming...		2025-10-03 07:17:06
>> finding overlap peak in gene scan region...		2025-10-03 07:17:06
>> dealing with left peak not your gene scan region...		2025-10-03 07:17:06
>> merging two set peaks...		2025-10-03 07:17:06
>> calculating distance and dealing with gene strand...		2025-10-03 07:17:06
>> merging all info together ...		2025-10-03 07:17:06
>> done		2025-10-03 07:17:06
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-10-03 07:17:08
>> merging all info together...		2025-10-03 07:17:08
>> done		2025-10-03 07:17:08
>> checking seqlevels match...		2025-10-03 07:17:08
>> 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...		2025-10-03 07:17:08
>> checking seqlevels match...		2025-10-03 07:17:08
>> 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...		2025-10-03 07:17:09
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2025-10-03 07:17:09
>> checking seqlevels match...		2025-10-03 07:17:09
>> 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...		2025-10-03 07:17:10
>> calculating cor and pvalue, which may be time consuming...		2025-10-03 07:17:10
>> merging all info together...		2025-10-03 07:17:11
>> done		2025-10-03 07:17:11
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 
 80.638   1.474  82.315 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit4.0880.1474.435
calcRP_coverage6.1610.1246.303
calcRP_region6.7230.0646.805
enhancerPromoterCor3.1550.0643.226
findIT_MARA0.5690.0000.569
findIT_TFHit1.0570.0081.067
findIT_TTPair0.0890.0000.090
findIT_enrichFisher0.1890.0040.194
findIT_enrichWilcox0.2160.0040.220
findIT_regionRP7.4850.0567.561
getAssocPairNumber1.4530.0001.458
integrate_ChIP_RNA2.6460.0442.698
integrate_replicates0.0000.0020.003
jaccard_findIT_TTpair0.1220.0030.125
jaccard_findIT_enrichFisher0.2570.0040.262
loadPeakFile0.0760.0000.076
mm_geneBound1.5110.0081.523
mm_geneScan1.4860.0081.498
mm_nearestGene1.4070.0201.432
peakGeneCor3.0070.0313.048
plot_annoDistance2.2340.0202.260
plot_peakGeneAlias_summary2.5970.0962.700
plot_peakGeneCor4.1160.0484.177
test_geneSet000