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This page was generated on 2025-01-14 11:44 -0500 (Tue, 14 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4767
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4487
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4450
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4405
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4398
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Package 711/2281HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.13.0  (landing page)
Guandong Shang
Snapshot Date: 2025-01-13 13:40 -0500 (Mon, 13 Jan 2025)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: devel
git_last_commit: 30235ec
git_last_commit_date: 2024-10-29 11:01:40 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for FindIT2 on lconway

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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-01-13 20:30:44 -0500 (Mon, 13 Jan 2025)
EndedAt: 2025-01-13 20:37:14 -0500 (Mon, 13 Jan 2025)
EllapsedTime: 389.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.13.0’
* 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 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 7.583  0.199   7.857
calcRP_coverage 5.145  0.529   5.735
calcRP_region   5.396  0.151   5.705
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-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)

Tests output

FindIT2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: 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...		2025-01-13 20:36:05
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:06
>> preparing weight info...		2025-01-13 20:36:06
>> loading E50h_sampleChr5.bw info...		2025-01-13 20:36:06
------------
>> extracting and calcluating Chr5 signal...		2025-01-13 20:36:06
>> dealing with Chr5 left gene signal...		2025-01-13 20:36:10
>> norming Chr5RP accoring to the whole Chr RP...		2025-01-13 20:36:10
>> merging all Chr RP together...		2025-01-13 20:36:10
>> done		2025-01-13 20:36:10
>> checking seqlevels match...		2025-01-13 20:36:10
>> 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...		2025-01-13 20:36:10
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:11
>> finding overlap peak in gene scan region...		2025-01-13 20:36:11
>> dealing with left peak not your gene scan region...		2025-01-13 20:36:11
>> merging two set peaks...		2025-01-13 20:36:12
>> calculating distance and dealing with gene strand...		2025-01-13 20:36:12
>> merging all info together ...		2025-01-13 20:36:12
>> done		2025-01-13 20:36:12
>> calculating peakCenter to TSS using peak-gene pair...		2025-01-13 20:36:12
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-01-13 20:36:13
>> calculating RP using centerToTSS and peak score2025-01-13 20:36:13
>> merging all info together		2025-01-13 20:36:15
>> done		2025-01-13 20:36:16
>> calculating peakCenter to TSS using peak-gene pair...		2025-01-13 20:36:16
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-01-13 20:36:17
>> calculating RP using centerToTSS and peak score2025-01-13 20:36:17
>> merging all info together		2025-01-13 20:36:20
>> done		2025-01-13 20:36:20
>> checking seqlevels match...		2025-01-13 20:36:20
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2025-01-13 20:36:20
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:21
>> finding overlap peak in gene scan region...		2025-01-13 20:36:21
>> dealing with left peak not your gene scan region...		2025-01-13 20:36:21
>> merging two set peaks...		2025-01-13 20:36:22
>> calculating distance and dealing with gene strand...		2025-01-13 20:36:22
>> merging all info together ...		2025-01-13 20:36:22
>> done		2025-01-13 20:36:22
>> calculating peakCenter to TSS using peak-gene pair...		2025-01-13 20:36:22
>> calculating RP using centerToTSS and TF hit		2025-01-13 20:36:23
>> merging all info together		2025-01-13 20:36:23
>> done		2025-01-13 20:36:23
>> calculating peakCenter to TSS using peak-gene pair...		2025-01-13 20:36:23
>> calculating RP using centerToTSS and TF hit		2025-01-13 20:36:24
>> merging all info together		2025-01-13 20:36:24
>> done		2025-01-13 20:36:25
>> checking seqlevels match...		2025-01-13 20:36:25
>> 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...		2025-01-13 20:36:25
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:26
>> finding overlap peak in gene scan region...		2025-01-13 20:36:26
>> dealing with left peak not your gene scan region...		2025-01-13 20:36:26
>> merging two set peaks...		2025-01-13 20:36:26
>> calculating distance and dealing with gene strand...		2025-01-13 20:36:26
>> merging all info together ...		2025-01-13 20:36:26
>> done		2025-01-13 20:36:27
>> calculating peakCenter to TSS using peak-gene pair...		2025-01-13 20:36:27
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-01-13 20:36:27
>> calculating RP using centerToTSS and peak score2025-01-13 20:36:27
>> merging all info together		2025-01-13 20:36:29
>> done		2025-01-13 20:36:30
>> extracting RP info from regionRP...		2025-01-13 20:36:30
>> dealing with TF_GR_databse...		2025-01-13 20:36:31
>> calculating percent and p-value...		2025-01-13 20:36:31
>> dealing withE5_0h_R1...		2025-01-13 20:36:31
>> dealing withE5_0h_R2...		2025-01-13 20:36:31
>> dealing withE5_4h_R1...		2025-01-13 20:36:31
>> dealing withE5_4h_R2...		2025-01-13 20:36:31
>> dealing withE5_8h_R1...		2025-01-13 20:36:31
>> dealing withE5_8h_R2...		2025-01-13 20:36:31
>> dealing withE5_16h_R1...		2025-01-13 20:36:31
>> dealing withE5_16h_R2...		2025-01-13 20:36:31
>> dealing withE5_24h_R1...		2025-01-13 20:36:31
>> dealing withE5_24h_R2...		2025-01-13 20:36:31
>> dealing withE5_48h_R1...		2025-01-13 20:36:31
>> dealing withE5_48h_R2...		2025-01-13 20:36:31
>> dealing withE5_48h_R3...		2025-01-13 20:36:31
>> dealing withE5_72h_R1...		2025-01-13 20:36:31
>> dealing withE5_72h_R2...		2025-01-13 20:36:31
>> dealing withE5_72h_R3...		2025-01-13 20:36:31
>> merging all info together...		2025-01-13 20:36:31
>> done		2025-01-13 20:36:31
>> preparing gene features information...		2025-01-13 20:36:32
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:32
>> calculating p-value for each TF, which may be time consuming...		2025-01-13 20:36:32
>> merging all info together...		2025-01-13 20:36:33
>> done		2025-01-13 20:36:33
>> dealing with TF_GR_database...		2025-01-13 20:36:33
>> calculating coef and converting into z-score using INT...		2025-01-13 20:36:33
>> dealing with E5_0h_R1...		2025-01-13 20:36:33
>> dealing with E5_0h_R2...		2025-01-13 20:36:33
>> dealing with E5_4h_R1...		2025-01-13 20:36:33
>> dealing with E5_4h_R2...		2025-01-13 20:36:33
>> dealing with E5_8h_R1...		2025-01-13 20:36:33
>> dealing with E5_8h_R2...		2025-01-13 20:36:33
>> dealing with E5_16h_R1...		2025-01-13 20:36:33
>> dealing with E5_16h_R2...		2025-01-13 20:36:33
>> dealing with E5_24h_R1...		2025-01-13 20:36:34
>> dealing with E5_24h_R2...		2025-01-13 20:36:34
>> dealing with E5_48h_R1...		2025-01-13 20:36:34
>> dealing with E5_48h_R2...		2025-01-13 20:36:34
>> dealing with E5_48h_R3...		2025-01-13 20:36:34
>> dealing with E5_72h_R1...		2025-01-13 20:36:34
>> dealing with E5_72h_R2...		2025-01-13 20:36:34
>> dealing with E5_72h_R3...		2025-01-13 20:36:34
>> merging all info together...		2025-01-13 20:36:34
>> done		2025-01-13 20:36:34
>> checking seqlevels match...		2025-01-13 20:36:34
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2025-01-13 20:36:34
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:35
>> finding overlap peak in gene scan region...		2025-01-13 20:36:35
>> dealing with left peak not your gene scan region...		2025-01-13 20:36:35
>> merging two set peaks...		2025-01-13 20:36:36
>> calculating distance and dealing with gene strand...		2025-01-13 20:36:36
>> merging all info together ...		2025-01-13 20:36:36
>> done		2025-01-13 20:36:36
>> calculating peakCenter to TSS using peak-gene pair...		2025-01-13 20:36:36
>> calculating RP using centerToTSS and TF hit		2025-01-13 20:36:38
>> merging all info together		2025-01-13 20:36:38
>> done		2025-01-13 20:36:38
>> checking seqlevels match...		2025-01-13 20:36:38
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2025-01-13 20:36:38
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2025-01-13 20:36:41
>> 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...		2025-01-13 20:36:41
>> 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...		2025-01-13 20:36:41
>> finding nearest gene and calculating distance...		2025-01-13 20:36:42
>> dealing with gene strand ...		2025-01-13 20:36:42
>> merging all info together ...		2025-01-13 20:36:42
>> done		2025-01-13 20:36:42
>> checking seqlevels match...		2025-01-13 20:36:42
>> 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...		2025-01-13 20:36:43
>> 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...		2025-01-13 20:36:43
>> finding nearest gene and calculating distance...		2025-01-13 20:36:43
>> dealing with gene strand ...		2025-01-13 20:36:43
>> merging all info together ...		2025-01-13 20:36:43
>> done		2025-01-13 20:36:44
>> checking seqlevels match...		2025-01-13 20:36:44
>> 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...		2025-01-13 20:36:44
>> 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...		2025-01-13 20:36:44
>> finding nearest gene and calculating distance...		2025-01-13 20:36:45
>> dealing with gene strand ...		2025-01-13 20:36:45
>> merging all info together ...		2025-01-13 20:36:45
>> done		2025-01-13 20:36:45
>> checking seqlevels match...		2025-01-13 20:36:46
>> 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...		2025-01-13 20:36:46
>> 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...		2025-01-13 20:36:46
>> finding nearest gene and calculating distance...		2025-01-13 20:36:47
>> dealing with gene strand ...		2025-01-13 20:36:47
>> merging all info together ...		2025-01-13 20:36:47
>> done		2025-01-13 20:36:47
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2025-01-13 20:36:48
>> 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
>> checking seqlevels match...		2025-01-13 20:36:48
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2025-01-13 20:36:48
>> finding nearest gene and calculating distance...		2025-01-13 20:36:49
>> dealing with gene strand ...		2025-01-13 20:36:49
>> merging all info together ...		2025-01-13 20:36:49
>> done		2025-01-13 20:36:49
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2025-01-13 20:36:50
>> 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
>> checking seqlevels match...		2025-01-13 20:36:51
>> 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...		2025-01-13 20:36:52
>> checking seqlevels match...		2025-01-13 20:36:53
>> 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
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:54
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-01-13 20:36:55
>> merging all info together...		2025-01-13 20:36:55
>> done		2025-01-13 20:36:56
>> checking seqlevels match...		2025-01-13 20:36:56
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2025-01-13 20:36:56
>> checking seqlevels match...		2025-01-13 20:36:56
>> 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...		2025-01-13 20:36:57
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2025-01-13 20:36:57
>> checking seqlevels match...		2025-01-13 20:36:57
>> 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...		2025-01-13 20:36:58
>> calculating cor and pvalue, which may be time consuming...		2025-01-13 20:36:58
>> merging all info together...		2025-01-13 20:36:58
>> done		2025-01-13 20:36:58
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-01-13 20:36:58
>> merging all info together...		2025-01-13 20:36:58
>> done		2025-01-13 20:36:58
>> checking seqlevels match...		2025-01-13 20:36:59
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2025-01-13 20:36:59
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:36:59
>> finding overlap peak in gene scan region...		2025-01-13 20:36:59
>> dealing with left peak not your gene scan region...		2025-01-13 20:36:59
>> merging two set peaks...		2025-01-13 20:37:00
>> calculating distance and dealing with gene strand...		2025-01-13 20:37:00
>> merging all info together ...		2025-01-13 20:37:00
>> done		2025-01-13 20:37:00
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-01-13 20:37:01
>> merging all info together...		2025-01-13 20:37:01
>> done		2025-01-13 20:37:01
>> checking seqlevels match...		2025-01-13 20:37:01
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2025-01-13 20:37:01
>> checking seqlevels match...		2025-01-13 20:37:01
>> 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
>> some scan range may cross Chr bound, trimming...		2025-01-13 20:37:02
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2025-01-13 20:37:02
>> checking seqlevels match...		2025-01-13 20:37:02
>> 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...		2025-01-13 20:37:03
>> calculating cor and pvalue, which may be time consuming...		2025-01-13 20:37:03
>> merging all info together...		2025-01-13 20:37:03
>> done		2025-01-13 20:37:03
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 
 70.502   2.638  73.701

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0000.0010.001
calcRP_TFHit3.1260.1593.364
calcRP_coverage5.1450.5295.735
calcRP_region5.3960.1515.705
enhancerPromoterCor3.1440.0813.267
findIT_MARA0.4970.0120.511
findIT_TFHit1.1110.0321.152
findIT_TTPair0.0890.0070.096
findIT_enrichFisher0.1860.0050.195
findIT_enrichWilcox0.2100.0050.216
findIT_regionRP7.5830.1997.857
getAssocPairNumber1.2920.0371.346
integrate_ChIP_RNA2.1370.0552.213
integrate_replicates0.0020.0010.003
jaccard_findIT_TTpair0.1040.0050.109
jaccard_findIT_enrichFisher0.2110.0040.216
loadPeakFile0.0600.0020.062
mm_geneBound1.2530.0351.300
mm_geneScan1.2950.0511.354
mm_nearestGene1.1170.0321.155
peakGeneCor3.1190.0863.223
plot_annoDistance1.5410.0311.581
plot_peakGeneAlias_summary1.3980.0541.459
plot_peakGeneCor3.0000.0643.079
test_geneSet0.0000.0000.001