Multiple platform build/check report for BioC 3.19 - CHECK results for FindIT2 on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for FindIT2 on kjohnson1

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: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2024-10-17 21:41:53 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 21:48:59 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 426.3 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FindIT2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FindIT2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 6.461  0.180   6.680
calcRP_coverage 5.142  0.658   5.884
calcRP_region   5.198  0.209   5.454
* 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/4.4-arm64/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) {
+     stop("unable to load TxDb.Athaliana.BioMart.plantsmart28")
+ }
Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28
> 
> test_check("FindIT2")
>> preparing gene features information...		2024-10-17 21:47:45
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:47:46
>> preparing weight info...		2024-10-17 21:47:47
>> loading E50h_sampleChr5.bw info...		2024-10-17 21:47:47
------------
>> extracting and calcluating Chr5 signal...		2024-10-17 21:47:47
>> dealing with Chr5 left gene signal...		2024-10-17 21:47:52
>> norming Chr5RP accoring to the whole Chr RP...		2024-10-17 21:47:52
>> merging all Chr RP together...		2024-10-17 21:47:52
>> done		2024-10-17 21:47:52
>> checking seqlevels match...		2024-10-17 21:47:52
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-10-17 21:47:52
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:47:53
>> finding overlap peak in gene scan region...		2024-10-17 21:47:53
>> dealing with left peak not your gene scan region...		2024-10-17 21:47:53
>> merging two set peaks...		2024-10-17 21:47:54
>> calculating distance and dealing with gene strand...		2024-10-17 21:47:54
>> merging all info together ...		2024-10-17 21:47:54
>> done		2024-10-17 21:47:54
>> calculating peakCenter to TSS using peak-gene pair...		2024-10-17 21:47:54
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-10-17 21:47:55
>> calculating RP using centerToTSS and peak score2024-10-17 21:47:55
>> merging all info together		2024-10-17 21:47:57
>> done		2024-10-17 21:47:58
>> calculating peakCenter to TSS using peak-gene pair...		2024-10-17 21:47:58
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-10-17 21:47:59
>> calculating RP using centerToTSS and peak score2024-10-17 21:47:59
>> merging all info together		2024-10-17 21:48:02
>> done		2024-10-17 21:48:02
>> checking seqlevels match...		2024-10-17 21:48:02
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-10-17 21:48:02
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:03
>> finding overlap peak in gene scan region...		2024-10-17 21:48:03
>> dealing with left peak not your gene scan region...		2024-10-17 21:48:03
>> merging two set peaks...		2024-10-17 21:48:04
>> calculating distance and dealing with gene strand...		2024-10-17 21:48:04
>> merging all info together ...		2024-10-17 21:48:04
>> done		2024-10-17 21:48:04
>> calculating peakCenter to TSS using peak-gene pair...		2024-10-17 21:48:04
>> calculating RP using centerToTSS and TF hit		2024-10-17 21:48:06
>> merging all info together		2024-10-17 21:48:06
>> done		2024-10-17 21:48:06
>> calculating peakCenter to TSS using peak-gene pair...		2024-10-17 21:48:06
>> calculating RP using centerToTSS and TF hit		2024-10-17 21:48:06
>> merging all info together		2024-10-17 21:48:06
>> done		2024-10-17 21:48:06
>> checking seqlevels match...		2024-10-17 21:48:07
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-10-17 21:48:07
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:08
>> finding overlap peak in gene scan region...		2024-10-17 21:48:08
>> dealing with left peak not your gene scan region...		2024-10-17 21:48:08
>> merging two set peaks...		2024-10-17 21:48:08
>> calculating distance and dealing with gene strand...		2024-10-17 21:48:08
>> merging all info together ...		2024-10-17 21:48:08
>> done		2024-10-17 21:48:09
>> calculating peakCenter to TSS using peak-gene pair...		2024-10-17 21:48:09
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-10-17 21:48:09
>> calculating RP using centerToTSS and peak score2024-10-17 21:48:09
>> merging all info together		2024-10-17 21:48:11
>> done		2024-10-17 21:48:12
>> extracting RP info from regionRP...		2024-10-17 21:48:13
>> dealing with TF_GR_databse...		2024-10-17 21:48:13
>> calculating percent and p-value...		2024-10-17 21:48:13
>> dealing withE5_0h_R1...		2024-10-17 21:48:13
>> dealing withE5_0h_R2...		2024-10-17 21:48:13
>> dealing withE5_4h_R1...		2024-10-17 21:48:13
>> dealing withE5_4h_R2...		2024-10-17 21:48:13
>> dealing withE5_8h_R1...		2024-10-17 21:48:13
>> dealing withE5_8h_R2...		2024-10-17 21:48:13
>> dealing withE5_16h_R1...		2024-10-17 21:48:13
>> dealing withE5_16h_R2...		2024-10-17 21:48:13
>> dealing withE5_24h_R1...		2024-10-17 21:48:13
>> dealing withE5_24h_R2...		2024-10-17 21:48:13
>> dealing withE5_48h_R1...		2024-10-17 21:48:13
>> dealing withE5_48h_R2...		2024-10-17 21:48:13
>> dealing withE5_48h_R3...		2024-10-17 21:48:13
>> dealing withE5_72h_R1...		2024-10-17 21:48:13
>> dealing withE5_72h_R2...		2024-10-17 21:48:13
>> dealing withE5_72h_R3...		2024-10-17 21:48:13
>> merging all info together...		2024-10-17 21:48:13
>> done		2024-10-17 21:48:14
>> preparing gene features information...		2024-10-17 21:48:14
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:15
>> calculating p-value for each TF, which may be time consuming...		2024-10-17 21:48:15
>> merging all info together...		2024-10-17 21:48:15
>> done		2024-10-17 21:48:15
>> dealing with TF_GR_database...		2024-10-17 21:48:15
>> calculating coef and converting into z-score using INT...		2024-10-17 21:48:15
>> dealing with E5_0h_R1...		2024-10-17 21:48:15
>> dealing with E5_0h_R2...		2024-10-17 21:48:15
>> dealing with E5_4h_R1...		2024-10-17 21:48:17
>> dealing with E5_4h_R2...		2024-10-17 21:48:17
>> dealing with E5_8h_R1...		2024-10-17 21:48:17
>> dealing with E5_8h_R2...		2024-10-17 21:48:17
>> dealing with E5_16h_R1...		2024-10-17 21:48:17
>> dealing with E5_16h_R2...		2024-10-17 21:48:17
>> dealing with E5_24h_R1...		2024-10-17 21:48:17
>> dealing with E5_24h_R2...		2024-10-17 21:48:17
>> dealing with E5_48h_R1...		2024-10-17 21:48:17
>> dealing with E5_48h_R2...		2024-10-17 21:48:17
>> dealing with E5_48h_R3...		2024-10-17 21:48:17
>> dealing with E5_72h_R1...		2024-10-17 21:48:17
>> dealing with E5_72h_R2...		2024-10-17 21:48:17
>> dealing with E5_72h_R3...		2024-10-17 21:48:17
>> merging all info together...		2024-10-17 21:48:17
>> done		2024-10-17 21:48:18
>> checking seqlevels match...		2024-10-17 21:48:18
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-10-17 21:48:18
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:19
>> finding overlap peak in gene scan region...		2024-10-17 21:48:19
>> dealing with left peak not your gene scan region...		2024-10-17 21:48:19
>> merging two set peaks...		2024-10-17 21:48:19
>> calculating distance and dealing with gene strand...		2024-10-17 21:48:19
>> merging all info together ...		2024-10-17 21:48:19
>> done		2024-10-17 21:48:19
>> calculating peakCenter to TSS using peak-gene pair...		2024-10-17 21:48:19
>> calculating RP using centerToTSS and TF hit		2024-10-17 21:48:20
>> merging all info together		2024-10-17 21:48:20
>> done		2024-10-17 21:48:20
>> checking seqlevels match...		2024-10-17 21:48:20
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-10-17 21:48:20
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-10-17 21:48:24
>> 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
>> checking seqlevels match...		2024-10-17 21:48:24
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-10-17 21:48:24
>> finding nearest gene and calculating distance...		2024-10-17 21:48:25
>> dealing with gene strand ...		2024-10-17 21:48:25
>> merging all info together ...		2024-10-17 21:48:25
>> done		2024-10-17 21:48:25
>> checking seqlevels match...		2024-10-17 21:48:25
>> 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
>> checking seqlevels match...		2024-10-17 21:48:25
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-10-17 21:48:25
>> finding nearest gene and calculating distance...		2024-10-17 21:48:26
>> dealing with gene strand ...		2024-10-17 21:48:26
>> merging all info together ...		2024-10-17 21:48:26
>> done		2024-10-17 21:48:26
>> checking seqlevels match...		2024-10-17 21:48:27
>> 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
>> checking seqlevels match...		2024-10-17 21:48:27
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-10-17 21:48:27
>> finding nearest gene and calculating distance...		2024-10-17 21:48:29
>> dealing with gene strand ...		2024-10-17 21:48:29
>> merging all info together ...		2024-10-17 21:48:29
>> done		2024-10-17 21:48:29
>> checking seqlevels match...		2024-10-17 21:48:30
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-10-17 21:48:30
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-10-17 21:48:30
>> finding nearest gene and calculating distance...		2024-10-17 21:48:31
>> dealing with gene strand ...		2024-10-17 21:48:31
>> merging all info together ...		2024-10-17 21:48:31
>> done		2024-10-17 21:48:31
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-10-17 21:48:32
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-10-17 21:48:32
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-10-17 21:48:32
>> finding nearest gene and calculating distance...		2024-10-17 21:48:33
>> dealing with gene strand ...		2024-10-17 21:48:33
>> merging all info together ...		2024-10-17 21:48:33
>> done		2024-10-17 21:48:33
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-10-17 21:48:34
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-10-17 21:48:35
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:36
>> checking seqlevels match...		2024-10-17 21:48:37
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:38
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-10-17 21:48:39
>> merging all info together...		2024-10-17 21:48:39
>> done		2024-10-17 21:48:39
>> checking seqlevels match...		2024-10-17 21:48:39
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2024-10-17 21:48:39
>> checking seqlevels match...		2024-10-17 21:48:39
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:40
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-10-17 21:48:40
>> checking seqlevels match...		2024-10-17 21:48:40
>> 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
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:41
>> calculating cor and pvalue, which may be time consuming...		2024-10-17 21:48:41
>> merging all info together...		2024-10-17 21:48:41
>> done		2024-10-17 21:48:42
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-10-17 21:48:42
>> merging all info together...		2024-10-17 21:48:42
>> done		2024-10-17 21:48:42
>> checking seqlevels match...		2024-10-17 21:48:42
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-10-17 21:48:42
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:43
>> finding overlap peak in gene scan region...		2024-10-17 21:48:43
>> dealing with left peak not your gene scan region...		2024-10-17 21:48:43
>> merging two set peaks...		2024-10-17 21:48:43
>> calculating distance and dealing with gene strand...		2024-10-17 21:48:43
>> merging all info together ...		2024-10-17 21:48:43
>> done		2024-10-17 21:48:43
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-10-17 21:48:45
>> merging all info together...		2024-10-17 21:48:45
>> done		2024-10-17 21:48:45
>> checking seqlevels match...		2024-10-17 21:48:45
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2024-10-17 21:48:45
>> checking seqlevels match...		2024-10-17 21:48:45
>> 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
>> some scan range may cross Chr bound, trimming...		2024-10-17 21:48:46
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-10-17 21:48:46
>> checking seqlevels match...		2024-10-17 21:48:46
>> 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...		2024-10-17 21:48:47
>> calculating cor and pvalue, which may be time consuming...		2024-10-17 21:48:47
>> merging all info together...		2024-10-17 21:48:47
>> done		2024-10-17 21:48:48
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 
 74.327   3.745  79.254

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

name	user	system	elapsed
TF_target_database	0	0	0
calcRP_TFHit	4.396	0.160	4.610
calcRP_coverage	5.142	0.658	5.884
calcRP_region	5.198	0.209	5.454
enhancerPromoterCor	3.024	0.168	3.207
findIT_MARA	0.494	0.020	0.517
findIT_TFHit	1.141	0.064	1.210
findIT_TTPair	0.096	0.006	0.103
findIT_enrichFisher	0.165	0.005	0.171
findIT_enrichWilcox	0.179	0.004	0.184
findIT_regionRP	6.461	0.180	6.680
getAssocPairNumber	1.453	0.047	1.522
integrate_ChIP_RNA	2.474	0.074	2.566
integrate_replicates	0.002	0.000	0.003
jaccard_findIT_TTpair	0.118	0.007	0.126
jaccard_findIT_enrichFisher	0.220	0.004	0.225
loadPeakFile	0.066	0.001	0.069
mm_geneBound	1.450	0.029	1.490
mm_geneScan	1.523	0.043	1.590
mm_nearestGene	1.291	0.036	1.331
peakGeneCor	2.503	0.051	2.574
plot_annoDistance	1.765	0.041	1.821
plot_peakGeneAlias_summary	1.611	0.044	1.665
plot_peakGeneCor	3.211	0.053	3.276
test_geneSet	0.000	0.000	0.001