Multiple platform build/check report for BioC 3.20 - CHECK results for FindIT2 on teran2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 teran2

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: 1.12.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FindIT2_1.12.0.tar.gz

StartedAt: 2024-11-20 02:57:24 -0500 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 03:04:43 -0500 (Wed, 20 Nov 2024)

EllapsedTime: 439.4 seconds

RetCode: 0

Status: OK

CheckDir: FindIT2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FindIT2_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FindIT2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.12.0’
* 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 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
calcRP_coverage 4.238  0.943   7.288
calcRP_region   4.369  0.078   5.378
* 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-3.20-bioc/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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

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, saveRDS, 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...		2024-11-20 03:02:45
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:02:46
>> preparing weight info...		2024-11-20 03:02:46
>> loading E50h_sampleChr5.bw info...		2024-11-20 03:02:46
------------
>> extracting and calcluating Chr5 signal...		2024-11-20 03:02:46
>> dealing with Chr5 left gene signal...		2024-11-20 03:02:51
>> norming Chr5RP accoring to the whole Chr RP...		2024-11-20 03:02:51
>> merging all Chr RP together...		2024-11-20 03:02:51
>> done		2024-11-20 03:02:51
>> checking seqlevels match...		2024-11-20 03:02:51
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-11-20 03:02:51
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:02:53
>> finding overlap peak in gene scan region...		2024-11-20 03:02:53
>> dealing with left peak not your gene scan region...		2024-11-20 03:02:53
>> merging two set peaks...		2024-11-20 03:02:53
>> calculating distance and dealing with gene strand...		2024-11-20 03:02:53
>> merging all info together ...		2024-11-20 03:02:53
>> done		2024-11-20 03:02:53
>> calculating peakCenter to TSS using peak-gene pair...		2024-11-20 03:02:53
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-11-20 03:02:54
>> calculating RP using centerToTSS and peak score2024-11-20 03:02:54
>> merging all info together		2024-11-20 03:02:55
>> done		2024-11-20 03:02:56
>> calculating peakCenter to TSS using peak-gene pair...		2024-11-20 03:02:56
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-11-20 03:02:57
>> calculating RP using centerToTSS and peak score2024-11-20 03:02:57
>> merging all info together		2024-11-20 03:02:59
>> done		2024-11-20 03:03:00
>> checking seqlevels match...		2024-11-20 03:03:00
>> 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...		2024-11-20 03:03:00
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:01
>> finding overlap peak in gene scan region...		2024-11-20 03:03:01
>> dealing with left peak not your gene scan region...		2024-11-20 03:03:01
>> merging two set peaks...		2024-11-20 03:03:01
>> calculating distance and dealing with gene strand...		2024-11-20 03:03:01
>> merging all info together ...		2024-11-20 03:03:01
>> done		2024-11-20 03:03:01
>> calculating peakCenter to TSS using peak-gene pair...		2024-11-20 03:03:01
>> calculating RP using centerToTSS and TF hit		2024-11-20 03:03:02
>> merging all info together		2024-11-20 03:03:02
>> done		2024-11-20 03:03:02
>> calculating peakCenter to TSS using peak-gene pair...		2024-11-20 03:03:02
>> calculating RP using centerToTSS and TF hit		2024-11-20 03:03:03
>> merging all info together		2024-11-20 03:03:03
>> done		2024-11-20 03:03:03
>> checking seqlevels match...		2024-11-20 03:03:04
>> 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...		2024-11-20 03:03:04
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:05
>> finding overlap peak in gene scan region...		2024-11-20 03:03:05
>> dealing with left peak not your gene scan region...		2024-11-20 03:03:05
>> merging two set peaks...		2024-11-20 03:03:05
>> calculating distance and dealing with gene strand...		2024-11-20 03:03:05
>> merging all info together ...		2024-11-20 03:03:05
>> done		2024-11-20 03:03:05
>> calculating peakCenter to TSS using peak-gene pair...		2024-11-20 03:03:05
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-11-20 03:03:05
>> calculating RP using centerToTSS and peak score2024-11-20 03:03:05
>> merging all info together		2024-11-20 03:03:07
>> done		2024-11-20 03:03:07
>> extracting RP info from regionRP...		2024-11-20 03:03:08
>> dealing with TF_GR_databse...		2024-11-20 03:03:08
>> calculating percent and p-value...		2024-11-20 03:03:08
>> dealing withE5_0h_R1...		2024-11-20 03:03:08
>> dealing withE5_0h_R2...		2024-11-20 03:03:08
>> dealing withE5_4h_R1...		2024-11-20 03:03:08
>> dealing withE5_4h_R2...		2024-11-20 03:03:08
>> dealing withE5_8h_R1...		2024-11-20 03:03:08
>> dealing withE5_8h_R2...		2024-11-20 03:03:08
>> dealing withE5_16h_R1...		2024-11-20 03:03:08
>> dealing withE5_16h_R2...		2024-11-20 03:03:08
>> dealing withE5_24h_R1...		2024-11-20 03:03:08
>> dealing withE5_24h_R2...		2024-11-20 03:03:08
>> dealing withE5_48h_R1...		2024-11-20 03:03:08
>> dealing withE5_48h_R2...		2024-11-20 03:03:08
>> dealing withE5_48h_R3...		2024-11-20 03:03:08
>> dealing withE5_72h_R1...		2024-11-20 03:03:08
>> dealing withE5_72h_R2...		2024-11-20 03:03:08
>> dealing withE5_72h_R3...		2024-11-20 03:03:08
>> merging all info together...		2024-11-20 03:03:09
>> done		2024-11-20 03:03:09
>> preparing gene features information...		2024-11-20 03:03:09
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:09
>> calculating p-value for each TF, which may be time consuming...		2024-11-20 03:03:09
>> merging all info together...		2024-11-20 03:03:10
>> done		2024-11-20 03:03:10
>> dealing with TF_GR_database...		2024-11-20 03:03:10
>> calculating coef and converting into z-score using INT...		2024-11-20 03:03:10
>> dealing with E5_0h_R1...		2024-11-20 03:03:10
>> dealing with E5_0h_R2...		2024-11-20 03:03:10
>> dealing with E5_4h_R1...		2024-11-20 03:03:10
>> dealing with E5_4h_R2...		2024-11-20 03:03:10
>> dealing with E5_8h_R1...		2024-11-20 03:03:10
>> dealing with E5_8h_R2...		2024-11-20 03:03:10
>> dealing with E5_16h_R1...		2024-11-20 03:03:10
>> dealing with E5_16h_R2...		2024-11-20 03:03:11
>> dealing with E5_24h_R1...		2024-11-20 03:03:11
>> dealing with E5_24h_R2...		2024-11-20 03:03:11
>> dealing with E5_48h_R1...		2024-11-20 03:03:11
>> dealing with E5_48h_R2...		2024-11-20 03:03:11
>> dealing with E5_48h_R3...		2024-11-20 03:03:11
>> dealing with E5_72h_R1...		2024-11-20 03:03:11
>> dealing with E5_72h_R2...		2024-11-20 03:03:11
>> dealing with E5_72h_R3...		2024-11-20 03:03:11
>> merging all info together...		2024-11-20 03:03:11
>> done		2024-11-20 03:03:11
>> checking seqlevels match...		2024-11-20 03:03:11
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-11-20 03:03:11
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:12
>> finding overlap peak in gene scan region...		2024-11-20 03:03:12
>> dealing with left peak not your gene scan region...		2024-11-20 03:03:12
>> merging two set peaks...		2024-11-20 03:03:12
>> calculating distance and dealing with gene strand...		2024-11-20 03:03:12
>> merging all info together ...		2024-11-20 03:03:12
>> done		2024-11-20 03:03:12
>> calculating peakCenter to TSS using peak-gene pair...		2024-11-20 03:03:12
>> calculating RP using centerToTSS and TF hit		2024-11-20 03:03:13
>> merging all info together		2024-11-20 03:03:13
>> done		2024-11-20 03:03:13
>> checking seqlevels match...		2024-11-20 03:03:13
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-11-20 03:03:13
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-11-20 03:03:15
>> 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...		2024-11-20 03:03:15
>> 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...		2024-11-20 03:03:15
>> finding nearest gene and calculating distance...		2024-11-20 03:03:16
>> dealing with gene strand ...		2024-11-20 03:03:16
>> merging all info together ...		2024-11-20 03:03:16
>> done		2024-11-20 03:03:16
>> checking seqlevels match...		2024-11-20 03:03:16
>> 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...		2024-11-20 03:03:16
>> 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...		2024-11-20 03:03:16
>> finding nearest gene and calculating distance...		2024-11-20 03:03:16
>> dealing with gene strand ...		2024-11-20 03:03:16
>> merging all info together ...		2024-11-20 03:03:16
>> done		2024-11-20 03:03:16
>> checking seqlevels match...		2024-11-20 03:03:19
>> 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...		2024-11-20 03:03:19
>> 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...		2024-11-20 03:03:19
>> finding nearest gene and calculating distance...		2024-11-20 03:03:20
>> dealing with gene strand ...		2024-11-20 03:03:20
>> merging all info together ...		2024-11-20 03:03:20
>> done		2024-11-20 03:03:20
>> checking seqlevels match...		2024-11-20 03:03:21
>> 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...		2024-11-20 03:03:21
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-11-20 03:03:21
>> finding nearest gene and calculating distance...		2024-11-20 03:03:21
>> dealing with gene strand ...		2024-11-20 03:03:21
>> merging all info together ...		2024-11-20 03:03:21
>> done		2024-11-20 03:03:21
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-11-20 03:03:23
>> 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...		2024-11-20 03:03:23
>> 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...		2024-11-20 03:03:23
>> finding nearest gene and calculating distance...		2024-11-20 03:03:23
>> dealing with gene strand ...		2024-11-20 03:03:23
>> merging all info together ...		2024-11-20 03:03:23
>> done		2024-11-20 03:03:23
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-11-20 03:03:24
>> 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...		2024-11-20 03:03:25
>> 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
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:25
>> checking seqlevels match...		2024-11-20 03:03:26
>> 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...		2024-11-20 03:03:26
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-11-20 03:03:28
>> merging all info together...		2024-11-20 03:03:28
>> done		2024-11-20 03:03:28
>> checking seqlevels match...		2024-11-20 03:03:28
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2024-11-20 03:03:28
>> checking seqlevels match...		2024-11-20 03:03:28
>> 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
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:29
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-11-20 03:03:29
>> checking seqlevels match...		2024-11-20 03:03:29
>> 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
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:29
>> calculating cor and pvalue, which may be time consuming...		2024-11-20 03:03:29
>> merging all info together...		2024-11-20 03:03:30
>> done		2024-11-20 03:03:30
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-11-20 03:03:30
>> merging all info together...		2024-11-20 03:03:30
>> done		2024-11-20 03:03:30
>> checking seqlevels match...		2024-11-20 03:03:30
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-11-20 03:03:30
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:30
>> finding overlap peak in gene scan region...		2024-11-20 03:03:30
>> dealing with left peak not your gene scan region...		2024-11-20 03:03:30
>> merging two set peaks...		2024-11-20 03:03:30
>> calculating distance and dealing with gene strand...		2024-11-20 03:03:30
>> merging all info together ...		2024-11-20 03:03:30
>> done		2024-11-20 03:03:30
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-11-20 03:03:32
>> merging all info together...		2024-11-20 03:03:32
>> done		2024-11-20 03:03:32
>> checking seqlevels match...		2024-11-20 03:03:32
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2024-11-20 03:03:32
>> checking seqlevels match...		2024-11-20 03:03:32
>> 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
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:33
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-11-20 03:03:33
>> checking seqlevels match...		2024-11-20 03:03:33
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-11-20 03:03:33
>> calculating cor and pvalue, which may be time consuming...		2024-11-20 03:03:33
>> merging all info together...		2024-11-20 03:03:34
>> done		2024-11-20 03:03:34
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 
 52.517   1.632  63.642

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

name	user	system	elapsed
TF_target_database	0	0	0
calcRP_TFHit	1.909	0.109	3.287
calcRP_coverage	4.238	0.943	7.288
calcRP_region	4.369	0.078	5.378
enhancerPromoterCor	3.253	0.022	4.301
findIT_MARA	0.282	0.013	0.295
findIT_TFHit	0.554	0.080	0.646
findIT_TTPair	0.049	0.002	0.051
findIT_enrichFisher	0.103	0.001	0.105
findIT_enrichWilcox	0.114	0.000	0.114
findIT_regionRP	4.426	0.051	4.730
getAssocPairNumber	0.731	0.002	0.800
integrate_ChIP_RNA	1.242	0.002	1.264
integrate_replicates	0.001	0.000	0.001
jaccard_findIT_TTpair	0.066	0.001	0.066
jaccard_findIT_enrichFisher	0.134	0.001	0.135
loadPeakFile	0.04	0.00	0.04
mm_geneBound	0.744	0.003	0.757
mm_geneScan	1.662	0.002	1.926
mm_nearestGene	0.705	0.006	0.899
peakGeneCor	1.513	0.008	1.564
plot_annoDistance	1.497	0.000	1.852
plot_peakGeneAlias_summary	0.865	0.009	0.922
plot_peakGeneCor	2.985	0.011	3.409
test_geneSet	0	0	0