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CHECK results for FindIT2 on kunpeng1


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Package 670/2171HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.5.0  (landing page)
Guandong Shang
Snapshot Date: 2023-02-27 07:53:22 -0000 (Mon, 27 Feb 2023)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: master
git_last_commit: db4c20d
git_last_commit_date: 2022-11-01 15:25:15 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: FindIT2
Version: 1.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings FindIT2_1.5.0.tar.gz
StartedAt: 2023-02-28 03:19:54 -0000 (Tue, 28 Feb 2023)
EndedAt: 2023-02-28 03:28:35 -0000 (Tue, 28 Feb 2023)
EllapsedTime: 520.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings FindIT2_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.5.0’
* 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 R 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
calcRP_coverage 9.815  0.752  10.568
findIT_regionRP 9.749  0.148   9.896
calcRP_region   7.012  0.180   7.195
calcRP_TFHit    4.739  0.196   5.068
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘FindIT2.Rmd’ using ‘UTF-8’... OK
 NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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...		2023-02-28 03:25:38
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:25:40
>> preparing weight info...		2023-02-28 03:25:40
>> loading E50h_sampleChr5.bw info...		2023-02-28 03:25:40
------------
>> extracting and calcluating Chr5 signal...		2023-02-28 03:25:41
>> dealing with Chr5 left gene signal...		2023-02-28 03:25:49
>> norming Chr5RP accoring to the whole Chr RP...		2023-02-28 03:25:49
>> merging all Chr RP together...		2023-02-28 03:25:49
>> done		2023-02-28 03:25:49
>> checking seqlevels match...		2023-02-28 03:25:50
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-02-28 03:25:50
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:25:51
>> finding overlap peak in gene scan region...		2023-02-28 03:25:51
>> dealing with left peak not your gene scan region...		2023-02-28 03:25:51
>> merging two set peaks...		2023-02-28 03:25:51
>> calculating distance and dealing with gene strand...		2023-02-28 03:25:51
>> merging all info together ...		2023-02-28 03:25:51
>> done		2023-02-28 03:25:52
>> calculating peakCenter to TSS using peak-gene pair...		2023-02-28 03:25:52
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-02-28 03:25:53
>> calculating RP using centerToTSS and peak score2023-02-28 03:25:53
>> merging all info together		2023-02-28 03:25:56
>> done		2023-02-28 03:25:57
>> calculating peakCenter to TSS using peak-gene pair...		2023-02-28 03:25:57
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-02-28 03:25:58
>> calculating RP using centerToTSS and peak score2023-02-28 03:25:58
>> merging all info together		2023-02-28 03:26:02
>> done		2023-02-28 03:26:03
>> checking seqlevels match...		2023-02-28 03:26:03
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-02-28 03:26:03
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:04
>> finding overlap peak in gene scan region...		2023-02-28 03:26:04
>> dealing with left peak not your gene scan region...		2023-02-28 03:26:04
>> merging two set peaks...		2023-02-28 03:26:04
>> calculating distance and dealing with gene strand...		2023-02-28 03:26:05
>> merging all info together ...		2023-02-28 03:26:05
>> done		2023-02-28 03:26:05
>> calculating peakCenter to TSS using peak-gene pair...		2023-02-28 03:26:05
>> calculating RP using centerToTSS and TF hit		2023-02-28 03:26:06
>> merging all info together		2023-02-28 03:26:06
>> done		2023-02-28 03:26:06
>> calculating peakCenter to TSS using peak-gene pair...		2023-02-28 03:26:06
>> calculating RP using centerToTSS and TF hit		2023-02-28 03:26:07
>> merging all info together		2023-02-28 03:26:07
>> done		2023-02-28 03:26:07
>> checking seqlevels match...		2023-02-28 03:26:08
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-02-28 03:26:08
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:10
>> finding overlap peak in gene scan region...		2023-02-28 03:26:10
>> dealing with left peak not your gene scan region...		2023-02-28 03:26:10
>> merging two set peaks...		2023-02-28 03:26:11
>> calculating distance and dealing with gene strand...		2023-02-28 03:26:11
>> merging all info together ...		2023-02-28 03:26:11
>> done		2023-02-28 03:26:11
>> calculating peakCenter to TSS using peak-gene pair...		2023-02-28 03:26:11
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-02-28 03:26:12
>> calculating RP using centerToTSS and peak score2023-02-28 03:26:12
>> merging all info together		2023-02-28 03:26:15
>> done		2023-02-28 03:26:15
>> extracting RP info from regionRP...		2023-02-28 03:26:16
>> dealing with TF_GR_databse...		2023-02-28 03:26:16
>> calculating percent and p-value...		2023-02-28 03:26:16
>> dealing withE5_0h_R1...		2023-02-28 03:26:16
>> dealing withE5_0h_R2...		2023-02-28 03:26:17
>> dealing withE5_4h_R1...		2023-02-28 03:26:17
>> dealing withE5_4h_R2...		2023-02-28 03:26:17
>> dealing withE5_8h_R1...		2023-02-28 03:26:17
>> dealing withE5_8h_R2...		2023-02-28 03:26:17
>> dealing withE5_16h_R1...		2023-02-28 03:26:17
>> dealing withE5_16h_R2...		2023-02-28 03:26:17
>> dealing withE5_24h_R1...		2023-02-28 03:26:17
>> dealing withE5_24h_R2...		2023-02-28 03:26:17
>> dealing withE5_48h_R1...		2023-02-28 03:26:17
>> dealing withE5_48h_R2...		2023-02-28 03:26:17
>> dealing withE5_48h_R3...		2023-02-28 03:26:17
>> dealing withE5_72h_R1...		2023-02-28 03:26:17
>> dealing withE5_72h_R2...		2023-02-28 03:26:17
>> dealing withE5_72h_R3...		2023-02-28 03:26:18
>> merging all info together...		2023-02-28 03:26:18
>> done		2023-02-28 03:26:18
>> preparing gene features information...		2023-02-28 03:26:18
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:19
>> calculating p-value for each TF, which may be time consuming...		2023-02-28 03:26:19
>> merging all info together...		2023-02-28 03:26:19
>> done		2023-02-28 03:26:19
>> dealing with TF_GR_database...		2023-02-28 03:26:19
>> calculating coef and converting into z-score using INT...		2023-02-28 03:26:20
>> dealing with E5_0h_R1...		2023-02-28 03:26:20
>> dealing with E5_0h_R2...		2023-02-28 03:26:20
>> dealing with E5_4h_R1...		2023-02-28 03:26:20
>> dealing with E5_4h_R2...		2023-02-28 03:26:20
>> dealing with E5_8h_R1...		2023-02-28 03:26:20
>> dealing with E5_8h_R2...		2023-02-28 03:26:20
>> dealing with E5_16h_R1...		2023-02-28 03:26:20
>> dealing with E5_16h_R2...		2023-02-28 03:26:20
>> dealing with E5_24h_R1...		2023-02-28 03:26:21
>> dealing with E5_24h_R2...		2023-02-28 03:26:21
>> dealing with E5_48h_R1...		2023-02-28 03:26:21
>> dealing with E5_48h_R2...		2023-02-28 03:26:21
>> dealing with E5_48h_R3...		2023-02-28 03:26:21
>> dealing with E5_72h_R1...		2023-02-28 03:26:21
>> dealing with E5_72h_R2...		2023-02-28 03:26:21
>> dealing with E5_72h_R3...		2023-02-28 03:26:21
>> merging all info together...		2023-02-28 03:26:21
>> done		2023-02-28 03:26:22
>> checking seqlevels match...		2023-02-28 03:26:22
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-02-28 03:26:22
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:23
>> finding overlap peak in gene scan region...		2023-02-28 03:26:23
>> dealing with left peak not your gene scan region...		2023-02-28 03:26:23
>> merging two set peaks...		2023-02-28 03:26:23
>> calculating distance and dealing with gene strand...		2023-02-28 03:26:23
>> merging all info together ...		2023-02-28 03:26:23
>> done		2023-02-28 03:26:23
>> calculating peakCenter to TSS using peak-gene pair...		2023-02-28 03:26:23
>> calculating RP using centerToTSS and TF hit		2023-02-28 03:26:24
>> merging all info together		2023-02-28 03:26:24
>> done		2023-02-28 03:26:25
>> checking seqlevels match...		2023-02-28 03:26:25
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-02-28 03:26:25
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-02-28 03:26:29
>> 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
>> checking seqlevels match...		2023-02-28 03:26:30
>> 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...		2023-02-28 03:26:30
>> finding nearest gene and calculating distance...		2023-02-28 03:26:31
>> dealing with gene strand ...		2023-02-28 03:26:31
>> merging all info together ...		2023-02-28 03:26:31
>> done		2023-02-28 03:26:31
>> checking seqlevels match...		2023-02-28 03:26:31
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2023-02-28 03:26:31
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-02-28 03:26:31
>> finding nearest gene and calculating distance...		2023-02-28 03:26:32
>> dealing with gene strand ...		2023-02-28 03:26:32
>> merging all info together ...		2023-02-28 03:26:32
>> done		2023-02-28 03:26:32
>> checking seqlevels match...		2023-02-28 03:26:33
>> 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
>> checking seqlevels match...		2023-02-28 03:26:34
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-02-28 03:26:34
>> finding nearest gene and calculating distance...		2023-02-28 03:26:35
>> dealing with gene strand ...		2023-02-28 03:26:35
>> merging all info together ...		2023-02-28 03:26:35
>> done		2023-02-28 03:26:35
>> checking seqlevels match...		2023-02-28 03:26:36
>> 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...		2023-02-28 03:26:36
>> 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...		2023-02-28 03:26:36
>> finding nearest gene and calculating distance...		2023-02-28 03:26:37
>> dealing with gene strand ...		2023-02-28 03:26:37
>> merging all info together ...		2023-02-28 03:26:37
>> done		2023-02-28 03:26:37
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-02-28 03:26:38
>> 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...		2023-02-28 03:26:39
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-02-28 03:26:39
>> finding nearest gene and calculating distance...		2023-02-28 03:26:40
>> dealing with gene strand ...		2023-02-28 03:26:40
>> merging all info together ...		2023-02-28 03:26:40
>> done		2023-02-28 03:26:40
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-02-28 03:26:41
>> 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...		2023-02-28 03:26:42
>> 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
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:44
>> checking seqlevels match...		2023-02-28 03:26:45
>> 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...		2023-02-28 03:26:46
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-02-28 03:26:47
>> merging all info together...		2023-02-28 03:26:48
>> done		2023-02-28 03:26:48
>> checking seqlevels match...		2023-02-28 03:26:48
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2023-02-28 03:26:48
>> checking seqlevels match...		2023-02-28 03:26:48
>> 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
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:49
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-02-28 03:26:49
>> checking seqlevels match...		2023-02-28 03:26:49
>> 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
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:50
>> calculating cor and pvalue, which may be time consuming...		2023-02-28 03:26:51
>> merging all info together...		2023-02-28 03:26:51
>> done		2023-02-28 03:26:51
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-02-28 03:26:51
>> merging all info together...		2023-02-28 03:26:51
>> done		2023-02-28 03:26:51
>> checking seqlevels match...		2023-02-28 03:26:51
>> 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...		2023-02-28 03:26:51
>> some scan range may cross Chr bound, trimming...		2023-02-28 03:26:53
>> finding overlap peak in gene scan region...		2023-02-28 03:26:53
>> dealing with left peak not your gene scan region...		2023-02-28 03:26:53
>> merging two set peaks...		2023-02-28 03:26:53
>> calculating distance and dealing with gene strand...		2023-02-28 03:26:53
>> merging all info together ...		2023-02-28 03:26:53
>> done		2023-02-28 03:26:53
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-02-28 03:26:54
>> merging all info together...		2023-02-28 03:26:54
>> done		2023-02-28 03:26:55
>> checking seqlevels match...		2023-02-28 03:26:55
>> 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...		2023-02-28 03:26:55
>> checking seqlevels match...		2023-02-28 03:26:55
>> 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...		2023-02-28 03:26:56
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-02-28 03:26:56
>> checking seqlevels match...		2023-02-28 03:26:56
>> 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...		2023-02-28 03:26:57
>> calculating cor and pvalue, which may be time consuming...		2023-02-28 03:26:58
>> merging all info together...		2023-02-28 03:26:58
>> done		2023-02-28 03:26:58
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 
 93.520   2.193  95.702

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit4.7390.1965.068
calcRP_coverage 9.815 0.75210.568
calcRP_region7.0120.1807.195
enhancerPromoterCor3.7970.0483.845
findIT_MARA0.6410.0320.673
findIT_TFHit1.3620.0081.370
findIT_TTPair0.1560.0000.157
findIT_enrichFisher0.2570.0040.261
findIT_enrichWilcox0.2780.0040.282
findIT_regionRP9.7490.1489.896
getAssocPairNumber1.5550.0521.607
integrate_ChIP_RNA2.7500.0442.795
integrate_replicates0.0030.0000.003
jaccard_findIT_TTpair0.2060.0080.214
jaccard_findIT_enrichFisher0.3380.0000.338
loadPeakFile0.0790.0000.078
mm_geneBound1.6300.0361.666
mm_geneScan1.6010.0201.621
mm_nearestGene1.4930.0001.493
peakGeneCor3.1900.0283.217
plot_annoDistance1.9530.0201.973
plot_peakGeneAlias_summary1.8070.0141.820
plot_peakGeneCor4.1340.0364.171
test_geneSet0.0000.0000.001