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Package 677/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.4.0  (landing page)
Guandong Shang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: RELEASE_3_16
git_last_commit: 081e7ae
git_last_commit_date: 2022-11-01 11:25:15 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FindIT2
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-04-10 20:12:44 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:18:04 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 319.2 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/FindIT2.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.4.0’
* 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
findIT_regionRP 5.674  0.174   5.866
calcRP_coverage 4.353  0.801   5.179
* 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 ... 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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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...		2023-04-10 20:17:03
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:05
>> preparing weight info...		2023-04-10 20:17:05
>> loading E50h_sampleChr5.bw info...		2023-04-10 20:17:05
------------
>> extracting and calcluating Chr5 signal...		2023-04-10 20:17:05
>> dealing with Chr5 left gene signal...		2023-04-10 20:17:08
>> norming Chr5RP accoring to the whole Chr RP...		2023-04-10 20:17:09
>> merging all Chr RP together...		2023-04-10 20:17:09
>> done		2023-04-10 20:17:09
>> checking seqlevels match...		2023-04-10 20:17:09
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-04-10 20:17:09
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:10
>> finding overlap peak in gene scan region...		2023-04-10 20:17:10
>> dealing with left peak not your gene scan region...		2023-04-10 20:17:10
>> merging two set peaks...		2023-04-10 20:17:10
>> calculating distance and dealing with gene strand...		2023-04-10 20:17:10
>> merging all info together ...		2023-04-10 20:17:10
>> done		2023-04-10 20:17:10
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-10 20:17:10
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-04-10 20:17:11
>> calculating RP using centerToTSS and peak score2023-04-10 20:17:11
>> merging all info together		2023-04-10 20:17:13
>> done		2023-04-10 20:17:14
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-10 20:17:14
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-04-10 20:17:15
>> calculating RP using centerToTSS and peak score2023-04-10 20:17:15
>> merging all info together		2023-04-10 20:17:18
>> done		2023-04-10 20:17:18
>> checking seqlevels match...		2023-04-10 20:17:18
>> 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...		2023-04-10 20:17:18
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:19
>> finding overlap peak in gene scan region...		2023-04-10 20:17:19
>> dealing with left peak not your gene scan region...		2023-04-10 20:17:19
>> merging two set peaks...		2023-04-10 20:17:19
>> calculating distance and dealing with gene strand...		2023-04-10 20:17:19
>> merging all info together ...		2023-04-10 20:17:19
>> done		2023-04-10 20:17:19
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-10 20:17:19
>> calculating RP using centerToTSS and TF hit		2023-04-10 20:17:20
>> merging all info together		2023-04-10 20:17:20
>> done		2023-04-10 20:17:20
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-10 20:17:20
>> calculating RP using centerToTSS and TF hit		2023-04-10 20:17:21
>> merging all info together		2023-04-10 20:17:21
>> done		2023-04-10 20:17:21
>> checking seqlevels match...		2023-04-10 20:17:22
>> 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...		2023-04-10 20:17:22
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:22
>> finding overlap peak in gene scan region...		2023-04-10 20:17:22
>> dealing with left peak not your gene scan region...		2023-04-10 20:17:22
>> merging two set peaks...		2023-04-10 20:17:22
>> calculating distance and dealing with gene strand...		2023-04-10 20:17:22
>> merging all info together ...		2023-04-10 20:17:23
>> done		2023-04-10 20:17:23
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-10 20:17:23
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-04-10 20:17:23
>> calculating RP using centerToTSS and peak score2023-04-10 20:17:23
>> merging all info together		2023-04-10 20:17:25
>> done		2023-04-10 20:17:25
>> extracting RP info from regionRP...		2023-04-10 20:17:26
>> dealing with TF_GR_databse...		2023-04-10 20:17:26
>> calculating percent and p-value...		2023-04-10 20:17:26
>> dealing withE5_0h_R1...		2023-04-10 20:17:26
>> dealing withE5_0h_R2...		2023-04-10 20:17:26
>> dealing withE5_4h_R1...		2023-04-10 20:17:26
>> dealing withE5_4h_R2...		2023-04-10 20:17:26
>> dealing withE5_8h_R1...		2023-04-10 20:17:26
>> dealing withE5_8h_R2...		2023-04-10 20:17:26
>> dealing withE5_16h_R1...		2023-04-10 20:17:26
>> dealing withE5_16h_R2...		2023-04-10 20:17:26
>> dealing withE5_24h_R1...		2023-04-10 20:17:26
>> dealing withE5_24h_R2...		2023-04-10 20:17:26
>> dealing withE5_48h_R1...		2023-04-10 20:17:26
>> dealing withE5_48h_R2...		2023-04-10 20:17:27
>> dealing withE5_48h_R3...		2023-04-10 20:17:27
>> dealing withE5_72h_R1...		2023-04-10 20:17:27
>> dealing withE5_72h_R2...		2023-04-10 20:17:27
>> dealing withE5_72h_R3...		2023-04-10 20:17:27
>> merging all info together...		2023-04-10 20:17:27
>> done		2023-04-10 20:17:27
>> preparing gene features information...		2023-04-10 20:17:27
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:28
>> calculating p-value for each TF, which may be time consuming...		2023-04-10 20:17:28
>> merging all info together...		2023-04-10 20:17:28
>> done		2023-04-10 20:17:28
>> dealing with TF_GR_database...		2023-04-10 20:17:28
>> calculating coef and converting into z-score using INT...		2023-04-10 20:17:28
>> dealing with E5_0h_R1...		2023-04-10 20:17:28
>> dealing with E5_0h_R2...		2023-04-10 20:17:28
>> dealing with E5_4h_R1...		2023-04-10 20:17:28
>> dealing with E5_4h_R2...		2023-04-10 20:17:28
>> dealing with E5_8h_R1...		2023-04-10 20:17:28
>> dealing with E5_8h_R2...		2023-04-10 20:17:29
>> dealing with E5_16h_R1...		2023-04-10 20:17:29
>> dealing with E5_16h_R2...		2023-04-10 20:17:29
>> dealing with E5_24h_R1...		2023-04-10 20:17:29
>> dealing with E5_24h_R2...		2023-04-10 20:17:29
>> dealing with E5_48h_R1...		2023-04-10 20:17:29
>> dealing with E5_48h_R2...		2023-04-10 20:17:29
>> dealing with E5_48h_R3...		2023-04-10 20:17:29
>> dealing with E5_72h_R1...		2023-04-10 20:17:29
>> dealing with E5_72h_R2...		2023-04-10 20:17:29
>> dealing with E5_72h_R3...		2023-04-10 20:17:29
>> merging all info together...		2023-04-10 20:17:29
>> done		2023-04-10 20:17:29
>> checking seqlevels match...		2023-04-10 20:17:30
>> 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...		2023-04-10 20:17:30
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:30
>> finding overlap peak in gene scan region...		2023-04-10 20:17:30
>> dealing with left peak not your gene scan region...		2023-04-10 20:17:30
>> merging two set peaks...		2023-04-10 20:17:30
>> calculating distance and dealing with gene strand...		2023-04-10 20:17:31
>> merging all info together ...		2023-04-10 20:17:31
>> done		2023-04-10 20:17:31
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-10 20:17:31
>> calculating RP using centerToTSS and TF hit		2023-04-10 20:17:32
>> merging all info together		2023-04-10 20:17:32
>> done		2023-04-10 20:17:32
>> checking seqlevels match...		2023-04-10 20:17:32
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-04-10 20:17:33
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-04-10 20:17:35
>> 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
>> checking seqlevels match...		2023-04-10 20:17:35
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-04-10 20:17:35
>> finding nearest gene and calculating distance...		2023-04-10 20:17:36
>> dealing with gene strand ...		2023-04-10 20:17:36
>> merging all info together ...		2023-04-10 20:17:36
>> done		2023-04-10 20:17:36
>> checking seqlevels match...		2023-04-10 20:17:36
>> 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...		2023-04-10 20:17:36
>> 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...		2023-04-10 20:17:36
>> finding nearest gene and calculating distance...		2023-04-10 20:17:37
>> dealing with gene strand ...		2023-04-10 20:17:37
>> merging all info together ...		2023-04-10 20:17:37
>> done		2023-04-10 20:17:37
>> checking seqlevels match...		2023-04-10 20:17:38
>> 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...		2023-04-10 20:17:38
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-04-10 20:17:38
>> finding nearest gene and calculating distance...		2023-04-10 20:17:38
>> dealing with gene strand ...		2023-04-10 20:17:38
>> merging all info together ...		2023-04-10 20:17:38
>> done		2023-04-10 20:17:38
>> checking seqlevels match...		2023-04-10 20:17:39
>> 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
>> checking seqlevels match...		2023-04-10 20:17:39
>> 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...		2023-04-10 20:17:39
>> finding nearest gene and calculating distance...		2023-04-10 20:17:40
>> dealing with gene strand ...		2023-04-10 20:17:40
>> merging all info together ...		2023-04-10 20:17:40
>> done		2023-04-10 20:17:40
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-04-10 20:17:41
>> 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...		2023-04-10 20:17:41
>> 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...		2023-04-10 20:17:41
>> finding nearest gene and calculating distance...		2023-04-10 20:17:42
>> dealing with gene strand ...		2023-04-10 20:17:42
>> merging all info together ...		2023-04-10 20:17:42
>> done		2023-04-10 20:17:42
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-04-10 20:17:43
>> 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
>> checking seqlevels match...		2023-04-10 20:17:44
>> 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
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:44
>> checking seqlevels match...		2023-04-10 20:17:45
>> 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...		2023-04-10 20:17:46
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-04-10 20:17:47
>> merging all info together...		2023-04-10 20:17:47
>> done		2023-04-10 20:17:47
>> checking seqlevels match...		2023-04-10 20:17:48
>> 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...		2023-04-10 20:17:48
>> checking seqlevels match...		2023-04-10 20:17:48
>> 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...		2023-04-10 20:17:48
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-04-10 20:17:49
>> checking seqlevels match...		2023-04-10 20:17:49
>> 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...		2023-04-10 20:17:49
>> calculating cor and pvalue, which may be time consuming...		2023-04-10 20:17:50
>> merging all info together...		2023-04-10 20:17:50
>> done		2023-04-10 20:17:50
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-04-10 20:17:50
>> merging all info together...		2023-04-10 20:17:50
>> done		2023-04-10 20:17:50
>> checking seqlevels match...		2023-04-10 20:17:50
>> 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...		2023-04-10 20:17:50
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:51
>> finding overlap peak in gene scan region...		2023-04-10 20:17:51
>> dealing with left peak not your gene scan region...		2023-04-10 20:17:51
>> merging two set peaks...		2023-04-10 20:17:51
>> calculating distance and dealing with gene strand...		2023-04-10 20:17:51
>> merging all info together ...		2023-04-10 20:17:51
>> done		2023-04-10 20:17:51
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-04-10 20:17:52
>> merging all info together...		2023-04-10 20:17:52
>> done		2023-04-10 20:17:52
>> checking seqlevels match...		2023-04-10 20:17:52
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2023-04-10 20:17:52
>> checking seqlevels match...		2023-04-10 20:17:52
>> 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
>> some scan range may cross Chr bound, trimming...		2023-04-10 20:17:53
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-04-10 20:17:53
>> checking seqlevels match...		2023-04-10 20:17:53
>> 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...		2023-04-10 20:17:54
>> calculating cor and pvalue, which may be time consuming...		2023-04-10 20:17:54
>> merging all info together...		2023-04-10 20:17:54
>> done		2023-04-10 20:17:54
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 
 60.117   2.816  63.132 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0000.0020.003
calcRP_TFHit3.4840.1433.709
calcRP_coverage4.3530.8015.179
calcRP_region4.2440.1604.410
enhancerPromoterCor2.5900.1042.699
findIT_MARA0.4190.0090.429
findIT_TFHit1.0360.0541.093
findIT_TTPair0.0830.0070.090
findIT_enrichFisher0.1490.0030.151
findIT_enrichWilcox0.1590.0030.162
findIT_regionRP5.6740.1745.866
getAssocPairNumber1.0350.0201.056
integrate_ChIP_RNA1.9500.0722.027
integrate_replicates0.0020.0010.003
jaccard_findIT_TTpair0.1150.0060.121
jaccard_findIT_enrichFisher0.1800.0040.184
loadPeakFile0.0600.0010.061
mm_geneBound1.1820.0271.212
mm_geneScan1.1520.0451.201
mm_nearestGene1.7790.0611.846
peakGeneCor1.7200.0861.813
plot_annoDistance1.1470.0361.183
plot_peakGeneAlias_summary1.1630.0241.191
plot_peakGeneCor2.3370.1202.460
test_geneSet0.0000.0000.001