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This page was generated on 2022-01-24 13:07:37 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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CHECK results for FindIT2 on machv2


To the developers/maintainers of the FindIT2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindIT2.git to
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raw results

Package 642/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.0.3  (landing page)
Guandong Shang
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: RELEASE_3_14
git_last_commit: e395076
git_last_commit_date: 2021-12-28 22:21:52 -0500 (Tue, 28 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FindIT2
Version: 1.0.3
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_1.0.3.tar.gz
StartedAt: 2022-01-23 13:02:58 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 13:11:31 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 513.5 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_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/FindIT2.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.0.3’
* 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     10.539  0.124  10.689
calcRP_region        8.585  0.155   8.748
calcRP_coverage      6.516  0.963   7.488
calcRP_TFHit         5.787  0.199   6.074
peakGeneCor          5.207  0.059   5.275
plot_peakGeneCor     5.188  0.069   5.262
enhancerPromoterCor  5.003  0.050   5.060
* 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/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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, 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...		2022-01-23 13:09:46
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:09:49
>> preparing weight info...		2022-01-23 13:09:49
>> loading E50h_sampleChr5.bw info...		2022-01-23 13:09:49
------------
>> extracting and calcluating Chr5 signal...		2022-01-23 13:09:49
>> dealing with Chr5 left gene signal...		2022-01-23 13:09:54
>> norming Chr5RP accoring to the whole Chr RP...		2022-01-23 13:09:54
>> merging all Chr RP together...		2022-01-23 13:09:54
>> done		2022-01-23 13:09:54
>> checking seqlevels match...		2022-01-23 13:09:54
>> 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...		2022-01-23 13:09:54
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:09:56
>> finding overlap peak in gene scan region...		2022-01-23 13:09:56
>> dealing with left peak not your gene scan region...		2022-01-23 13:09:56
>> merging two set peaks...		2022-01-23 13:09:56
>> calculating distance and dealing with gene strand...		2022-01-23 13:09:56
>> merging all info together ...		2022-01-23 13:09:57
>> done		2022-01-23 13:09:57
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 13:09:57
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 13:09:59
>> calculating RP using centerToTSS and peak score2022-01-23 13:09:59
>> merging all info together		2022-01-23 13:10:03
>> done		2022-01-23 13:10:04
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 13:10:04
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 13:10:05
>> calculating RP using centerToTSS and peak score2022-01-23 13:10:05
>> merging all info together		2022-01-23 13:10:10
>> done		2022-01-23 13:10:11
>> checking seqlevels match...		2022-01-23 13:10:11
>> 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...		2022-01-23 13:10:11
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:10:12
>> finding overlap peak in gene scan region...		2022-01-23 13:10:12
>> dealing with left peak not your gene scan region...		2022-01-23 13:10:13
>> merging two set peaks...		2022-01-23 13:10:13
>> calculating distance and dealing with gene strand...		2022-01-23 13:10:13
>> merging all info together ...		2022-01-23 13:10:13
>> done		2022-01-23 13:10:13
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 13:10:13
>> calculating RP using centerToTSS and TF hit		2022-01-23 13:10:14
>> merging all info together		2022-01-23 13:10:15
>> done		2022-01-23 13:10:15
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 13:10:15
>> calculating RP using centerToTSS and TF hit		2022-01-23 13:10:16
>> merging all info together		2022-01-23 13:10:16
>> done		2022-01-23 13:10:16
>> checking seqlevels match...		2022-01-23 13:10:17
>> 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...		2022-01-23 13:10:18
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:10:19
>> finding overlap peak in gene scan region...		2022-01-23 13:10:19
>> dealing with left peak not your gene scan region...		2022-01-23 13:10:19
>> merging two set peaks...		2022-01-23 13:10:19
>> calculating distance and dealing with gene strand...		2022-01-23 13:10:19
>> merging all info together ...		2022-01-23 13:10:19
>> done		2022-01-23 13:10:20
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 13:10:20
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 13:10:21
>> calculating RP using centerToTSS and peak score2022-01-23 13:10:21
>> merging all info together		2022-01-23 13:10:25
>> done		2022-01-23 13:10:25
>> extracting RP info from regionRP...		2022-01-23 13:10:26
>> dealing with TF_GR_databse...		2022-01-23 13:10:27
>> calculating percent and p-value...		2022-01-23 13:10:27
>> dealing withE5_0h_R1...		2022-01-23 13:10:27
>> dealing withE5_0h_R2...		2022-01-23 13:10:27
>> dealing withE5_4h_R1...		2022-01-23 13:10:27
>> dealing withE5_4h_R2...		2022-01-23 13:10:27
>> dealing withE5_8h_R1...		2022-01-23 13:10:27
>> dealing withE5_8h_R2...		2022-01-23 13:10:27
>> dealing withE5_16h_R1...		2022-01-23 13:10:27
>> dealing withE5_16h_R2...		2022-01-23 13:10:27
>> dealing withE5_24h_R1...		2022-01-23 13:10:27
>> dealing withE5_24h_R2...		2022-01-23 13:10:27
>> dealing withE5_48h_R1...		2022-01-23 13:10:27
>> dealing withE5_48h_R2...		2022-01-23 13:10:27
>> dealing withE5_48h_R3...		2022-01-23 13:10:27
>> dealing withE5_72h_R1...		2022-01-23 13:10:27
>> dealing withE5_72h_R2...		2022-01-23 13:10:27
>> dealing withE5_72h_R3...		2022-01-23 13:10:27
>> merging all info together...		2022-01-23 13:10:27
>> done		2022-01-23 13:10:28
>> preparing gene features information...		2022-01-23 13:10:28
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:10:30
>> calculating p-value for each TF, which may be time consuming...		2022-01-23 13:10:30
>> merging all info together...		2022-01-23 13:10:30
>> done		2022-01-23 13:10:30
>> dealing with TF_GR_database...		2022-01-23 13:10:31
>> calculating coef and converting into z-score using INT...		2022-01-23 13:10:31
>> dealing withE5_0h_R1...		2022-01-23 13:10:31
>> dealing withE5_0h_R2...		2022-01-23 13:10:31
>> dealing withE5_4h_R1...		2022-01-23 13:10:31
>> dealing withE5_4h_R2...		2022-01-23 13:10:32
>> dealing withE5_8h_R1...		2022-01-23 13:10:32
>> dealing withE5_8h_R2...		2022-01-23 13:10:32
>> dealing withE5_16h_R1...		2022-01-23 13:10:32
>> dealing withE5_16h_R2...		2022-01-23 13:10:32
>> dealing withE5_24h_R1...		2022-01-23 13:10:32
>> dealing withE5_24h_R2...		2022-01-23 13:10:32
>> dealing withE5_48h_R1...		2022-01-23 13:10:33
>> dealing withE5_48h_R2...		2022-01-23 13:10:33
>> dealing withE5_48h_R3...		2022-01-23 13:10:33
>> dealing withE5_72h_R1...		2022-01-23 13:10:33
>> dealing withE5_72h_R2...		2022-01-23 13:10:33
>> dealing withE5_72h_R3...		2022-01-23 13:10:33
>> merging all info together...		2022-01-23 13:10:33
>> done		2022-01-23 13:10:34
>> checking seqlevels match...		2022-01-23 13:10:34
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-23 13:10:34
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:10:35
>> finding overlap peak in gene scan region...		2022-01-23 13:10:35
>> dealing with left peak not your gene scan region...		2022-01-23 13:10:35
>> merging two set peaks...		2022-01-23 13:10:35
>> calculating distance and dealing with gene strand...		2022-01-23 13:10:36
>> merging all info together ...		2022-01-23 13:10:36
>> done		2022-01-23 13:10:36
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 13:10:36
>> calculating RP using centerToTSS and TF hit		2022-01-23 13:10:37
>> merging all info together		2022-01-23 13:10:37
>> done		2022-01-23 13:10:37
>> checking seqlevels match...		2022-01-23 13:10:38
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 13:10:38
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 13:10:44
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-01-23 13:10:44
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 13:10:44
>> finding nearest gene and calculating distance...		2022-01-23 13:10:46
>> dealing with gene strand ...		2022-01-23 13:10:46
>> merging all info together ...		2022-01-23 13:10:46
>> done		2022-01-23 13:10:46
>> checking seqlevels match...		2022-01-23 13:10:46
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-01-23 13:10:46
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 13:10:46
>> finding nearest gene and calculating distance...		2022-01-23 13:10:48
>> dealing with gene strand ...		2022-01-23 13:10:48
>> merging all info together ...		2022-01-23 13:10:48
>> done		2022-01-23 13:10:48
>> checking seqlevels match...		2022-01-23 13:10:49
>> 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
>> checking seqlevels match...		2022-01-23 13:10:49
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 13:10:50
>> finding nearest gene and calculating distance...		2022-01-23 13:10:51
>> dealing with gene strand ...		2022-01-23 13:10:51
>> merging all info together ...		2022-01-23 13:10:51
>> done		2022-01-23 13:10:51
>> checking seqlevels match...		2022-01-23 13:10:52
>> 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
>> checking seqlevels match...		2022-01-23 13:10:53
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 13:10:53
>> finding nearest gene and calculating distance...		2022-01-23 13:10:54
>> dealing with gene strand ...		2022-01-23 13:10:54
>> merging all info together ...		2022-01-23 13:10:54
>> done		2022-01-23 13:10:54
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 13:10:56
>> 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
>> checking seqlevels match...		2022-01-23 13:10:56
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 13:10:56
>> finding nearest gene and calculating distance...		2022-01-23 13:10:57
>> dealing with gene strand ...		2022-01-23 13:10:57
>> merging all info together ...		2022-01-23 13:10:57
>> done		2022-01-23 13:10:57
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 13:10:59
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-01-23 13:11:01
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:11:02
>> checking seqlevels match...		2022-01-23 13:11:04
>> 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:11:06
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 13:11:08
>> merging all info together...		2022-01-23 13:11:09
>> done		2022-01-23 13:11:09
>> checking seqlevels match...		2022-01-23 13:11:09
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2022-01-23 13:11:09
>> checking seqlevels match...		2022-01-23 13:11:09
>> 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:11:10
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 13:11:11
>> checking seqlevels match...		2022-01-23 13:11:11
>> 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:11:12
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 13:11:12
>> merging all info together...		2022-01-23 13:11:13
>> done		2022-01-23 13:11:13
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 13:11:13
>> merging all info together...		2022-01-23 13:11:13
>> done		2022-01-23 13:11:13
>> checking seqlevels match...		2022-01-23 13:11:14
>> 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...		2022-01-23 13:11:14
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:11:15
>> finding overlap peak in gene scan region...		2022-01-23 13:11:15
>> dealing with left peak not your gene scan region...		2022-01-23 13:11:15
>> merging two set peaks...		2022-01-23 13:11:15
>> calculating distance and dealing with gene strand...		2022-01-23 13:11:15
>> merging all info together ...		2022-01-23 13:11:15
>> done		2022-01-23 13:11:15
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 13:11:17
>> merging all info together...		2022-01-23 13:11:17
>> done		2022-01-23 13:11:17
>> checking seqlevels match...		2022-01-23 13:11:18
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2022-01-23 13:11:18
>> checking seqlevels match...		2022-01-23 13:11:18
>> 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:11:19
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 13:11:19
>> checking seqlevels match...		2022-01-23 13:11:20
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-01-23 13:11:21
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 13:11:21
>> merging all info together...		2022-01-23 13:11:22
>> done		2022-01-23 13:11:22
Joining, by = "feature_id"
Joining, by = "feature_id"
`geom_smooth()` using formula 'y ~ x'
Joining, by = "feature_id"
Joining, by = "feature_id"
`geom_smooth()` using formula 'y ~ x'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
111.851   2.557 114.498 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0000.0010.001
calcRP_TFHit5.7870.1996.074
calcRP_coverage6.5160.9637.488
calcRP_region8.5850.1558.748
enhancerPromoterCor5.0030.0505.060
findIT_MARA0.5960.0080.606
findIT_TFHit1.8290.0331.863
findIT_TTPair0.1120.0060.118
findIT_enrichFisher0.3150.0040.319
findIT_enrichWilcox0.3070.0050.313
findIT_regionRP10.539 0.12410.689
getAssocPairNumber2.1660.0342.202
integrate_ChIP_RNA3.5750.0413.622
integrate_replicates0.0030.0010.005
jaccard_findIT_TTpair0.1160.0080.124
jaccard_findIT_enrichFisher0.3270.0040.330
loadPeakFile0.1290.0020.130
mm_geneBound2.8290.0312.866
mm_geneScan2.2220.0232.249
mm_nearestGene1.8940.0211.919
peakGeneCor5.2070.0595.275
plot_annoDistance2.4980.0282.538
plot_peakGeneAlias_summary2.2900.0202.313
plot_peakGeneCor5.1880.0695.262
test_geneSet0.0010.0020.002