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This page was generated on 2022-10-19 13:21:29 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
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CHECK results for FindIT2 on palomino3


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 664/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.2.3  (landing page)
Guandong Shang
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: RELEASE_3_15
git_last_commit: 17dec46
git_last_commit_date: 2022-05-25 06:53:22 -0400 (Wed, 25 May 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FindIT2
Version: 1.2.3
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FindIT2_1.2.3.tar.gz
StartedAt: 2022-10-19 00:14:15 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 00:20:27 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 371.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FindIT2_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/FindIT2.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FindIT2/DESCRIPTION' ... OK
* this is package 'FindIT2' version '1.2.3'
* 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 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 8.16   0.22    8.38
calcRP_region   5.24   0.10    5.33
calcRP_TFHit    4.41   0.18   11.78
* 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:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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 version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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")
>> checking seqlevels match...		2022-10-19 12:19:14 AM
>> 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...		2022-10-19 12:19:14 AM
>> some scan range may cross Chr bound, trimming...		2022-10-19 12:19:16 AM
>> finding overlap peak in gene scan region...		2022-10-19 12:19:16 AM
>> dealing with left peak not your gene scan region...		2022-10-19 12:19:16 AM
>> merging two set peaks...		2022-10-19 12:19:17 AM
>> calculating distance and dealing with gene strand...		2022-10-19 12:19:17 AM
>> merging all info together ...		2022-10-19 12:19:17 AM
>> done		2022-10-19 12:19:17 AM
>> calculating peakCenter to TSS using peak-gene pair...		2022-10-19 12:19:17 AM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-10-19 12:19:18 AM
>> calculating RP using centerToTSS and peak score2022-10-19 12:19:18 AM
>> merging all info together		2022-10-19 12:19:20 AM
>> done		2022-10-19 12:19:21 AM
>> calculating peakCenter to TSS using peak-gene pair...		2022-10-19 12:19:21 AM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-10-19 12:19:23 AM
>> calculating RP using centerToTSS and peak score2022-10-19 12:19:23 AM
>> merging all info together		2022-10-19 12:19:26 AM
>> done		2022-10-19 12:19:27 AM
>> checking seqlevels match...		2022-10-19 12:19:27 AM
>> 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...		2022-10-19 12:19:27 AM
>> some scan range may cross Chr bound, trimming...		2022-10-19 12:19:28 AM
>> finding overlap peak in gene scan region...		2022-10-19 12:19:28 AM
>> dealing with left peak not your gene scan region...		2022-10-19 12:19:28 AM
>> merging two set peaks...		2022-10-19 12:19:28 AM
>> calculating distance and dealing with gene strand...		2022-10-19 12:19:28 AM
>> merging all info together ...		2022-10-19 12:19:28 AM
>> done		2022-10-19 12:19:28 AM
>> calculating peakCenter to TSS using peak-gene pair...		2022-10-19 12:19:28 AM
>> calculating RP using centerToTSS and TF hit		2022-10-19 12:19:29 AM
>> merging all info together		2022-10-19 12:19:29 AM
>> done		2022-10-19 12:19:29 AM
>> calculating peakCenter to TSS using peak-gene pair...		2022-10-19 12:19:29 AM
>> calculating RP using centerToTSS and TF hit		2022-10-19 12:19:30 AM
>> merging all info together		2022-10-19 12:19:30 AM
>> done		2022-10-19 12:19:30 AM
>> checking seqlevels match...		2022-10-19 12:19:31 AM
>> 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...		2022-10-19 12:19:31 AM
>> some scan range may cross Chr bound, trimming...		2022-10-19 12:19:32 AM
>> finding overlap peak in gene scan region...		2022-10-19 12:19:32 AM
>> dealing with left peak not your gene scan region...		2022-10-19 12:19:32 AM
>> merging two set peaks...		2022-10-19 12:19:32 AM
>> calculating distance and dealing with gene strand...		2022-10-19 12:19:32 AM
>> merging all info together ...		2022-10-19 12:19:32 AM
>> done		2022-10-19 12:19:32 AM
>> calculating peakCenter to TSS using peak-gene pair...		2022-10-19 12:19:32 AM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-10-19 12:19:33 AM
>> calculating RP using centerToTSS and peak score2022-10-19 12:19:33 AM
>> merging all info together		2022-10-19 12:19:36 AM
>> done		2022-10-19 12:19:36 AM
>> extracting RP info from regionRP...		2022-10-19 12:19:37 AM
>> dealing with TF_GR_databse...		2022-10-19 12:19:37 AM
>> calculating percent and p-value...		2022-10-19 12:19:37 AM
>> dealing withE5_0h_R1...		2022-10-19 12:19:37 AM
>> dealing withE5_0h_R2...		2022-10-19 12:19:37 AM
>> dealing withE5_4h_R1...		2022-10-19 12:19:37 AM
>> dealing withE5_4h_R2...		2022-10-19 12:19:37 AM
>> dealing withE5_8h_R1...		2022-10-19 12:19:37 AM
>> dealing withE5_8h_R2...		2022-10-19 12:19:37 AM
>> dealing withE5_16h_R1...		2022-10-19 12:19:37 AM
>> dealing withE5_16h_R2...		2022-10-19 12:19:37 AM
>> dealing withE5_24h_R1...		2022-10-19 12:19:37 AM
>> dealing withE5_24h_R2...		2022-10-19 12:19:37 AM
>> dealing withE5_48h_R1...		2022-10-19 12:19:37 AM
>> dealing withE5_48h_R2...		2022-10-19 12:19:37 AM
>> dealing withE5_48h_R3...		2022-10-19 12:19:37 AM
>> dealing withE5_72h_R1...		2022-10-19 12:19:37 AM
>> dealing withE5_72h_R2...		2022-10-19 12:19:38 AM
>> dealing withE5_72h_R3...		2022-10-19 12:19:38 AM
>> merging all info together...		2022-10-19 12:19:38 AM
>> done		2022-10-19 12:19:38 AM
>> preparing gene features information...		2022-10-19 12:19:38 AM
>> some scan range may cross Chr bound, trimming...		2022-10-19 12:19:39 AM
>> calculating p-value for each TF, which may be time consuming...		2022-10-19 12:19:39 AM
>> merging all info together...		2022-10-19 12:19:39 AM
>> done		2022-10-19 12:19:39 AM
>> dealing with TF_GR_database...		2022-10-19 12:19:39 AM
>> calculating coef and converting into z-score using INT...		2022-10-19 12:19:39 AM
>> dealing with E5_0h_R1...		2022-10-19 12:19:39 AM
>> dealing with E5_0h_R2...		2022-10-19 12:19:40 AM
>> dealing with E5_4h_R1...		2022-10-19 12:19:40 AM
>> dealing with E5_4h_R2...		2022-10-19 12:19:40 AM
>> dealing with E5_8h_R1...		2022-10-19 12:19:40 AM
>> dealing with E5_8h_R2...		2022-10-19 12:19:40 AM
>> dealing with E5_16h_R1...		2022-10-19 12:19:40 AM
>> dealing with E5_16h_R2...		2022-10-19 12:19:40 AM
>> dealing with E5_24h_R1...		2022-10-19 12:19:40 AM
>> dealing with E5_24h_R2...		2022-10-19 12:19:40 AM
>> dealing with E5_48h_R1...		2022-10-19 12:19:41 AM
>> dealing with E5_48h_R2...		2022-10-19 12:19:41 AM
>> dealing with E5_48h_R3...		2022-10-19 12:19:41 AM
>> dealing with E5_72h_R1...		2022-10-19 12:19:41 AM
>> dealing with E5_72h_R2...		2022-10-19 12:19:41 AM
>> dealing with E5_72h_R3...		2022-10-19 12:19:41 AM
>> merging all info together...		2022-10-19 12:19:41 AM
>> done		2022-10-19 12:19:41 AM
>> checking seqlevels match...		2022-10-19 12:19:41 AM
>> 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...		2022-10-19 12:19:42 AM
>> some scan range may cross Chr bound, trimming...		2022-10-19 12:19:42 AM
>> finding overlap peak in gene scan region...		2022-10-19 12:19:42 AM
>> dealing with left peak not your gene scan region...		2022-10-19 12:19:43 AM
>> merging two set peaks...		2022-10-19 12:19:43 AM
>> calculating distance and dealing with gene strand...		2022-10-19 12:19:43 AM
>> merging all info together ...		2022-10-19 12:19:43 AM
>> done		2022-10-19 12:19:43 AM
>> calculating peakCenter to TSS using peak-gene pair...		2022-10-19 12:19:43 AM
>> calculating RP using centerToTSS and TF hit		2022-10-19 12:19:44 AM
>> merging all info together		2022-10-19 12:19:44 AM
>> done		2022-10-19 12:19:44 AM
>> checking seqlevels match...		2022-10-19 12:19:45 AM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-10-19 12:19:45 AM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-10-19 12:19:50 AM
>> 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...		2022-10-19 12:19:50 AM
>> 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...		2022-10-19 12:19:50 AM
>> finding nearest gene and calculating distance...		2022-10-19 12:19:51 AM
>> dealing with gene strand ...		2022-10-19 12:19:51 AM
>> merging all info together ...		2022-10-19 12:19:51 AM
>> done		2022-10-19 12:19:51 AM
>> checking seqlevels match...		2022-10-19 12:19:51 AM
>> 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...		2022-10-19 12:19:52 AM
>> 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...		2022-10-19 12:19:52 AM
>> finding nearest gene and calculating distance...		2022-10-19 12:19:52 AM
>> dealing with gene strand ...		2022-10-19 12:19:53 AM
>> merging all info together ...		2022-10-19 12:19:53 AM
>> done		2022-10-19 12:19:53 AM
>> checking seqlevels match...		2022-10-19 12:19:54 AM
>> 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...		2022-10-19 12:19:54 AM
>> 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...		2022-10-19 12:19:54 AM
>> finding nearest gene and calculating distance...		2022-10-19 12:19:55 AM
>> dealing with gene strand ...		2022-10-19 12:19:55 AM
>> merging all info together ...		2022-10-19 12:19:55 AM
>> done		2022-10-19 12:19:55 AM
>> checking seqlevels match...		2022-10-19 12:19:56 AM
>> 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...		2022-10-19 12:19:56 AM
>> 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...		2022-10-19 12:19:56 AM
>> finding nearest gene and calculating distance...		2022-10-19 12:19:57 AM
>> dealing with gene strand ...		2022-10-19 12:19:57 AM
>> merging all info together ...		2022-10-19 12:19:57 AM
>> done		2022-10-19 12:19:57 AM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-10-19 12:19:58 AM
>> 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...		2022-10-19 12:19:58 AM
>> 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...		2022-10-19 12:19:58 AM
>> finding nearest gene and calculating distance...		2022-10-19 12:19:59 AM
>> dealing with gene strand ...		2022-10-19 12:19:59 AM
>> merging all info together ...		2022-10-19 12:19:59 AM
>> done		2022-10-19 12:19:59 AM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-10-19 12:20:00 AM
>> 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...		2022-10-19 12:20:01 AM
>> 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...		2022-10-19 12:20:03 AM
>> checking seqlevels match...		2022-10-19 12:20:03 AM
>> 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...		2022-10-19 12:20:04 AM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-10-19 12:20:06 AM
>> merging all info together...		2022-10-19 12:20:06 AM
>> done		2022-10-19 12:20:06 AM
>> checking seqlevels match...		2022-10-19 12:20:06 AM
>> 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...		2022-10-19 12:20:06 AM
>> checking seqlevels match...		2022-10-19 12:20:06 AM
>> 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...		2022-10-19 12:20:07 AM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-10-19 12:20:08 AM
>> checking seqlevels match...		2022-10-19 12:20:08 AM
>> 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...		2022-10-19 12:20:09 AM
>> calculating cor and pvalue, which may be time consuming...		2022-10-19 12:20:09 AM
>> merging all info together...		2022-10-19 12:20:09 AM
>> done		2022-10-19 12:20:09 AM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-10-19 12:20:09 AM
>> merging all info together...		2022-10-19 12:20:09 AM
>> done		2022-10-19 12:20:09 AM
>> checking seqlevels match...		2022-10-19 12:20:10 AM
>> 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...		2022-10-19 12:20:10 AM
>> some scan range may cross Chr bound, trimming...		2022-10-19 12:20:11 AM
>> finding overlap peak in gene scan region...		2022-10-19 12:20:11 AM
>> dealing with left peak not your gene scan region...		2022-10-19 12:20:11 AM
>> merging two set peaks...		2022-10-19 12:20:11 AM
>> calculating distance and dealing with gene strand...		2022-10-19 12:20:11 AM
>> merging all info together ...		2022-10-19 12:20:11 AM
>> done		2022-10-19 12:20:11 AM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-10-19 12:20:12 AM
>> merging all info together...		2022-10-19 12:20:12 AM
>> done		2022-10-19 12:20:12 AM
>> checking seqlevels match...		2022-10-19 12:20:12 AM
>> 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...		2022-10-19 12:20:12 AM
>> checking seqlevels match...		2022-10-19 12:20:13 AM
>> 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...		2022-10-19 12:20:13 AM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-10-19 12:20:14 AM
>> checking seqlevels match...		2022-10-19 12:20:14 AM
>> 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...		2022-10-19 12:20:15 AM
>> calculating cor and pvalue, which may be time consuming...		2022-10-19 12:20:15 AM
>> merging all info together...		2022-10-19 12:20:16 AM
>> done		2022-10-19 12:20:16 AM
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 63 ]
> 
> proc.time()
   user  system elapsed 
  72.23    2.53   74.71 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit 4.41 0.1811.78
calcRP_coverage0.070.000.06
calcRP_region5.240.105.33
enhancerPromoterCor3.810.173.98
findIT_MARA0.420.080.50
findIT_TFHit0.940.091.03
findIT_TTPair0.150.050.21
findIT_enrichFisher0.180.000.17
findIT_enrichWilcox0.180.000.18
findIT_regionRP8.160.228.38
getAssocPairNumber1.410.041.45
integrate_ChIP_RNA2.250.072.32
integrate_replicates000
jaccard_findIT_TTpair0.150.060.21
jaccard_findIT_enrichFisher0.240.000.24
loadPeakFile0.080.000.08
mm_geneBound1.420.051.47
mm_geneScan1.220.011.28
mm_nearestGene1.060.081.14
peakGeneCor2.610.122.73
plot_annoDistance1.530.051.58
plot_peakGeneAlias_summary1.280.021.29
plot_peakGeneCor3.110.063.17
test_geneSet000