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HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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CHECK results for FindIT2 on nebbiolo2


To the developers/maintainers of the FindIT2 package:
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raw results

Package 692/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.5.0  (landing page)
Guandong Shang
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: devel
git_last_commit: db4c20d
git_last_commit_date: 2022-11-01 11:25:15 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  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/site-library --timings FindIT2_1.5.0.tar.gz
StartedAt: 2023-04-12 06:16:21 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 06:23:59 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 458.5 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/site-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) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
findIT_regionRP 6.888  0.180   7.068
calcRP_coverage 4.188  0.888   5.076
* 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/site-library’
* installing *source* package ‘FindIT2’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FindIT2)

Tests output

FindIT2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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...		2023-04-12 06:21:54
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:21:56
>> preparing weight info...		2023-04-12 06:21:56
>> loading E50h_sampleChr5.bw info...		2023-04-12 06:21:56
------------
>> extracting and calcluating Chr5 signal...		2023-04-12 06:21:56
>> dealing with Chr5 left gene signal...		2023-04-12 06:22:00
>> norming Chr5RP accoring to the whole Chr RP...		2023-04-12 06:22:00
>> merging all Chr RP together...		2023-04-12 06:22:00
>> done		2023-04-12 06:22:00
>> checking seqlevels match...		2023-04-12 06:22:00
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-04-12 06:22:00
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:01
>> finding overlap peak in gene scan region...		2023-04-12 06:22:01
>> dealing with left peak not your gene scan region...		2023-04-12 06:22:01
>> merging two set peaks...		2023-04-12 06:22:01
>> calculating distance and dealing with gene strand...		2023-04-12 06:22:01
>> merging all info together ...		2023-04-12 06:22:01
>> done		2023-04-12 06:22:01
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-12 06:22:01
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-04-12 06:22:02
>> calculating RP using centerToTSS and peak score2023-04-12 06:22:02
>> merging all info together		2023-04-12 06:22:04
>> done		2023-04-12 06:22:05
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-12 06:22:05
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-04-12 06:22:06
>> calculating RP using centerToTSS and peak score2023-04-12 06:22:06
>> merging all info together		2023-04-12 06:22:08
>> done		2023-04-12 06:22:08
>> checking seqlevels match...		2023-04-12 06:22:09
>> 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...		2023-04-12 06:22:09
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:09
>> finding overlap peak in gene scan region...		2023-04-12 06:22:09
>> dealing with left peak not your gene scan region...		2023-04-12 06:22:09
>> merging two set peaks...		2023-04-12 06:22:10
>> calculating distance and dealing with gene strand...		2023-04-12 06:22:10
>> merging all info together ...		2023-04-12 06:22:10
>> done		2023-04-12 06:22:10
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-12 06:22:10
>> calculating RP using centerToTSS and TF hit		2023-04-12 06:22:10
>> merging all info together		2023-04-12 06:22:10
>> done		2023-04-12 06:22:11
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-12 06:22:11
>> calculating RP using centerToTSS and TF hit		2023-04-12 06:22:12
>> merging all info together		2023-04-12 06:22:12
>> done		2023-04-12 06:22:12
>> checking seqlevels match...		2023-04-12 06:22:13
>> 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...		2023-04-12 06:22:13
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:14
>> finding overlap peak in gene scan region...		2023-04-12 06:22:14
>> dealing with left peak not your gene scan region...		2023-04-12 06:22:14
>> merging two set peaks...		2023-04-12 06:22:14
>> calculating distance and dealing with gene strand...		2023-04-12 06:22:14
>> merging all info together ...		2023-04-12 06:22:14
>> done		2023-04-12 06:22:14
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-12 06:22:14
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-04-12 06:22:16
>> calculating RP using centerToTSS and peak score2023-04-12 06:22:16
>> merging all info together		2023-04-12 06:22:18
>> done		2023-04-12 06:22:18
>> extracting RP info from regionRP...		2023-04-12 06:22:19
>> dealing with TF_GR_databse...		2023-04-12 06:22:19
>> calculating percent and p-value...		2023-04-12 06:22:19
>> dealing withE5_0h_R1...		2023-04-12 06:22:19
>> dealing withE5_0h_R2...		2023-04-12 06:22:19
>> dealing withE5_4h_R1...		2023-04-12 06:22:19
>> dealing withE5_4h_R2...		2023-04-12 06:22:19
>> dealing withE5_8h_R1...		2023-04-12 06:22:19
>> dealing withE5_8h_R2...		2023-04-12 06:22:19
>> dealing withE5_16h_R1...		2023-04-12 06:22:19
>> dealing withE5_16h_R2...		2023-04-12 06:22:19
>> dealing withE5_24h_R1...		2023-04-12 06:22:19
>> dealing withE5_24h_R2...		2023-04-12 06:22:19
>> dealing withE5_48h_R1...		2023-04-12 06:22:19
>> dealing withE5_48h_R2...		2023-04-12 06:22:19
>> dealing withE5_48h_R3...		2023-04-12 06:22:19
>> dealing withE5_72h_R1...		2023-04-12 06:22:20
>> dealing withE5_72h_R2...		2023-04-12 06:22:20
>> dealing withE5_72h_R3...		2023-04-12 06:22:20
>> merging all info together...		2023-04-12 06:22:20
>> done		2023-04-12 06:22:20
>> preparing gene features information...		2023-04-12 06:22:20
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:21
>> calculating p-value for each TF, which may be time consuming...		2023-04-12 06:22:21
>> merging all info together...		2023-04-12 06:22:21
>> done		2023-04-12 06:22:21
>> dealing with TF_GR_database...		2023-04-12 06:22:21
>> calculating coef and converting into z-score using INT...		2023-04-12 06:22:21
>> dealing with E5_0h_R1...		2023-04-12 06:22:21
>> dealing with E5_0h_R2...		2023-04-12 06:22:21
>> dealing with E5_4h_R1...		2023-04-12 06:22:21
>> dealing with E5_4h_R2...		2023-04-12 06:22:21
>> dealing with E5_8h_R1...		2023-04-12 06:22:21
>> dealing with E5_8h_R2...		2023-04-12 06:22:22
>> dealing with E5_16h_R1...		2023-04-12 06:22:22
>> dealing with E5_16h_R2...		2023-04-12 06:22:22
>> dealing with E5_24h_R1...		2023-04-12 06:22:22
>> dealing with E5_24h_R2...		2023-04-12 06:22:22
>> dealing with E5_48h_R1...		2023-04-12 06:22:22
>> dealing with E5_48h_R2...		2023-04-12 06:22:22
>> dealing with E5_48h_R3...		2023-04-12 06:22:22
>> dealing with E5_72h_R1...		2023-04-12 06:22:22
>> dealing with E5_72h_R2...		2023-04-12 06:22:22
>> dealing with E5_72h_R3...		2023-04-12 06:22:22
>> merging all info together...		2023-04-12 06:22:22
>> done		2023-04-12 06:22:22
>> checking seqlevels match...		2023-04-12 06:22:23
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-04-12 06:22:23
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:23
>> finding overlap peak in gene scan region...		2023-04-12 06:22:23
>> dealing with left peak not your gene scan region...		2023-04-12 06:22:23
>> merging two set peaks...		2023-04-12 06:22:23
>> calculating distance and dealing with gene strand...		2023-04-12 06:22:24
>> merging all info together ...		2023-04-12 06:22:24
>> done		2023-04-12 06:22:24
>> calculating peakCenter to TSS using peak-gene pair...		2023-04-12 06:22:24
>> calculating RP using centerToTSS and TF hit		2023-04-12 06:22:24
>> merging all info together		2023-04-12 06:22:24
>> done		2023-04-12 06:22:24
>> checking seqlevels match...		2023-04-12 06:22:25
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-04-12 06:22:25
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-04-12 06:22:28
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2023-04-12 06:22:28
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-04-12 06:22:28
>> finding nearest gene and calculating distance...		2023-04-12 06:22:29
>> dealing with gene strand ...		2023-04-12 06:22:29
>> merging all info together ...		2023-04-12 06:22:29
>> done		2023-04-12 06:22:29
>> checking seqlevels match...		2023-04-12 06:22:29
>> 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...		2023-04-12 06:22:29
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-04-12 06:22:29
>> finding nearest gene and calculating distance...		2023-04-12 06:22:30
>> dealing with gene strand ...		2023-04-12 06:22:30
>> merging all info together ...		2023-04-12 06:22:30
>> done		2023-04-12 06:22:30
>> checking seqlevels match...		2023-04-12 06:22:31
>> 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...		2023-04-12 06:22:31
>> 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...		2023-04-12 06:22:31
>> finding nearest gene and calculating distance...		2023-04-12 06:22:31
>> dealing with gene strand ...		2023-04-12 06:22:31
>> merging all info together ...		2023-04-12 06:22:31
>> done		2023-04-12 06:22:32
>> checking seqlevels match...		2023-04-12 06:22:32
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2023-04-12 06:22:32
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-04-12 06:22:32
>> finding nearest gene and calculating distance...		2023-04-12 06:22:33
>> dealing with gene strand ...		2023-04-12 06:22:33
>> merging all info together ...		2023-04-12 06:22:33
>> done		2023-04-12 06:22:33
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-04-12 06:22:34
>> 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
>> checking seqlevels match...		2023-04-12 06:22:34
>> 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...		2023-04-12 06:22:34
>> finding nearest gene and calculating distance...		2023-04-12 06:22:35
>> dealing with gene strand ...		2023-04-12 06:22:35
>> merging all info together ...		2023-04-12 06:22:35
>> done		2023-04-12 06:22:35
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-04-12 06:22:36
>> 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...		2023-04-12 06:22:37
>> 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...		2023-04-12 06:22:38
>> checking seqlevels match...		2023-04-12 06:22:38
>> 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
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:39
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-04-12 06:22:40
>> merging all info together...		2023-04-12 06:22:40
>> done		2023-04-12 06:22:40
>> checking seqlevels match...		2023-04-12 06:22:40
>> 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...		2023-04-12 06:22:40
>> checking seqlevels match...		2023-04-12 06:22:40
>> 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...		2023-04-12 06:22:41
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-04-12 06:22:42
>> checking seqlevels match...		2023-04-12 06:22:42
>> 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...		2023-04-12 06:22:42
>> calculating cor and pvalue, which may be time consuming...		2023-04-12 06:22:43
>> merging all info together...		2023-04-12 06:22:43
>> done		2023-04-12 06:22:43
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-04-12 06:22:43
>> merging all info together...		2023-04-12 06:22:43
>> done		2023-04-12 06:22:43
>> checking seqlevels match...		2023-04-12 06:22:43
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-04-12 06:22:43
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:44
>> finding overlap peak in gene scan region...		2023-04-12 06:22:44
>> dealing with left peak not your gene scan region...		2023-04-12 06:22:44
>> merging two set peaks...		2023-04-12 06:22:44
>> calculating distance and dealing with gene strand...		2023-04-12 06:22:44
>> merging all info together ...		2023-04-12 06:22:44
>> done		2023-04-12 06:22:44
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-04-12 06:22:45
>> merging all info together...		2023-04-12 06:22:45
>> done		2023-04-12 06:22:45
>> checking seqlevels match...		2023-04-12 06:22:45
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2023-04-12 06:22:45
>> checking seqlevels match...		2023-04-12 06:22:45
>> 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...		2023-04-12 06:22:46
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-04-12 06:22:46
>> checking seqlevels match...		2023-04-12 06:22:46
>> 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
>> some scan range may cross Chr bound, trimming...		2023-04-12 06:22:48
>> calculating cor and pvalue, which may be time consuming...		2023-04-12 06:22:49
>> merging all info together...		2023-04-12 06:22:49
>> done		2023-04-12 06:22:49
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 
 64.807   2.109  66.904

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0010.0000.001
calcRP_TFHit3.6150.0913.766
calcRP_coverage4.1880.8885.076
calcRP_region4.7510.1244.875
enhancerPromoterCor2.9280.0923.020
findIT_MARA0.4550.0080.462
findIT_TFHit0.9730.0160.989
findIT_TTPair0.0740.0040.078
findIT_enrichFisher0.1580.0040.162
findIT_enrichWilcox0.2520.0080.260
findIT_regionRP6.8880.1807.068
getAssocPairNumber1.0550.0241.080
integrate_ChIP_RNA1.9190.0161.934
integrate_replicates0.0020.0000.002
jaccard_findIT_TTpair0.1050.0040.109
jaccard_findIT_enrichFisher0.1980.0120.210
loadPeakFile0.0490.0080.057
mm_geneBound1.1870.0281.215
mm_geneScan1.3100.0121.321
mm_nearestGene1.0510.0921.143
peakGeneCor2.1820.0162.198
plot_annoDistance1.4230.0161.440
plot_peakGeneAlias_summary1.2570.0001.258
plot_peakGeneCor2.590.022.61
test_geneSet000