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CHECK results for FindIT2 on nebbiolo2

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raw results

Package 642/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.0.2  (landing page)
Guandong Shang
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: RELEASE_3_14
git_last_commit: af8aa7b
git_last_commit_date: 2021-11-23 08:01:16 -0500 (Tue, 23 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: FindIT2
Version: 1.0.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FindIT2_1.0.2.tar.gz
StartedAt: 2021-11-25 09:25:13 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 09:30:27 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 314.1 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FindIT2_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/FindIT2.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.0.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FindIT2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
calcRP_coverage 4.980  0.936   5.917
findIT_regionRP 5.412  0.056   5.469
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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, 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...		2021-11-25 09:29:32
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:29:34
>> preparing weight info...		2021-11-25 09:29:34
>> loading E50h_sampleChr5.bwinfo...		2021-11-25 09:29:34
------------
>> extracting and calcluating Chr5signal...		2021-11-25 09:29:35
>> dealing with Chr5left gene signal...		2021-11-25 09:29:37
>> norming Chr5RP accoring to the whole Chr RP...		2021-11-25 09:29:37
>> merging all Chr RP together...		2021-11-25 09:29:37
>> done		2021-11-25 09:29:37
>> checking seqlevels match...		2021-11-25 09:29:37
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2021-11-25 09:29:37
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:29:38
>> finding overlap peak in gene scan region...		2021-11-25 09:29:38
>> dealing with left peak not your gene scan region...		2021-11-25 09:29:38
>> merging two set peaks...		2021-11-25 09:29:39
>> calculating distance and dealing with gene strand...		2021-11-25 09:29:39
>> merging all info together ...		2021-11-25 09:29:39
>> done		2021-11-25 09:29:39
>> calculating peakCenter to TSS using peak-gene pair...		2021-11-25 09:29:39
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2021-11-25 09:29:40
>> calculating RP using centerToTSS and peak score2021-11-25 09:29:40
>> merging all info together		2021-11-25 09:29:42
>> done		2021-11-25 09:29:43
>> calculating peakCenter to TSS using peak-gene pair...		2021-11-25 09:29:43
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2021-11-25 09:29:43
>> calculating RP using centerToTSS and peak score2021-11-25 09:29:43
>> merging all info together		2021-11-25 09:29:46
>> done		2021-11-25 09:29:46
>> checking seqlevels match...		2021-11-25 09:29:46
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2021-11-25 09:29:46
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:29:47
>> finding overlap peak in gene scan region...		2021-11-25 09:29:47
>> dealing with left peak not your gene scan region...		2021-11-25 09:29:47
>> merging two set peaks...		2021-11-25 09:29:47
>> calculating distance and dealing with gene strand...		2021-11-25 09:29:47
>> merging all info together ...		2021-11-25 09:29:47
>> done		2021-11-25 09:29:47
>> calculating peakCenter to TSS using peak-gene pair...		2021-11-25 09:29:47
>> calculating RP using centerToTSS and TF hit		2021-11-25 09:29:48
>> merging all info together		2021-11-25 09:29:48
>> done		2021-11-25 09:29:48
>> calculating peakCenter to TSS using peak-gene pair...		2021-11-25 09:29:48
>> calculating RP using centerToTSS and TF hit		2021-11-25 09:29:50
>> merging all info together		2021-11-25 09:29:50
>> done		2021-11-25 09:29:50
>> checking seqlevels match...		2021-11-25 09:29:51
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2021-11-25 09:29:51
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:29:51
>> finding overlap peak in gene scan region...		2021-11-25 09:29:51
>> dealing with left peak not your gene scan region...		2021-11-25 09:29:51
>> merging two set peaks...		2021-11-25 09:29:52
>> calculating distance and dealing with gene strand...		2021-11-25 09:29:52
>> merging all info together ...		2021-11-25 09:29:52
>> done		2021-11-25 09:29:52
>> calculating peakCenter to TSS using peak-gene pair...		2021-11-25 09:29:52
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2021-11-25 09:29:52
>> calculating RP using centerToTSS and peak score2021-11-25 09:29:52
>> merging all info together		2021-11-25 09:29:54
>> done		2021-11-25 09:29:54
>> extracting RP info from regionRP...		2021-11-25 09:29:55
>> dealing with TF_GR_databse...		2021-11-25 09:29:55
>> calculating percent and p-value...		2021-11-25 09:29:55
>> dealing withE5_0h_R1...		2021-11-25 09:29:55
>> dealing withE5_0h_R2...		2021-11-25 09:29:55
>> dealing withE5_4h_R1...		2021-11-25 09:29:55
>> dealing withE5_4h_R2...		2021-11-25 09:29:55
>> dealing withE5_8h_R1...		2021-11-25 09:29:55
>> dealing withE5_8h_R2...		2021-11-25 09:29:55
>> dealing withE5_16h_R1...		2021-11-25 09:29:55
>> dealing withE5_16h_R2...		2021-11-25 09:29:55
>> dealing withE5_24h_R1...		2021-11-25 09:29:55
>> dealing withE5_24h_R2...		2021-11-25 09:29:55
>> dealing withE5_48h_R1...		2021-11-25 09:29:55
>> dealing withE5_48h_R2...		2021-11-25 09:29:55
>> dealing withE5_48h_R3...		2021-11-25 09:29:55
>> dealing withE5_72h_R1...		2021-11-25 09:29:56
>> dealing withE5_72h_R2...		2021-11-25 09:29:56
>> dealing withE5_72h_R3...		2021-11-25 09:29:56
>> merging all info together...		2021-11-25 09:29:56
>> done		2021-11-25 09:29:56
>> preparing gene features information...		2021-11-25 09:29:56
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:29:57
>> calculating p-value for each TF, which may be time consuming...		2021-11-25 09:29:57
>> merging all info together...		2021-11-25 09:29:57
>> done		2021-11-25 09:29:57
>> dealing with TF_GR_database...		2021-11-25 09:29:57
>> calculating coef and converting into z-score using INT...		2021-11-25 09:29:57
>> dealing withE5_0h_R1...		2021-11-25 09:29:57
>> dealing withE5_0h_R2...		2021-11-25 09:29:57
>> dealing withE5_4h_R1...		2021-11-25 09:29:57
>> dealing withE5_4h_R2...		2021-11-25 09:29:57
>> dealing withE5_8h_R1...		2021-11-25 09:29:58
>> dealing withE5_8h_R2...		2021-11-25 09:29:58
>> dealing withE5_16h_R1...		2021-11-25 09:29:58
>> dealing withE5_16h_R2...		2021-11-25 09:29:58
>> dealing withE5_24h_R1...		2021-11-25 09:29:58
>> dealing withE5_24h_R2...		2021-11-25 09:29:58
>> dealing withE5_48h_R1...		2021-11-25 09:29:58
>> dealing withE5_48h_R2...		2021-11-25 09:29:58
>> dealing withE5_48h_R3...		2021-11-25 09:29:58
>> dealing withE5_72h_R1...		2021-11-25 09:29:58
>> dealing withE5_72h_R2...		2021-11-25 09:29:58
>> dealing withE5_72h_R3...		2021-11-25 09:29:58
>> merging all info together...		2021-11-25 09:29:58
>> done		2021-11-25 09:29:58
>> checking seqlevels match...		2021-11-25 09:29:59
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2021-11-25 09:29:59
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:29:59
>> finding overlap peak in gene scan region...		2021-11-25 09:29:59
>> dealing with left peak not your gene scan region...		2021-11-25 09:29:59
>> merging two set peaks...		2021-11-25 09:30:00
>> calculating distance and dealing with gene strand...		2021-11-25 09:30:00
>> merging all info together ...		2021-11-25 09:30:00
>> done		2021-11-25 09:30:00
>> calculating peakCenter to TSS using peak-gene pair...		2021-11-25 09:30:00
>> calculating RP using centerToTSS and TF hit		2021-11-25 09:30:01
>> merging all info together		2021-11-25 09:30:01
>> done		2021-11-25 09:30:01
>> checking seqlevels match...		2021-11-25 09:30:01
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2021-11-25 09:30:01
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2021-11-25 09:30:04
>> 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
>> checking seqlevels match...		2021-11-25 09:30:04
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2021-11-25 09:30:04
>> finding nearest gene and calculating distance...		2021-11-25 09:30:06
>> dealing with gene strand ...		2021-11-25 09:30:06
>> merging all info together ...		2021-11-25 09:30:06
>> done		2021-11-25 09:30:06
>> checking seqlevels match...		2021-11-25 09:30:06
>> 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...		2021-11-25 09:30:06
>> 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...		2021-11-25 09:30:06
>> finding nearest gene and calculating distance...		2021-11-25 09:30:07
>> dealing with gene strand ...		2021-11-25 09:30:07
>> merging all info together ...		2021-11-25 09:30:07
>> done		2021-11-25 09:30:07
>> checking seqlevels match...		2021-11-25 09:30:08
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2021-11-25 09:30:08
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2021-11-25 09:30:08
>> finding nearest gene and calculating distance...		2021-11-25 09:30:09
>> dealing with gene strand ...		2021-11-25 09:30:09
>> merging all info together ...		2021-11-25 09:30:09
>> done		2021-11-25 09:30:09
>> checking seqlevels match...		2021-11-25 09:30:10
>> 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...		2021-11-25 09:30:10
>> 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...		2021-11-25 09:30:10
>> finding nearest gene and calculating distance...		2021-11-25 09:30:10
>> dealing with gene strand ...		2021-11-25 09:30:11
>> merging all info together ...		2021-11-25 09:30:11
>> done		2021-11-25 09:30:11
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2021-11-25 09:30:11
>> 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
>> checking seqlevels match...		2021-11-25 09:30:12
>> 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...		2021-11-25 09:30:12
>> finding nearest gene and calculating distance...		2021-11-25 09:30:12
>> dealing with gene strand ...		2021-11-25 09:30:12
>> merging all info together ...		2021-11-25 09:30:12
>> done		2021-11-25 09:30:12
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2021-11-25 09:30:13
>> 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
>> checking seqlevels match...		2021-11-25 09:30:14
>> 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
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:30:15
>> checking seqlevels match...		2021-11-25 09:30:15
>> 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...		2021-11-25 09:30:16
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2021-11-25 09:30:17
>> merging all info together...		2021-11-25 09:30:17
>> done		2021-11-25 09:30:17
>> checking seqlevels match...		2021-11-25 09:30:17
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2021-11-25 09:30:17
>> checking seqlevels match...		2021-11-25 09:30:17
>> 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
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:30:18
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2021-11-25 09:30:18
>> checking seqlevels match...		2021-11-25 09:30:18
>> 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...		2021-11-25 09:30:19
>> calculating cor and pvalue, which may be time consuming...		2021-11-25 09:30:19
>> merging all info together...		2021-11-25 09:30:19
>> done		2021-11-25 09:30:20
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2021-11-25 09:30:20
>> merging all info together...		2021-11-25 09:30:20
>> done		2021-11-25 09:30:20
>> checking seqlevels match...		2021-11-25 09:30:20
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2021-11-25 09:30:20
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:30:21
>> finding overlap peak in gene scan region...		2021-11-25 09:30:21
>> dealing with left peak not your gene scan region...		2021-11-25 09:30:21
>> merging two set peaks...		2021-11-25 09:30:21
>> calculating distance and dealing with gene strand...		2021-11-25 09:30:21
>> merging all info together ...		2021-11-25 09:30:21
>> done		2021-11-25 09:30:21
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2021-11-25 09:30:22
>> merging all info together...		2021-11-25 09:30:22
>> done		2021-11-25 09:30:22
>> checking seqlevels match...		2021-11-25 09:30:22
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2021-11-25 09:30:22
>> checking seqlevels match...		2021-11-25 09:30:22
>> 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
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:30:23
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2021-11-25 09:30:23
>> checking seqlevels match...		2021-11-25 09:30:23
>> 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
>> some scan range may cross Chr bound, trimming...		2021-11-25 09:30:24
>> calculating cor and pvalue, which may be time consuming...		2021-11-25 09:30:24
>> merging all info together...		2021-11-25 09:30:24
>> done		2021-11-25 09:30:24
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 
 61.273   1.212  62.474 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit2.8720.1533.084
calcRP_coverage4.9800.9365.917
calcRP_region4.4160.2684.684
enhancerPromoterCor3.4730.0363.509
findIT_MARA0.2900.0040.294
findIT_TFHit0.9400.0560.997
findIT_TTPair0.0650.0000.066
findIT_enrichFisher0.1610.0000.162
findIT_enrichWilcox0.1760.0000.177
findIT_regionRP5.4120.0565.469
getAssocPairNumber1.1540.0081.163
integrate_ChIP_RNA2.0480.0072.055
integrate_replicates0.0010.0000.002
jaccard_findIT_TTpair0.0790.0000.079
jaccard_findIT_enrichFisher0.1970.0000.196
loadPeakFile0.0650.0000.064
mm_geneBound1.1760.0081.183
mm_geneScan1.2450.0081.253
mm_nearestGene1.0600.0001.061
peakGeneCor2.1070.0002.107
plot_annoDistance1.4130.0121.425
plot_peakGeneAlias_summary1.2960.0041.301
plot_peakGeneCor2.6230.0042.627
test_geneSet000