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This page was generated on 2022-04-13 12:07:59 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (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: 2022-04-12 13:17:45 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:26:30 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 524.9 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 4.1.3 (2022-03-10)
* 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  12.007  0.126  12.163
calcRP_region     8.707  0.176   8.891
calcRP_coverage   6.215  0.852   7.078
calcRP_TFHit      5.939  0.197   6.219
plot_peakGeneCor  5.331  0.063   5.397
* 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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...		2022-04-12 13:24:45
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:24:47
>> preparing weight info...		2022-04-12 13:24:47
>> loading E50h_sampleChr5.bw info...		2022-04-12 13:24:47
------------
>> extracting and calcluating Chr5 signal...		2022-04-12 13:24:47
>> dealing with Chr5 left gene signal...		2022-04-12 13:24:52
>> norming Chr5RP accoring to the whole Chr RP...		2022-04-12 13:24:53
>> merging all Chr RP together...		2022-04-12 13:24:53
>> done		2022-04-12 13:24:53
>> checking seqlevels match...		2022-04-12 13:24:53
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-04-12 13:24:53
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:24:55
>> finding overlap peak in gene scan region...		2022-04-12 13:24:55
>> dealing with left peak not your gene scan region...		2022-04-12 13:24:55
>> merging two set peaks...		2022-04-12 13:24:55
>> calculating distance and dealing with gene strand...		2022-04-12 13:24:55
>> merging all info together ...		2022-04-12 13:24:55
>> done		2022-04-12 13:24:55
>> calculating peakCenter to TSS using peak-gene pair...		2022-04-12 13:24:55
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-04-12 13:24:57
>> calculating RP using centerToTSS and peak score2022-04-12 13:24:57
>> merging all info together		2022-04-12 13:25:00
>> done		2022-04-12 13:25:02
>> calculating peakCenter to TSS using peak-gene pair...		2022-04-12 13:25:02
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-04-12 13:25:03
>> calculating RP using centerToTSS and peak score2022-04-12 13:25:03
>> merging all info together		2022-04-12 13:25:08
>> done		2022-04-12 13:25:09
>> checking seqlevels match...		2022-04-12 13:25:09
>> 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...		2022-04-12 13:25:09
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:25:11
>> finding overlap peak in gene scan region...		2022-04-12 13:25:11
>> dealing with left peak not your gene scan region...		2022-04-12 13:25:11
>> merging two set peaks...		2022-04-12 13:25:11
>> calculating distance and dealing with gene strand...		2022-04-12 13:25:12
>> merging all info together ...		2022-04-12 13:25:12
>> done		2022-04-12 13:25:12
>> calculating peakCenter to TSS using peak-gene pair...		2022-04-12 13:25:12
>> calculating RP using centerToTSS and TF hit		2022-04-12 13:25:13
>> merging all info together		2022-04-12 13:25:13
>> done		2022-04-12 13:25:13
>> calculating peakCenter to TSS using peak-gene pair...		2022-04-12 13:25:13
>> calculating RP using centerToTSS and TF hit		2022-04-12 13:25:15
>> merging all info together		2022-04-12 13:25:15
>> done		2022-04-12 13:25:15
>> checking seqlevels match...		2022-04-12 13:25:16
>> 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...		2022-04-12 13:25:16
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:25:18
>> finding overlap peak in gene scan region...		2022-04-12 13:25:18
>> dealing with left peak not your gene scan region...		2022-04-12 13:25:18
>> merging two set peaks...		2022-04-12 13:25:18
>> calculating distance and dealing with gene strand...		2022-04-12 13:25:18
>> merging all info together ...		2022-04-12 13:25:18
>> done		2022-04-12 13:25:18
>> calculating peakCenter to TSS using peak-gene pair...		2022-04-12 13:25:18
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-04-12 13:25:20
>> calculating RP using centerToTSS and peak score2022-04-12 13:25:20
>> merging all info together		2022-04-12 13:25:23
>> done		2022-04-12 13:25:24
>> extracting RP info from regionRP...		2022-04-12 13:25:25
>> dealing with TF_GR_databse...		2022-04-12 13:25:25
>> calculating percent and p-value...		2022-04-12 13:25:25
>> dealing withE5_0h_R1...		2022-04-12 13:25:25
>> dealing withE5_0h_R2...		2022-04-12 13:25:26
>> dealing withE5_4h_R1...		2022-04-12 13:25:26
>> dealing withE5_4h_R2...		2022-04-12 13:25:26
>> dealing withE5_8h_R1...		2022-04-12 13:25:26
>> dealing withE5_8h_R2...		2022-04-12 13:25:26
>> dealing withE5_16h_R1...		2022-04-12 13:25:26
>> dealing withE5_16h_R2...		2022-04-12 13:25:26
>> dealing withE5_24h_R1...		2022-04-12 13:25:26
>> dealing withE5_24h_R2...		2022-04-12 13:25:26
>> dealing withE5_48h_R1...		2022-04-12 13:25:26
>> dealing withE5_48h_R2...		2022-04-12 13:25:26
>> dealing withE5_48h_R3...		2022-04-12 13:25:26
>> dealing withE5_72h_R1...		2022-04-12 13:25:26
>> dealing withE5_72h_R2...		2022-04-12 13:25:26
>> dealing withE5_72h_R3...		2022-04-12 13:25:26
>> merging all info together...		2022-04-12 13:25:26
>> done		2022-04-12 13:25:27
>> preparing gene features information...		2022-04-12 13:25:27
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:25:28
>> calculating p-value for each TF, which may be time consuming...		2022-04-12 13:25:28
>> merging all info together...		2022-04-12 13:25:29
>> done		2022-04-12 13:25:29
>> dealing with TF_GR_database...		2022-04-12 13:25:29
>> calculating coef and converting into z-score using INT...		2022-04-12 13:25:29
>> dealing withE5_0h_R1...		2022-04-12 13:25:29
>> dealing withE5_0h_R2...		2022-04-12 13:25:30
>> dealing withE5_4h_R1...		2022-04-12 13:25:30
>> dealing withE5_4h_R2...		2022-04-12 13:25:30
>> dealing withE5_8h_R1...		2022-04-12 13:25:30
>> dealing withE5_8h_R2...		2022-04-12 13:25:30
>> dealing withE5_16h_R1...		2022-04-12 13:25:31
>> dealing withE5_16h_R2...		2022-04-12 13:25:31
>> dealing withE5_24h_R1...		2022-04-12 13:25:31
>> dealing withE5_24h_R2...		2022-04-12 13:25:31
>> dealing withE5_48h_R1...		2022-04-12 13:25:31
>> dealing withE5_48h_R2...		2022-04-12 13:25:31
>> dealing withE5_48h_R3...		2022-04-12 13:25:32
>> dealing withE5_72h_R1...		2022-04-12 13:25:32
>> dealing withE5_72h_R2...		2022-04-12 13:25:32
>> dealing withE5_72h_R3...		2022-04-12 13:25:32
>> merging all info together...		2022-04-12 13:25:32
>> done		2022-04-12 13:25:32
>> checking seqlevels match...		2022-04-12 13:25:33
>> 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...		2022-04-12 13:25:33
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:25:34
>> finding overlap peak in gene scan region...		2022-04-12 13:25:34
>> dealing with left peak not your gene scan region...		2022-04-12 13:25:34
>> merging two set peaks...		2022-04-12 13:25:34
>> calculating distance and dealing with gene strand...		2022-04-12 13:25:34
>> merging all info together ...		2022-04-12 13:25:34
>> done		2022-04-12 13:25:35
>> calculating peakCenter to TSS using peak-gene pair...		2022-04-12 13:25:35
>> calculating RP using centerToTSS and TF hit		2022-04-12 13:25:36
>> merging all info together		2022-04-12 13:25:36
>> done		2022-04-12 13:25:36
>> checking seqlevels match...		2022-04-12 13:25:37
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-04-12 13:25:37
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-04-12 13:25:42
>> 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
>> checking seqlevels match...		2022-04-12 13:25:43
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-04-12 13:25:43
>> finding nearest gene and calculating distance...		2022-04-12 13:25:44
>> dealing with gene strand ...		2022-04-12 13:25:45
>> merging all info together ...		2022-04-12 13:25:45
>> done		2022-04-12 13:25:45
>> checking seqlevels match...		2022-04-12 13:25:45
>> 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
>> checking seqlevels match...		2022-04-12 13:25:46
>> 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...		2022-04-12 13:25:46
>> finding nearest gene and calculating distance...		2022-04-12 13:25:47
>> dealing with gene strand ...		2022-04-12 13:25:47
>> merging all info together ...		2022-04-12 13:25:47
>> done		2022-04-12 13:25:47
>> checking seqlevels match...		2022-04-12 13:25:48
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-04-12 13:25:48
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-04-12 13:25:48
>> finding nearest gene and calculating distance...		2022-04-12 13:25:50
>> dealing with gene strand ...		2022-04-12 13:25:50
>> merging all info together ...		2022-04-12 13:25:50
>> done		2022-04-12 13:25:50
>> checking seqlevels match...		2022-04-12 13:25:51
>> 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
>> checking seqlevels match...		2022-04-12 13:25:52
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-04-12 13:25:52
>> finding nearest gene and calculating distance...		2022-04-12 13:25:53
>> dealing with gene strand ...		2022-04-12 13:25:53
>> merging all info together ...		2022-04-12 13:25:53
>> done		2022-04-12 13:25:53
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-04-12 13:25:54
>> 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
>> checking seqlevels match...		2022-04-12 13:25:55
>> 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...		2022-04-12 13:25:55
>> finding nearest gene and calculating distance...		2022-04-12 13:25:56
>> dealing with gene strand ...		2022-04-12 13:25:56
>> merging all info together ...		2022-04-12 13:25:56
>> done		2022-04-12 13:25:56
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-04-12 13:25:58
>> 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...		2022-04-12 13:25:59
>> 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
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:26:00
>> checking seqlevels match...		2022-04-12 13:26:02
>> 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...		2022-04-12 13:26:03
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-04-12 13:26:05
>> merging all info together...		2022-04-12 13:26:05
>> done		2022-04-12 13:26:06
>> checking seqlevels match...		2022-04-12 13:26:06
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2022-04-12 13:26:06
>> checking seqlevels match...		2022-04-12 13:26:06
>> 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
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:26:07
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-04-12 13:26:08
>> checking seqlevels match...		2022-04-12 13:26:08
>> 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
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:26:09
>> calculating cor and pvalue, which may be time consuming...		2022-04-12 13:26:10
>> merging all info together...		2022-04-12 13:26:10
>> done		2022-04-12 13:26:10
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-04-12 13:26:10
>> merging all info together...		2022-04-12 13:26:10
>> done		2022-04-12 13:26:11
>> checking seqlevels match...		2022-04-12 13:26:11
>> 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...		2022-04-12 13:26:11
>> some scan range may cross Chr bound, trimming...		2022-04-12 13:26:12
>> finding overlap peak in gene scan region...		2022-04-12 13:26:12
>> dealing with left peak not your gene scan region...		2022-04-12 13:26:12
>> merging two set peaks...		2022-04-12 13:26:13
>> calculating distance and dealing with gene strand...		2022-04-12 13:26:13
>> merging all info together ...		2022-04-12 13:26:13
>> done		2022-04-12 13:26:13
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-04-12 13:26:15
>> merging all info together...		2022-04-12 13:26:15
>> done		2022-04-12 13:26:15
>> checking seqlevels match...		2022-04-12 13:26:15
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2022-04-12 13:26:15
>> checking seqlevels match...		2022-04-12 13:26:15
>> 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...		2022-04-12 13:26:17
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-04-12 13:26:17
>> checking seqlevels match...		2022-04-12 13:26:17
>> 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...		2022-04-12 13:26:19
>> calculating cor and pvalue, which may be time consuming...		2022-04-12 13:26:19
>> merging all info together...		2022-04-12 13:26:19
>> done		2022-04-12 13:26:20
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 
111.304   2.756 114.183 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0010.0010.001
calcRP_TFHit5.9390.1976.219
calcRP_coverage6.2150.8527.078
calcRP_region8.7070.1768.891
enhancerPromoterCor4.9190.0504.975
findIT_MARA0.8450.0550.901
findIT_TFHit1.7790.0271.807
findIT_TTPair0.1560.0080.163
findIT_enrichFisher0.3460.0040.350
findIT_enrichWilcox0.3760.0060.383
findIT_regionRP12.007 0.12612.163
getAssocPairNumber2.3850.0232.412
integrate_ChIP_RNA4.7850.0464.839
integrate_replicates0.0030.0010.003
jaccard_findIT_TTpair0.2230.0060.229
jaccard_findIT_enrichFisher0.4450.0040.451
loadPeakFile0.1330.0020.135
mm_geneBound2.0560.0292.087
mm_geneScan2.0630.0182.084
mm_nearestGene1.9790.0282.009
peakGeneCor4.1450.0444.197
plot_annoDistance2.5210.0272.551
plot_peakGeneAlias_summary2.3720.0312.409
plot_peakGeneCor5.3310.0635.397
test_geneSet0.0010.0020.002