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HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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Package 723/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.10.0  (landing page)
Guandong Shang
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: RELEASE_3_19
git_last_commit: ca624b0
git_last_commit_date: 2024-04-30 11:35:36 -0400 (Tue, 30 Apr 2024)
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for FindIT2 on kjohnson3


To the developers/maintainers of the FindIT2 package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: FindIT2
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-05-06 21:32:37 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 21:34:51 -0400 (Mon, 06 May 2024)
EllapsedTime: 133.6 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/FindIT2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.10.0’
* 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 code 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-arm64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

The following objects are masked from 'package:base':

    expand.grid, I, 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...		2024-05-06 21:34:29
>> some scan range may cross Chr bound, trimming...		2024-05-06 21:34:30
>> preparing weight info...		2024-05-06 21:34:30
>> loading E50h_sampleChr5.bw info...		2024-05-06 21:34:30
------------
>> extracting and calcluating Chr5 signal...		2024-05-06 21:34:30
>> dealing with Chr5 left gene signal...		2024-05-06 21:34:32
>> norming Chr5RP accoring to the whole Chr RP...		2024-05-06 21:34:32
>> merging all Chr RP together...		2024-05-06 21:34:32
>> done		2024-05-06 21:34:32
>> checking seqlevels match...		2024-05-06 21:34:32
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-05-06 21:34:32
>> some scan range may cross Chr bound, trimming...		2024-05-06 21:34:32
>> finding overlap peak in gene scan region...		2024-05-06 21:34:32
>> dealing with left peak not your gene scan region...		2024-05-06 21:34:32
>> merging two set peaks...		2024-05-06 21:34:32
>> calculating distance and dealing with gene strand...		2024-05-06 21:34:32
>> merging all info together ...		2024-05-06 21:34:32
>> done		2024-05-06 21:34:32
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-06 21:34:32
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-05-06 21:34:33
>> calculating RP using centerToTSS and peak score2024-05-06 21:34:33
>> merging all info together		2024-05-06 21:34:33
>> done		2024-05-06 21:34:33
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-06 21:34:33
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-05-06 21:34:34
>> calculating RP using centerToTSS and peak score2024-05-06 21:34:34
>> merging all info together		2024-05-06 21:34:35
>> done		2024-05-06 21:34:35
>> checking seqlevels match...		2024-05-06 21:34:35
>> 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...		2024-05-06 21:34:35
>> some scan range may cross Chr bound, trimming...		2024-05-06 21:34:35
>> finding overlap peak in gene scan region...		2024-05-06 21:34:35
>> dealing with left peak not your gene scan region...		2024-05-06 21:34:35
>> merging two set peaks...		2024-05-06 21:34:35
>> calculating distance and dealing with gene strand...		2024-05-06 21:34:35
>> merging all info together ...		2024-05-06 21:34:35
>> done		2024-05-06 21:34:35
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-06 21:34:35
>> calculating RP using centerToTSS and TF hit		2024-05-06 21:34:35
>> merging all info together		2024-05-06 21:34:35
>> done		2024-05-06 21:34:35
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-06 21:34:35
>> calculating RP using centerToTSS and TF hit		2024-05-06 21:34:36
>> merging all info together		2024-05-06 21:34:36
>> done		2024-05-06 21:34:36
>> checking seqlevels match...		2024-05-06 21:34:36
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-05-06 21:34:36
>> some scan range may cross Chr bound, trimming...		2024-05-06 21:34:36
>> finding overlap peak in gene scan region...		2024-05-06 21:34:36
>> dealing with left peak not your gene scan region...		2024-05-06 21:34:36
>> merging two set peaks...		2024-05-06 21:34:37
>> calculating distance and dealing with gene strand...		2024-05-06 21:34:37
>> merging all info together ...		2024-05-06 21:34:37
>> done		2024-05-06 21:34:37
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-06 21:34:37
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-05-06 21:34:37
>> calculating RP using centerToTSS and peak score2024-05-06 21:34:37
>> merging all info together		2024-05-06 21:34:37
>> done		2024-05-06 21:34:37
>> extracting RP info from regionRP...		2024-05-06 21:34:38
>> dealing with TF_GR_databse...		2024-05-06 21:34:38
>> calculating percent and p-value...		2024-05-06 21:34:38
>> dealing withE5_0h_R1...		2024-05-06 21:34:38
>> dealing withE5_0h_R2...		2024-05-06 21:34:38
>> dealing withE5_4h_R1...		2024-05-06 21:34:38
>> dealing withE5_4h_R2...		2024-05-06 21:34:38
>> dealing withE5_8h_R1...		2024-05-06 21:34:38
>> dealing withE5_8h_R2...		2024-05-06 21:34:38
>> dealing withE5_16h_R1...		2024-05-06 21:34:38
>> dealing withE5_16h_R2...		2024-05-06 21:34:38
>> dealing withE5_24h_R1...		2024-05-06 21:34:38
>> dealing withE5_24h_R2...		2024-05-06 21:34:38
>> dealing withE5_48h_R1...		2024-05-06 21:34:38
>> dealing withE5_48h_R2...		2024-05-06 21:34:38
>> dealing withE5_48h_R3...		2024-05-06 21:34:38
>> dealing withE5_72h_R1...		2024-05-06 21:34:38
>> dealing withE5_72h_R2...		2024-05-06 21:34:38
>> dealing withE5_72h_R3...		2024-05-06 21:34:38
>> merging all info together...		2024-05-06 21:34:38
>> done		2024-05-06 21:34:38
>> preparing gene features information...		2024-05-06 21:34:38
>> some scan range may cross Chr bound, trimming...		2024-05-06 21:34:38
>> calculating p-value for each TF, which may be time consuming...		2024-05-06 21:34:38
>> merging all info together...		2024-05-06 21:34:38
>> done		2024-05-06 21:34:38
>> dealing with TF_GR_database...		2024-05-06 21:34:38
>> calculating coef and converting into z-score using INT...		2024-05-06 21:34:38
>> dealing with E5_0h_R1...		2024-05-06 21:34:38
>> dealing with E5_0h_R2...		2024-05-06 21:34:38
>> dealing with E5_4h_R1...		2024-05-06 21:34:38
>> dealing with E5_4h_R2...		2024-05-06 21:34:38
>> dealing with E5_8h_R1...		2024-05-06 21:34:38
>> dealing with E5_8h_R2...		2024-05-06 21:34:38
>> dealing with E5_16h_R1...		2024-05-06 21:34:39
>> dealing with E5_16h_R2...		2024-05-06 21:34:39
>> dealing with E5_24h_R1...		2024-05-06 21:34:39
>> dealing with E5_24h_R2...		2024-05-06 21:34:39
>> dealing with E5_48h_R1...		2024-05-06 21:34:39
>> dealing with E5_48h_R2...		2024-05-06 21:34:39
>> dealing with E5_48h_R3...		2024-05-06 21:34:39
>> dealing with E5_72h_R1...		2024-05-06 21:34:39
>> dealing with E5_72h_R2...		2024-05-06 21:34:39
>> dealing with E5_72h_R3...		2024-05-06 21:34:39
>> merging all info together...		2024-05-06 21:34:39
>> done		2024-05-06 21:34:39
>> checking seqlevels match...		2024-05-06 21:34:39
>> 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...		2024-05-06 21:34:39
>> some scan range may cross Chr bound, trimming...		2024-05-06 21:34:39
>> finding overlap peak in gene scan region...		2024-05-06 21:34:39
>> dealing with left peak not your gene scan region...		2024-05-06 21:34:39
>> merging two set peaks...		2024-05-06 21:34:39
>> calculating distance and dealing with gene strand...		2024-05-06 21:34:39
>> merging all info together ...		2024-05-06 21:34:39
>> done		2024-05-06 21:34:39
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-06 21:34:39
>> calculating RP using centerToTSS and TF hit		2024-05-06 21:34:39
>> merging all info together		2024-05-06 21:34:39
>> done		2024-05-06 21:34:39
>> checking seqlevels match...		2024-05-06 21:34:40
>> 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
>> checking seqlevels match...		2024-05-06 21:34:40
>> 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...		2024-05-06 21:34:41
>> checking seqlevels match...		2024-05-06 21:34:41
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-05-06 21:34:41
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-05-06 21:34:42
>> 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...		2024-05-06 21:34:42
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-05-06 21:34:42
>> finding nearest gene and calculating distance...		2024-05-06 21:34:42
>> dealing with gene strand ...		2024-05-06 21:34:42
>> merging all info together ...		2024-05-06 21:34:42
>> done		2024-05-06 21:34:42
>> checking seqlevels match...		2024-05-06 21:34:42
>> 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...		2024-05-06 21:34:42
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-05-06 21:34:42
>> finding nearest gene and calculating distance...		2024-05-06 21:34:42
>> dealing with gene strand ...		2024-05-06 21:34:42
>> merging all info together ...		2024-05-06 21:34:42
>> done		2024-05-06 21:34:42
>> checking seqlevels match...		2024-05-06 21:34:43
>> 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
>> checking seqlevels match...		2024-05-06 21:34:43
>> 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...		2024-05-06 21:34:43
>> finding nearest gene and calculating distance...		2024-05-06 21:34:43
>> dealing with gene strand ...		2024-05-06 21:34:43
>> merging all info together ...		2024-05-06 21:34:43
>> done		2024-05-06 21:34:43
>> checking seqlevels match...		2024-05-06 21:34:43
>> 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
>> checking seqlevels match...		2024-05-06 21:34:43
>> 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...		2024-05-06 21:34:43
>> finding nearest gene and calculating distance...		2024-05-06 21:34:43
>> dealing with gene strand ...		2024-05-06 21:34:43
>> merging all info together ...		2024-05-06 21:34:43
>> done		2024-05-06 21:34:43
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-05-06 21:34:44
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-05-06 21:34:44
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-05-06 21:34:44
>> finding nearest gene and calculating distance...		2024-05-06 21:34:44
>> dealing with gene strand ...		2024-05-06 21:34:44
>> merging all info together ...		2024-05-06 21:34:44
>> done		2024-05-06 21:34:44
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-05-06 21:34:44
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-05-06 21:34:44
>> some scan range may cross Chr bound, trimming...		2024-05-06 21:34:44
>> finding overlap peak in gene scan region...		2024-05-06 21:34:44
>> dealing with left peak not your gene scan region...		2024-05-06 21:34:44
>> merging two set peaks...		2024-05-06 21:34:44
>> calculating distance and dealing with gene strand...		2024-05-06 21:34:45
>> merging all info together ...		2024-05-06 21:34:45
>> done		2024-05-06 21:34:45
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-05-06 21:34:45
>> merging all info together...		2024-05-06 21:34:45
>> done		2024-05-06 21:34:45
>> checking seqlevels match...		2024-05-06 21:34:45
>> 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...		2024-05-06 21:34:45
>> checking seqlevels match...		2024-05-06 21:34:45
>> 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...		2024-05-06 21:34:45
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-05-06 21:34:45
>> checking seqlevels match...		2024-05-06 21:34:45
>> 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...		2024-05-06 21:34:45
>> calculating cor and pvalue, which may be time consuming...		2024-05-06 21:34:45
>> merging all info together...		2024-05-06 21:34:46
>> done		2024-05-06 21:34:46
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'
>> checking seqlevels match...		2024-05-06 21:34:46
>> 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...		2024-05-06 21:34:46
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-05-06 21:34:46
>> merging all info together...		2024-05-06 21:34:46
>> done		2024-05-06 21:34:46
>> checking seqlevels match...		2024-05-06 21:34:46
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2024-05-06 21:34:46
>> checking seqlevels match...		2024-05-06 21:34:46
>> 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...		2024-05-06 21:34:47
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-05-06 21:34:47
>> checking seqlevels match...		2024-05-06 21:34:47
>> 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...		2024-05-06 21:34:47
>> calculating cor and pvalue, which may be time consuming...		2024-05-06 21:34:47
>> merging all info together...		2024-05-06 21:34:47
>> done		2024-05-06 21:34:47
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-05-06 21:34:47
>> merging all info together...		2024-05-06 21:34:47
>> done		2024-05-06 21:34:47
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
 22.108   0.869  22.994

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0000.0000.001
calcRP_TFHit0.9230.0270.967
calcRP_coverage2.0790.3192.398
calcRP_region1.5140.0371.551
enhancerPromoterCor0.8710.0200.891
findIT_MARA0.1260.0020.129
findIT_TFHit0.3380.0120.350
findIT_TTPair0.0250.0020.028
findIT_enrichFisher0.0480.0020.049
findIT_enrichWilcox0.0530.0020.055
findIT_regionRP2.3980.0502.451
getAssocPairNumber0.3810.0130.394
integrate_ChIP_RNA0.6830.0260.708
integrate_replicates0.0010.0000.001
jaccard_findIT_TTpair0.0330.0020.035
jaccard_findIT_enrichFisher0.0630.0020.064
loadPeakFile0.0180.0000.018
mm_geneBound0.3820.0060.388
mm_geneScan0.3990.0150.415
mm_nearestGene0.3670.0170.384
peakGeneCor0.7390.0150.755
plot_annoDistance0.4680.0140.482
plot_peakGeneAlias_summary0.4330.0110.444
plot_peakGeneCor0.9340.0260.961
test_geneSet000