Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 730/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.14.0  (landing page)
Guandong Shang
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: RELEASE_3_21
git_last_commit: b0f7ffc
git_last_commit_date: 2025-04-15 12:34:18 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for FindIT2 on lconway

To the developers/maintainers of the FindIT2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindIT2.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2025-04-21 20:44:27 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 20:50:51 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 383.5 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FindIT2.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
findIT_regionRP 5.874  0.145   6.054
calcRP_region   5.288  0.161   5.495
* 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/4.5-x86_64/Resources/library’
* installing *source* package ‘FindIT2’ ...
** this is package ‘FindIT2’ version ‘1.14.0’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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':

    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...		2025-04-21 20:49:45
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:49:47
>> preparing weight info...		2025-04-21 20:49:47
>> loading E50h_sampleChr5.bw info...		2025-04-21 20:49:47
------------
>> extracting and calcluating Chr5 signal...		2025-04-21 20:49:47
>> dealing with Chr5 left gene signal...		2025-04-21 20:49:50
>> norming Chr5RP accoring to the whole Chr RP...		2025-04-21 20:49:50
>> merging all Chr RP together...		2025-04-21 20:49:50
>> done		2025-04-21 20:49:50
>> checking seqlevels match...		2025-04-21 20:49:51
>> 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...		2025-04-21 20:49:51
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:49:52
>> finding overlap peak in gene scan region...		2025-04-21 20:49:52
>> dealing with left peak not your gene scan region...		2025-04-21 20:49:52
>> merging two set peaks...		2025-04-21 20:49:52
>> calculating distance and dealing with gene strand...		2025-04-21 20:49:52
>> merging all info together ...		2025-04-21 20:49:52
>> done		2025-04-21 20:49:52
>> calculating peakCenter to TSS using peak-gene pair...		2025-04-21 20:49:52
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-04-21 20:49:53
>> calculating RP using centerToTSS and peak score2025-04-21 20:49:53
>> merging all info together		2025-04-21 20:49:55
>> done		2025-04-21 20:49:56
>> calculating peakCenter to TSS using peak-gene pair...		2025-04-21 20:49:56
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-04-21 20:49:57
>> calculating RP using centerToTSS and peak score2025-04-21 20:49:57
>> merging all info together		2025-04-21 20:50:00
>> done		2025-04-21 20:50:00
>> checking seqlevels match...		2025-04-21 20:50:01
>> 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...		2025-04-21 20:50:01
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:01
>> finding overlap peak in gene scan region...		2025-04-21 20:50:01
>> dealing with left peak not your gene scan region...		2025-04-21 20:50:01
>> merging two set peaks...		2025-04-21 20:50:02
>> calculating distance and dealing with gene strand...		2025-04-21 20:50:02
>> merging all info together ...		2025-04-21 20:50:02
>> done		2025-04-21 20:50:02
>> calculating peakCenter to TSS using peak-gene pair...		2025-04-21 20:50:02
>> calculating RP using centerToTSS and TF hit		2025-04-21 20:50:03
>> merging all info together		2025-04-21 20:50:03
>> done		2025-04-21 20:50:03
>> calculating peakCenter to TSS using peak-gene pair...		2025-04-21 20:50:03
>> calculating RP using centerToTSS and TF hit		2025-04-21 20:50:04
>> merging all info together		2025-04-21 20:50:04
>> done		2025-04-21 20:50:04
>> checking seqlevels match...		2025-04-21 20:50:05
>> 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...		2025-04-21 20:50:05
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:05
>> finding overlap peak in gene scan region...		2025-04-21 20:50:05
>> dealing with left peak not your gene scan region...		2025-04-21 20:50:05
>> merging two set peaks...		2025-04-21 20:50:06
>> calculating distance and dealing with gene strand...		2025-04-21 20:50:06
>> merging all info together ...		2025-04-21 20:50:06
>> done		2025-04-21 20:50:06
>> calculating peakCenter to TSS using peak-gene pair...		2025-04-21 20:50:06
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2025-04-21 20:50:07
>> calculating RP using centerToTSS and peak score2025-04-21 20:50:07
>> merging all info together		2025-04-21 20:50:10
>> done		2025-04-21 20:50:10
>> extracting RP info from regionRP...		2025-04-21 20:50:11
>> dealing with TF_GR_databse...		2025-04-21 20:50:11
>> calculating percent and p-value...		2025-04-21 20:50:11
>> dealing withE5_0h_R1...		2025-04-21 20:50:11
>> dealing withE5_0h_R2...		2025-04-21 20:50:11
>> dealing withE5_4h_R1...		2025-04-21 20:50:11
>> dealing withE5_4h_R2...		2025-04-21 20:50:11
>> dealing withE5_8h_R1...		2025-04-21 20:50:11
>> dealing withE5_8h_R2...		2025-04-21 20:50:11
>> dealing withE5_16h_R1...		2025-04-21 20:50:11
>> dealing withE5_16h_R2...		2025-04-21 20:50:11
>> dealing withE5_24h_R1...		2025-04-21 20:50:11
>> dealing withE5_24h_R2...		2025-04-21 20:50:11
>> dealing withE5_48h_R1...		2025-04-21 20:50:11
>> dealing withE5_48h_R2...		2025-04-21 20:50:11
>> dealing withE5_48h_R3...		2025-04-21 20:50:11
>> dealing withE5_72h_R1...		2025-04-21 20:50:11
>> dealing withE5_72h_R2...		2025-04-21 20:50:11
>> dealing withE5_72h_R3...		2025-04-21 20:50:11
>> merging all info together...		2025-04-21 20:50:11
>> done		2025-04-21 20:50:12
>> preparing gene features information...		2025-04-21 20:50:12
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:12
>> calculating p-value for each TF, which may be time consuming...		2025-04-21 20:50:12
>> merging all info together...		2025-04-21 20:50:13
>> done		2025-04-21 20:50:13
>> dealing with TF_GR_database...		2025-04-21 20:50:13
>> calculating coef and converting into z-score using INT...		2025-04-21 20:50:13
>> dealing with E5_0h_R1...		2025-04-21 20:50:13
>> dealing with E5_0h_R2...		2025-04-21 20:50:13
>> dealing with E5_4h_R1...		2025-04-21 20:50:13
>> dealing with E5_4h_R2...		2025-04-21 20:50:13
>> dealing with E5_8h_R1...		2025-04-21 20:50:13
>> dealing with E5_8h_R2...		2025-04-21 20:50:13
>> dealing with E5_16h_R1...		2025-04-21 20:50:13
>> dealing with E5_16h_R2...		2025-04-21 20:50:13
>> dealing with E5_24h_R1...		2025-04-21 20:50:14
>> dealing with E5_24h_R2...		2025-04-21 20:50:14
>> dealing with E5_48h_R1...		2025-04-21 20:50:14
>> dealing with E5_48h_R2...		2025-04-21 20:50:14
>> dealing with E5_48h_R3...		2025-04-21 20:50:14
>> dealing with E5_72h_R1...		2025-04-21 20:50:14
>> dealing with E5_72h_R2...		2025-04-21 20:50:14
>> dealing with E5_72h_R3...		2025-04-21 20:50:14
>> merging all info together...		2025-04-21 20:50:14
>> done		2025-04-21 20:50:14
>> checking seqlevels match...		2025-04-21 20:50:14
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2025-04-21 20:50:15
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:15
>> finding overlap peak in gene scan region...		2025-04-21 20:50:15
>> dealing with left peak not your gene scan region...		2025-04-21 20:50:15
>> merging two set peaks...		2025-04-21 20:50:15
>> calculating distance and dealing with gene strand...		2025-04-21 20:50:16
>> merging all info together ...		2025-04-21 20:50:16
>> done		2025-04-21 20:50:16
>> calculating peakCenter to TSS using peak-gene pair...		2025-04-21 20:50:16
>> calculating RP using centerToTSS and TF hit		2025-04-21 20:50:16
>> merging all info together		2025-04-21 20:50:16
>> done		2025-04-21 20:50:16
>> checking seqlevels match...		2025-04-21 20:50:17
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2025-04-21 20:50:17
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2025-04-21 20:50:20
>> 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
>> checking seqlevels match...		2025-04-21 20:50:20
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2025-04-21 20:50:20
>> finding nearest gene and calculating distance...		2025-04-21 20:50:21
>> dealing with gene strand ...		2025-04-21 20:50:21
>> merging all info together ...		2025-04-21 20:50:21
>> done		2025-04-21 20:50:21
>> checking seqlevels match...		2025-04-21 20:50:21
>> 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...		2025-04-21 20:50:21
>> 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...		2025-04-21 20:50:21
>> finding nearest gene and calculating distance...		2025-04-21 20:50:22
>> dealing with gene strand ...		2025-04-21 20:50:22
>> merging all info together ...		2025-04-21 20:50:22
>> done		2025-04-21 20:50:22
>> checking seqlevels match...		2025-04-21 20:50:23
>> 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
>> checking seqlevels match...		2025-04-21 20:50:23
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2025-04-21 20:50:23
>> finding nearest gene and calculating distance...		2025-04-21 20:50:24
>> dealing with gene strand ...		2025-04-21 20:50:24
>> merging all info together ...		2025-04-21 20:50:24
>> done		2025-04-21 20:50:24
>> checking seqlevels match...		2025-04-21 20:50:25
>> 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...		2025-04-21 20:50:25
>> 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...		2025-04-21 20:50:25
>> finding nearest gene and calculating distance...		2025-04-21 20:50:26
>> dealing with gene strand ...		2025-04-21 20:50:26
>> merging all info together ...		2025-04-21 20:50:26
>> done		2025-04-21 20:50:26
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2025-04-21 20:50:27
>> 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...		2025-04-21 20:50:27
>> 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...		2025-04-21 20:50:27
>> finding nearest gene and calculating distance...		2025-04-21 20:50:27
>> dealing with gene strand ...		2025-04-21 20:50:28
>> merging all info together ...		2025-04-21 20:50:28
>> done		2025-04-21 20:50:28
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2025-04-21 20:50:29
>> 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...		2025-04-21 20:50:29
>> 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
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:30
>> checking seqlevels match...		2025-04-21 20:50:31
>> 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
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:32
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-04-21 20:50:33
>> merging all info together...		2025-04-21 20:50:33
>> done		2025-04-21 20:50:33
>> checking seqlevels match...		2025-04-21 20:50:33
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2025-04-21 20:50:33
>> checking seqlevels match...		2025-04-21 20:50:33
>> 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
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:34
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2025-04-21 20:50:34
>> checking seqlevels match...		2025-04-21 20:50:34
>> 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
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:35
>> calculating cor and pvalue, which may be time consuming...		2025-04-21 20:50:35
>> merging all info together...		2025-04-21 20:50:35
>> done		2025-04-21 20:50:35
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-04-21 20:50:35
>> merging all info together...		2025-04-21 20:50:36
>> done		2025-04-21 20:50:36
>> checking seqlevels match...		2025-04-21 20:50:36
>> 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...		2025-04-21 20:50:36
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:37
>> finding overlap peak in gene scan region...		2025-04-21 20:50:37
>> dealing with left peak not your gene scan region...		2025-04-21 20:50:37
>> merging two set peaks...		2025-04-21 20:50:37
>> calculating distance and dealing with gene strand...		2025-04-21 20:50:37
>> merging all info together ...		2025-04-21 20:50:37
>> done		2025-04-21 20:50:37
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2025-04-21 20:50:38
>> merging all info together...		2025-04-21 20:50:38
>> done		2025-04-21 20:50:38
>> checking seqlevels match...		2025-04-21 20:50:38
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2025-04-21 20:50:38
>> checking seqlevels match...		2025-04-21 20:50:38
>> 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...		2025-04-21 20:50:39
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2025-04-21 20:50:39
>> checking seqlevels match...		2025-04-21 20:50:39
>> 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
>> some scan range may cross Chr bound, trimming...		2025-04-21 20:50:40
>> calculating cor and pvalue, which may be time consuming...		2025-04-21 20:50:40
>> merging all info together...		2025-04-21 20:50:41
>> done		2025-04-21 20:50:41
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 
 67.025   2.647  70.139 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0000.0000.001
calcRP_TFHit3.8560.1774.118
calcRP_coverage3.6800.6724.382
calcRP_region5.2880.1615.495
enhancerPromoterCor2.7300.0802.829
findIT_MARA0.5330.0160.557
findIT_TFHit1.0250.0231.056
findIT_TTPair0.0800.0070.088
findIT_enrichFisher0.1690.0050.175
findIT_enrichWilcox0.1810.0040.187
findIT_regionRP5.8740.1456.054
getAssocPairNumber1.3820.0351.432
integrate_ChIP_RNA2.2080.0642.288
integrate_replicates0.0030.0000.003
jaccard_findIT_TTpair0.1250.0050.131
jaccard_findIT_enrichFisher0.2370.0040.243
loadPeakFile0.0670.0020.071
mm_geneBound1.4000.0431.450
mm_geneScan1.3930.0381.441
mm_nearestGene2.0900.0552.160
peakGeneCor2.2900.1072.414
plot_annoDistance1.5770.0441.626
plot_peakGeneAlias_summary1.4550.0741.543
plot_peakGeneCor2.9360.0713.022
test_geneSet0.0000.0010.001