Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:39:12 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 723/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.10.0  (landing page)
Guandong Shang
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.10.0
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: 2024-05-03 21:55:48 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:02:43 -0400 (Fri, 03 May 2024)
EllapsedTime: 414.1 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/meat/FindIT2.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-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 Monterey 12.7.1
* 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
findIT_regionRP 8.132  0.192   8.409
calcRP_region   5.519  0.163   5.729
calcRP_coverage 4.975  0.631   5.661
* 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-x86_64/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 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

    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...		2024-05-03 22:01:28
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:01:30
>> preparing weight info...		2024-05-03 22:01:30
>> loading E50h_sampleChr5.bw info...		2024-05-03 22:01:30
------------
>> extracting and calcluating Chr5 signal...		2024-05-03 22:01:30
>> dealing with Chr5 left gene signal...		2024-05-03 22:01:34
>> norming Chr5RP accoring to the whole Chr RP...		2024-05-03 22:01:34
>> merging all Chr RP together...		2024-05-03 22:01:34
>> done		2024-05-03 22:01:34
>> checking seqlevels match...		2024-05-03 22:01:34
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-05-03 22:01:34
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:01:35
>> finding overlap peak in gene scan region...		2024-05-03 22:01:35
>> dealing with left peak not your gene scan region...		2024-05-03 22:01:35
>> merging two set peaks...		2024-05-03 22:01:36
>> calculating distance and dealing with gene strand...		2024-05-03 22:01:36
>> merging all info together ...		2024-05-03 22:01:36
>> done		2024-05-03 22:01:36
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-03 22:01:36
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-05-03 22:01:37
>> calculating RP using centerToTSS and peak score2024-05-03 22:01:37
>> merging all info together		2024-05-03 22:01:39
>> done		2024-05-03 22:01:40
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-03 22:01:40
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-05-03 22:01:41
>> calculating RP using centerToTSS and peak score2024-05-03 22:01:41
>> merging all info together		2024-05-03 22:01:44
>> done		2024-05-03 22:01:44
>> checking seqlevels match...		2024-05-03 22:01:45
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-05-03 22:01:45
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:01:46
>> finding overlap peak in gene scan region...		2024-05-03 22:01:46
>> dealing with left peak not your gene scan region...		2024-05-03 22:01:46
>> merging two set peaks...		2024-05-03 22:01:46
>> calculating distance and dealing with gene strand...		2024-05-03 22:01:46
>> merging all info together ...		2024-05-03 22:01:46
>> done		2024-05-03 22:01:46
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-03 22:01:46
>> calculating RP using centerToTSS and TF hit		2024-05-03 22:01:47
>> merging all info together		2024-05-03 22:01:47
>> done		2024-05-03 22:01:47
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-03 22:01:47
>> calculating RP using centerToTSS and TF hit		2024-05-03 22:01:49
>> merging all info together		2024-05-03 22:01:49
>> done		2024-05-03 22:01:49
>> checking seqlevels match...		2024-05-03 22:01:50
>> 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...		2024-05-03 22:01:50
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:01:51
>> finding overlap peak in gene scan region...		2024-05-03 22:01:51
>> dealing with left peak not your gene scan region...		2024-05-03 22:01:51
>> merging two set peaks...		2024-05-03 22:01:51
>> calculating distance and dealing with gene strand...		2024-05-03 22:01:51
>> merging all info together ...		2024-05-03 22:01:52
>> done		2024-05-03 22:01:52
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-03 22:01:52
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-05-03 22:01:52
>> calculating RP using centerToTSS and peak score2024-05-03 22:01:52
>> merging all info together		2024-05-03 22:01:54
>> done		2024-05-03 22:01:55
>> extracting RP info from regionRP...		2024-05-03 22:01:56
>> dealing with TF_GR_databse...		2024-05-03 22:01:56
>> calculating percent and p-value...		2024-05-03 22:01:56
>> dealing withE5_0h_R1...		2024-05-03 22:01:56
>> dealing withE5_0h_R2...		2024-05-03 22:01:56
>> dealing withE5_4h_R1...		2024-05-03 22:01:56
>> dealing withE5_4h_R2...		2024-05-03 22:01:56
>> dealing withE5_8h_R1...		2024-05-03 22:01:56
>> dealing withE5_8h_R2...		2024-05-03 22:01:56
>> dealing withE5_16h_R1...		2024-05-03 22:01:56
>> dealing withE5_16h_R2...		2024-05-03 22:01:56
>> dealing withE5_24h_R1...		2024-05-03 22:01:56
>> dealing withE5_24h_R2...		2024-05-03 22:01:56
>> dealing withE5_48h_R1...		2024-05-03 22:01:57
>> dealing withE5_48h_R2...		2024-05-03 22:01:57
>> dealing withE5_48h_R3...		2024-05-03 22:01:57
>> dealing withE5_72h_R1...		2024-05-03 22:01:57
>> dealing withE5_72h_R2...		2024-05-03 22:01:57
>> dealing withE5_72h_R3...		2024-05-03 22:01:57
>> merging all info together...		2024-05-03 22:01:57
>> done		2024-05-03 22:01:57
>> preparing gene features information...		2024-05-03 22:01:57
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:01:58
>> calculating p-value for each TF, which may be time consuming...		2024-05-03 22:01:58
>> merging all info together...		2024-05-03 22:01:58
>> done		2024-05-03 22:01:58
>> dealing with TF_GR_database...		2024-05-03 22:01:58
>> calculating coef and converting into z-score using INT...		2024-05-03 22:01:59
>> dealing with E5_0h_R1...		2024-05-03 22:01:59
>> dealing with E5_0h_R2...		2024-05-03 22:01:59
>> dealing with E5_4h_R1...		2024-05-03 22:01:59
>> dealing with E5_4h_R2...		2024-05-03 22:01:59
>> dealing with E5_8h_R1...		2024-05-03 22:01:59
>> dealing with E5_8h_R2...		2024-05-03 22:01:59
>> dealing with E5_16h_R1...		2024-05-03 22:01:59
>> dealing with E5_16h_R2...		2024-05-03 22:01:59
>> dealing with E5_24h_R1...		2024-05-03 22:01:59
>> dealing with E5_24h_R2...		2024-05-03 22:01:59
>> dealing with E5_48h_R1...		2024-05-03 22:01:59
>> dealing with E5_48h_R2...		2024-05-03 22:01:59
>> dealing with E5_48h_R3...		2024-05-03 22:02:00
>> dealing with E5_72h_R1...		2024-05-03 22:02:00
>> dealing with E5_72h_R2...		2024-05-03 22:02:00
>> dealing with E5_72h_R3...		2024-05-03 22:02:00
>> merging all info together...		2024-05-03 22:02:00
>> done		2024-05-03 22:02:00
>> checking seqlevels match...		2024-05-03 22:02:00
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-05-03 22:02:00
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:02:01
>> finding overlap peak in gene scan region...		2024-05-03 22:02:01
>> dealing with left peak not your gene scan region...		2024-05-03 22:02:01
>> merging two set peaks...		2024-05-03 22:02:01
>> calculating distance and dealing with gene strand...		2024-05-03 22:02:01
>> merging all info together ...		2024-05-03 22:02:02
>> done		2024-05-03 22:02:02
>> calculating peakCenter to TSS using peak-gene pair...		2024-05-03 22:02:02
>> calculating RP using centerToTSS and TF hit		2024-05-03 22:02:02
>> merging all info together		2024-05-03 22:02:02
>> done		2024-05-03 22:02:02
>> checking seqlevels match...		2024-05-03 22:02:03
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-05-03 22:02:03
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-05-03 22:02:07
>> 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...		2024-05-03 22:02:07
>> 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...		2024-05-03 22:02:07
>> finding nearest gene and calculating distance...		2024-05-03 22:02:08
>> dealing with gene strand ...		2024-05-03 22:02:08
>> merging all info together ...		2024-05-03 22:02:08
>> done		2024-05-03 22:02:08
>> checking seqlevels match...		2024-05-03 22:02:08
>> 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...		2024-05-03 22:02:08
>> 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...		2024-05-03 22:02:08
>> finding nearest gene and calculating distance...		2024-05-03 22:02:09
>> dealing with gene strand ...		2024-05-03 22:02:09
>> merging all info together ...		2024-05-03 22:02:09
>> done		2024-05-03 22:02:09
>> checking seqlevels match...		2024-05-03 22:02:10
>> 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...		2024-05-03 22:02:10
>> 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...		2024-05-03 22:02:11
>> finding nearest gene and calculating distance...		2024-05-03 22:02:12
>> dealing with gene strand ...		2024-05-03 22:02:13
>> merging all info together ...		2024-05-03 22:02:13
>> done		2024-05-03 22:02:13
>> checking seqlevels match...		2024-05-03 22:02:14
>> 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
>> checking seqlevels match...		2024-05-03 22:02:14
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-05-03 22:02:14
>> finding nearest gene and calculating distance...		2024-05-03 22:02:14
>> dealing with gene strand ...		2024-05-03 22:02:15
>> merging all info together ...		2024-05-03 22:02:15
>> done		2024-05-03 22:02:15
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-05-03 22:02:16
>> 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
>> checking seqlevels match...		2024-05-03 22:02:16
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-05-03 22:02:16
>> finding nearest gene and calculating distance...		2024-05-03 22:02:17
>> dealing with gene strand ...		2024-05-03 22:02:17
>> merging all info together ...		2024-05-03 22:02:17
>> done		2024-05-03 22:02:17
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-05-03 22:02:18
>> 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
>> checking seqlevels match...		2024-05-03 22:02:19
>> 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...		2024-05-03 22:02:20
>> checking seqlevels match...		2024-05-03 22:02:21
>> 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
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:02:22
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-05-03 22:02:23
>> merging all info together...		2024-05-03 22:02:23
>> done		2024-05-03 22:02:23
>> checking seqlevels match...		2024-05-03 22:02:23
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2024-05-03 22:02:23
>> checking seqlevels match...		2024-05-03 22:02:23
>> 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...		2024-05-03 22:02:24
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-05-03 22:02:25
>> checking seqlevels match...		2024-05-03 22:02:25
>> 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
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:02:26
>> calculating cor and pvalue, which may be time consuming...		2024-05-03 22:02:26
>> merging all info together...		2024-05-03 22:02:26
>> done		2024-05-03 22:02:26
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-05-03 22:02:26
>> merging all info together...		2024-05-03 22:02:26
>> done		2024-05-03 22:02:26
>> checking seqlevels match...		2024-05-03 22:02:27
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-05-03 22:02:27
>> some scan range may cross Chr bound, trimming...		2024-05-03 22:02:28
>> finding overlap peak in gene scan region...		2024-05-03 22:02:28
>> dealing with left peak not your gene scan region...		2024-05-03 22:02:28
>> merging two set peaks...		2024-05-03 22:02:28
>> calculating distance and dealing with gene strand...		2024-05-03 22:02:28
>> merging all info together ...		2024-05-03 22:02:28
>> done		2024-05-03 22:02:28
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-05-03 22:02:29
>> merging all info together...		2024-05-03 22:02:29
>> done		2024-05-03 22:02:29
>> checking seqlevels match...		2024-05-03 22:02:29
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2024-05-03 22:02:29
>> checking seqlevels match...		2024-05-03 22:02:29
>> 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...		2024-05-03 22:02:30
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-05-03 22:02:30
>> checking seqlevels match...		2024-05-03 22:02:30
>> 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...		2024-05-03 22:02:31
>> calculating cor and pvalue, which may be time consuming...		2024-05-03 22:02:32
>> merging all info together...		2024-05-03 22:02:32
>> done		2024-05-03 22:02:32
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 
 75.390   3.091  79.251 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0000.0000.001
calcRP_TFHit3.4630.1853.742
calcRP_coverage4.9750.6315.661
calcRP_region5.5190.1635.729
enhancerPromoterCor3.2590.1033.381
findIT_MARA0.5350.0260.565
findIT_TFHit1.2300.0431.285
findIT_TTPair0.0900.0070.099
findIT_enrichFisher0.1960.0060.205
findIT_enrichWilcox0.2190.0060.229
findIT_regionRP8.1320.1928.409
getAssocPairNumber1.3290.0371.379
integrate_ChIP_RNA2.3030.0852.418
integrate_replicates0.0020.0010.003
jaccard_findIT_TTpair0.1270.0070.141
jaccard_findIT_enrichFisher0.2440.0080.253
loadPeakFile0.0700.0030.073
mm_geneBound1.4660.0481.538
mm_geneScan1.4480.0441.511
mm_nearestGene1.3110.0661.387
peakGeneCor2.5790.0802.689
plot_annoDistance1.7450.0451.810
plot_peakGeneAlias_summary1.6080.0601.688
plot_peakGeneCor3.4880.0963.627
test_geneSet0.0000.0010.001