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CHECK results for FindIT2 on kunpeng1


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raw results

Package 689/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.7.0  (landing page)
Guandong Shang
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: devel
git_last_commit: 59594d0
git_last_commit_date: 2023-04-25 15:31:01 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: FindIT2
Version: 1.7.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings FindIT2_1.7.0.tar.gz
StartedAt: 2023-05-09 15:59:11 -0000 (Tue, 09 May 2023)
EndedAt: 2023-05-09 16:08:10 -0000 (Tue, 09 May 2023)
EllapsedTime: 538.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings FindIT2_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.7.0’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
calcRP_coverage 8.855  0.332   9.189
findIT_regionRP 8.266  0.084   8.351
calcRP_region   7.552  0.240   7.793
* 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 ...
  ‘FindIT2.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

FindIT2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(FindIT2)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, 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, 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...		2023-05-09 16:05:28
>> some scan range may cross Chr bound, trimming...		2023-05-09 16:05:29
>> preparing weight info...		2023-05-09 16:05:29
>> loading E50h_sampleChr5.bw info...		2023-05-09 16:05:29
------------
>> extracting and calcluating Chr5 signal...		2023-05-09 16:05:29
>> dealing with Chr5 left gene signal...		2023-05-09 16:05:38
>> norming Chr5RP accoring to the whole Chr RP...		2023-05-09 16:05:38
>> merging all Chr RP together...		2023-05-09 16:05:38
>> done		2023-05-09 16:05:38
>> checking seqlevels match...		2023-05-09 16:05:38
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-05-09 16:05:38
>> some scan range may cross Chr bound, trimming...		2023-05-09 16:05:39
>> finding overlap peak in gene scan region...		2023-05-09 16:05:39
>> dealing with left peak not your gene scan region...		2023-05-09 16:05:39
>> merging two set peaks...		2023-05-09 16:05:40
>> calculating distance and dealing with gene strand...		2023-05-09 16:05:40
>> merging all info together ...		2023-05-09 16:05:40
>> done		2023-05-09 16:05:40
>> calculating peakCenter to TSS using peak-gene pair...		2023-05-09 16:05:40
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-05-09 16:05:41
>> calculating RP using centerToTSS and peak score2023-05-09 16:05:41
>> merging all info together		2023-05-09 16:05:44
>> done		2023-05-09 16:05:45
>> calculating peakCenter to TSS using peak-gene pair...		2023-05-09 16:05:45
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-05-09 16:05:47
>> calculating RP using centerToTSS and peak score2023-05-09 16:05:47
>> merging all info together		2023-05-09 16:05:50
>> done		2023-05-09 16:05:51
>> checking seqlevels match...		2023-05-09 16:05:51
>> 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...		2023-05-09 16:05:51
>> some scan range may cross Chr bound, trimming...		2023-05-09 16:05:52
>> finding overlap peak in gene scan region...		2023-05-09 16:05:52
>> dealing with left peak not your gene scan region...		2023-05-09 16:05:52
>> merging two set peaks...		2023-05-09 16:05:53
>> calculating distance and dealing with gene strand...		2023-05-09 16:05:53
>> merging all info together ...		2023-05-09 16:05:53
>> done		2023-05-09 16:05:53
>> calculating peakCenter to TSS using peak-gene pair...		2023-05-09 16:05:53
>> calculating RP using centerToTSS and TF hit		2023-05-09 16:05:54
>> merging all info together		2023-05-09 16:05:54
>> done		2023-05-09 16:05:54
>> calculating peakCenter to TSS using peak-gene pair...		2023-05-09 16:05:54
>> calculating RP using centerToTSS and TF hit		2023-05-09 16:05:55
>> merging all info together		2023-05-09 16:05:55
>> done		2023-05-09 16:05:55
>> checking seqlevels match...		2023-05-09 16:05:56
>> 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...		2023-05-09 16:05:56
>> some scan range may cross Chr bound, trimming...		2023-05-09 16:05:57
>> finding overlap peak in gene scan region...		2023-05-09 16:05:57
>> dealing with left peak not your gene scan region...		2023-05-09 16:05:57
>> merging two set peaks...		2023-05-09 16:05:57
>> calculating distance and dealing with gene strand...		2023-05-09 16:05:57
>> merging all info together ...		2023-05-09 16:05:57
>> done		2023-05-09 16:05:57
>> calculating peakCenter to TSS using peak-gene pair...		2023-05-09 16:05:57
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-05-09 16:05:58
>> calculating RP using centerToTSS and peak score2023-05-09 16:05:58
>> merging all info together		2023-05-09 16:06:01
>> done		2023-05-09 16:06:01
>> extracting RP info from regionRP...		2023-05-09 16:06:02
>> dealing with TF_GR_databse...		2023-05-09 16:06:02
>> calculating percent and p-value...		2023-05-09 16:06:02
>> dealing withE5_0h_R1...		2023-05-09 16:06:02
>> dealing withE5_0h_R2...		2023-05-09 16:06:03
>> dealing withE5_4h_R1...		2023-05-09 16:06:03
>> dealing withE5_4h_R2...		2023-05-09 16:06:03
>> dealing withE5_8h_R1...		2023-05-09 16:06:03
>> dealing withE5_8h_R2...		2023-05-09 16:06:03
>> dealing withE5_16h_R1...		2023-05-09 16:06:03
>> dealing withE5_16h_R2...		2023-05-09 16:06:03
>> dealing withE5_24h_R1...		2023-05-09 16:06:03
>> dealing withE5_24h_R2...		2023-05-09 16:06:03
>> dealing withE5_48h_R1...		2023-05-09 16:06:03
>> dealing withE5_48h_R2...		2023-05-09 16:06:03
>> dealing withE5_48h_R3...		2023-05-09 16:06:03
>> dealing withE5_72h_R1...		2023-05-09 16:06:03
>> dealing withE5_72h_R2...		2023-05-09 16:06:03
>> dealing withE5_72h_R3...		2023-05-09 16:06:03
>> merging all info together...		2023-05-09 16:06:03
>> done		2023-05-09 16:06:04
>> preparing gene features information...		2023-05-09 16:06:04
>> some scan range may cross Chr bound, trimming...		2023-05-09 16:06:05
>> calculating p-value for each TF, which may be time consuming...		2023-05-09 16:06:05
>> merging all info together...		2023-05-09 16:06:05
>> done		2023-05-09 16:06:05
>> dealing with TF_GR_database...		2023-05-09 16:06:05
>> calculating coef and converting into z-score using INT...		2023-05-09 16:06:05
>> dealing with E5_0h_R1...		2023-05-09 16:06:05
>> dealing with E5_0h_R2...		2023-05-09 16:06:05
>> dealing with E5_4h_R1...		2023-05-09 16:06:06
>> dealing with E5_4h_R2...		2023-05-09 16:06:06
>> dealing with E5_8h_R1...		2023-05-09 16:06:06
>> dealing with E5_8h_R2...		2023-05-09 16:06:06
>> dealing with E5_16h_R1...		2023-05-09 16:06:06
>> dealing with E5_16h_R2...		2023-05-09 16:06:06
>> dealing with E5_24h_R1...		2023-05-09 16:06:06
>> dealing with E5_24h_R2...		2023-05-09 16:06:06
>> dealing with E5_48h_R1...		2023-05-09 16:06:06
>> dealing with E5_48h_R2...		2023-05-09 16:06:06
>> dealing with E5_48h_R3...		2023-05-09 16:06:07
>> dealing with E5_72h_R1...		2023-05-09 16:06:07
>> dealing with E5_72h_R2...		2023-05-09 16:06:07
>> dealing with E5_72h_R3...		2023-05-09 16:06:07
>> merging all info together...		2023-05-09 16:06:07
>> done		2023-05-09 16:06:07
>> checking seqlevels match...		2023-05-09 16:06:07
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-05-09 16:06:07
>> some scan range may cross Chr bound, trimming...		2023-05-09 16:06:09
>> finding overlap peak in gene scan region...		2023-05-09 16:06:09
>> dealing with left peak not your gene scan region...		2023-05-09 16:06:10
>> merging two set peaks...		2023-05-09 16:06:10
>> calculating distance and dealing with gene strand...		2023-05-09 16:06:10
>> merging all info together ...		2023-05-09 16:06:10
>> done		2023-05-09 16:06:10
>> calculating peakCenter to TSS using peak-gene pair...		2023-05-09 16:06:10
>> calculating RP using centerToTSS and TF hit		2023-05-09 16:06:11
>> merging all info together		2023-05-09 16:06:11
>> done		2023-05-09 16:06:11
>> checking seqlevels match...		2023-05-09 16:06:11
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-05-09 16:06:11
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-05-09 16:06:15
>> 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
>> checking seqlevels match...		2023-05-09 16:06:15
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-05-09 16:06:15
>> finding nearest gene and calculating distance...		2023-05-09 16:06:16
>> dealing with gene strand ...		2023-05-09 16:06:16
>> merging all info together ...		2023-05-09 16:06:16
>> done		2023-05-09 16:06:16
>> checking seqlevels match...		2023-05-09 16:06:16
>> 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...		2023-05-09 16:06:17
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-05-09 16:06:17
>> finding nearest gene and calculating distance...		2023-05-09 16:06:19
>> dealing with gene strand ...		2023-05-09 16:06:19
>> merging all info together ...		2023-05-09 16:06:19
>> done		2023-05-09 16:06:19
>> checking seqlevels match...		2023-05-09 16:06:20
>> 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...		2023-05-09 16:06:20
>> 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...		2023-05-09 16:06:20
>> finding nearest gene and calculating distance...		2023-05-09 16:06:21
>> dealing with gene strand ...		2023-05-09 16:06:21
>> merging all info together ...		2023-05-09 16:06:21
>> done		2023-05-09 16:06:21
>> checking seqlevels match...		2023-05-09 16:06:22
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2023-05-09 16:06:22
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-05-09 16:06:22
>> finding nearest gene and calculating distance...		2023-05-09 16:06:23
>> dealing with gene strand ...		2023-05-09 16:06:23
>> merging all info together ...		2023-05-09 16:06:23
>> done		2023-05-09 16:06:23
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-05-09 16:06:24
>> 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...		2023-05-09 16:06:24
>> 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...		2023-05-09 16:06:24
>> finding nearest gene and calculating distance...		2023-05-09 16:06:25
>> dealing with gene strand ...		2023-05-09 16:06:25
>> merging all info together ...		2023-05-09 16:06:25
>> done		2023-05-09 16:06:26
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-05-09 16:06:27
>> 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...		2023-05-09 16:06:28
>> 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...		2023-05-09 16:06:29
>> checking seqlevels match...		2023-05-09 16:06:30
>> 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...		2023-05-09 16:06:31
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-05-09 16:06:32
>> merging all info together...		2023-05-09 16:06:32
>> done		2023-05-09 16:06:32
>> checking seqlevels match...		2023-05-09 16:06:32
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2023-05-09 16:06:33
>> checking seqlevels match...		2023-05-09 16:06:33
>> 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...		2023-05-09 16:06:34
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-05-09 16:06:34
>> checking seqlevels match...		2023-05-09 16:06:34
>> 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...		2023-05-09 16:06:35
>> calculating cor and pvalue, which may be time consuming...		2023-05-09 16:06:35
>> merging all info together...		2023-05-09 16:06:35
>> done		2023-05-09 16:06:35
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-05-09 16:06:35
>> merging all info together...		2023-05-09 16:06:36
>> done		2023-05-09 16:06:36
>> checking seqlevels match...		2023-05-09 16:06:36
>> 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...		2023-05-09 16:06:36
>> some scan range may cross Chr bound, trimming...		2023-05-09 16:06:37
>> finding overlap peak in gene scan region...		2023-05-09 16:06:37
>> dealing with left peak not your gene scan region...		2023-05-09 16:06:37
>> merging two set peaks...		2023-05-09 16:06:37
>> calculating distance and dealing with gene strand...		2023-05-09 16:06:37
>> merging all info together ...		2023-05-09 16:06:37
>> done		2023-05-09 16:06:37
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-05-09 16:06:39
>> merging all info together...		2023-05-09 16:06:39
>> done		2023-05-09 16:06:39
>> checking seqlevels match...		2023-05-09 16:06:39
>> 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
>> using scanPromoter parameter to scan promoter for each gene...		2023-05-09 16:06:39
>> checking seqlevels match...		2023-05-09 16:06:39
>> 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...		2023-05-09 16:06:40
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-05-09 16:06:40
>> checking seqlevels match...		2023-05-09 16:06:40
>> 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...		2023-05-09 16:06:41
>> calculating cor and pvalue, which may be time consuming...		2023-05-09 16:06:42
>> merging all info together...		2023-05-09 16:06:42
>> done		2023-05-09 16:06:42
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 
 89.305   2.076  91.369

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit4.6590.1604.939
calcRP_coverage8.8550.3329.189
calcRP_region7.5520.2407.793
enhancerPromoterCor3.4910.0993.591
findIT_MARA0.5930.0040.596
findIT_TFHit1.2390.0121.251
findIT_TTPair0.0950.0030.100
findIT_enrichFisher0.1990.0040.202
findIT_enrichWilcox0.2210.0000.222
findIT_regionRP8.2660.0848.351
getAssocPairNumber1.6170.0071.624
integrate_ChIP_RNA2.8480.0322.880
integrate_replicates0.0020.0000.002
jaccard_findIT_TTpair0.1430.0030.146
jaccard_findIT_enrichFisher0.2840.0010.284
loadPeakFile0.0760.0000.076
mm_geneBound1.6310.0151.647
mm_geneScan1.6730.0291.701
mm_nearestGene1.5040.0031.508
peakGeneCor3.2930.0273.321
plot_annoDistance1.9530.0151.970
plot_peakGeneAlias_summary2.7980.1152.914
plot_peakGeneCor3.8490.0883.937
test_geneSet0.0010.0010.000