Build/check report for BioC 3.17 - CHECK results for FindIT2 on palomino5

Hostname	OS	Arch (*)	R version	Installed pkgs
palomino5	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"	4165
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: FindIT2

Version: 1.5.0

Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FindIT2_1.5.0.tar.gz

StartedAt: 2022-12-28 23:48:05 -0500 (Wed, 28 Dec 2022)

EndedAt: 2022-12-28 23:52:44 -0500 (Wed, 28 Dec 2022)

EllapsedTime: 279.1 seconds

RetCode: 0

Status: OK

CheckDir: FindIT2.Rcheck

Warnings: 0

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FindIT2_1.5.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/FindIT2.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FindIT2/DESCRIPTION' ... OK
* this is package 'FindIT2' version '1.5.0'
* 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 whether package 'FindIT2' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
findIT_regionRP 5.87   0.27    6.14
calcRP_region   5.27   0.22    5.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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)


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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")
>> checking seqlevels match...		2022-12-28 11:51:48 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-12-28 11:51:48 PM
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:51:50 PM
>> finding overlap peak in gene scan region...		2022-12-28 11:51:50 PM
>> dealing with left peak not your gene scan region...		2022-12-28 11:51:50 PM
>> merging two set peaks...		2022-12-28 11:51:50 PM
>> calculating distance and dealing with gene strand...		2022-12-28 11:51:50 PM
>> merging all info together ...		2022-12-28 11:51:50 PM
>> done		2022-12-28 11:51:50 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-12-28 11:51:50 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-12-28 11:51:51 PM
>> calculating RP using centerToTSS and peak score2022-12-28 11:51:51 PM
>> merging all info together		2022-12-28 11:51:53 PM
>> done		2022-12-28 11:51:54 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-12-28 11:51:54 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-12-28 11:51:55 PM
>> calculating RP using centerToTSS and peak score2022-12-28 11:51:55 PM
>> merging all info together		2022-12-28 11:51:58 PM
>> done		2022-12-28 11:51:58 PM
>> checking seqlevels match...		2022-12-28 11:51:58 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-12-28 11:51:58 PM
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:51:59 PM
>> finding overlap peak in gene scan region...		2022-12-28 11:51:59 PM
>> dealing with left peak not your gene scan region...		2022-12-28 11:51:59 PM
>> merging two set peaks...		2022-12-28 11:51:59 PM
>> calculating distance and dealing with gene strand...		2022-12-28 11:51:59 PM
>> merging all info together ...		2022-12-28 11:51:59 PM
>> done		2022-12-28 11:51:59 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-12-28 11:51:59 PM
>> calculating RP using centerToTSS and TF hit		2022-12-28 11:52:00 PM
>> merging all info together		2022-12-28 11:52:00 PM
>> done		2022-12-28 11:52:00 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-12-28 11:52:00 PM
>> calculating RP using centerToTSS and TF hit		2022-12-28 11:52:00 PM
>> merging all info together		2022-12-28 11:52:01 PM
>> done		2022-12-28 11:52:01 PM
>> checking seqlevels match...		2022-12-28 11:52:01 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-12-28 11:52:01 PM
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:02 PM
>> finding overlap peak in gene scan region...		2022-12-28 11:52:02 PM
>> dealing with left peak not your gene scan region...		2022-12-28 11:52:02 PM
>> merging two set peaks...		2022-12-28 11:52:02 PM
>> calculating distance and dealing with gene strand...		2022-12-28 11:52:02 PM
>> merging all info together ...		2022-12-28 11:52:02 PM
>> done		2022-12-28 11:52:02 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-12-28 11:52:02 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-12-28 11:52:03 PM
>> calculating RP using centerToTSS and peak score2022-12-28 11:52:03 PM
>> merging all info together		2022-12-28 11:52:05 PM
>> done		2022-12-28 11:52:05 PM
>> extracting RP info from regionRP...		2022-12-28 11:52:06 PM
>> dealing with TF_GR_databse...		2022-12-28 11:52:06 PM
>> calculating percent and p-value...		2022-12-28 11:52:06 PM
>> dealing withE5_0h_R1...		2022-12-28 11:52:06 PM
>> dealing withE5_0h_R2...		2022-12-28 11:52:06 PM
>> dealing withE5_4h_R1...		2022-12-28 11:52:06 PM
>> dealing withE5_4h_R2...		2022-12-28 11:52:06 PM
>> dealing withE5_8h_R1...		2022-12-28 11:52:06 PM
>> dealing withE5_8h_R2...		2022-12-28 11:52:06 PM
>> dealing withE5_16h_R1...		2022-12-28 11:52:06 PM
>> dealing withE5_16h_R2...		2022-12-28 11:52:06 PM
>> dealing withE5_24h_R1...		2022-12-28 11:52:06 PM
>> dealing withE5_24h_R2...		2022-12-28 11:52:06 PM
>> dealing withE5_48h_R1...		2022-12-28 11:52:06 PM
>> dealing withE5_48h_R2...		2022-12-28 11:52:06 PM
>> dealing withE5_48h_R3...		2022-12-28 11:52:06 PM
>> dealing withE5_72h_R1...		2022-12-28 11:52:07 PM
>> dealing withE5_72h_R2...		2022-12-28 11:52:07 PM
>> dealing withE5_72h_R3...		2022-12-28 11:52:07 PM
>> merging all info together...		2022-12-28 11:52:07 PM
>> done		2022-12-28 11:52:07 PM
>> preparing gene features information...		2022-12-28 11:52:07 PM
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:07 PM
>> calculating p-value for each TF, which may be time consuming...		2022-12-28 11:52:07 PM
>> merging all info together...		2022-12-28 11:52:08 PM
>> done		2022-12-28 11:52:08 PM
>> dealing with TF_GR_database...		2022-12-28 11:52:08 PM
>> calculating coef and converting into z-score using INT...		2022-12-28 11:52:08 PM
>> dealing with E5_0h_R1...		2022-12-28 11:52:08 PM
>> dealing with E5_0h_R2...		2022-12-28 11:52:08 PM
>> dealing with E5_4h_R1...		2022-12-28 11:52:08 PM
>> dealing with E5_4h_R2...		2022-12-28 11:52:08 PM
>> dealing with E5_8h_R1...		2022-12-28 11:52:08 PM
>> dealing with E5_8h_R2...		2022-12-28 11:52:08 PM
>> dealing with E5_16h_R1...		2022-12-28 11:52:08 PM
>> dealing with E5_16h_R2...		2022-12-28 11:52:08 PM
>> dealing with E5_24h_R1...		2022-12-28 11:52:08 PM
>> dealing with E5_24h_R2...		2022-12-28 11:52:08 PM
>> dealing with E5_48h_R1...		2022-12-28 11:52:09 PM
>> dealing with E5_48h_R2...		2022-12-28 11:52:09 PM
>> dealing with E5_48h_R3...		2022-12-28 11:52:09 PM
>> dealing with E5_72h_R1...		2022-12-28 11:52:09 PM
>> dealing with E5_72h_R2...		2022-12-28 11:52:09 PM
>> dealing with E5_72h_R3...		2022-12-28 11:52:09 PM
>> merging all info together...		2022-12-28 11:52:09 PM
>> done		2022-12-28 11:52:09 PM
>> checking seqlevels match...		2022-12-28 11:52:09 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-12-28 11:52:09 PM
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:10 PM
>> finding overlap peak in gene scan region...		2022-12-28 11:52:10 PM
>> dealing with left peak not your gene scan region...		2022-12-28 11:52:10 PM
>> merging two set peaks...		2022-12-28 11:52:10 PM
>> calculating distance and dealing with gene strand...		2022-12-28 11:52:10 PM
>> merging all info together ...		2022-12-28 11:52:10 PM
>> done		2022-12-28 11:52:10 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-12-28 11:52:10 PM
>> calculating RP using centerToTSS and TF hit		2022-12-28 11:52:11 PM
>> merging all info together		2022-12-28 11:52:11 PM
>> done		2022-12-28 11:52:11 PM
>> checking seqlevels match...		2022-12-28 11:52:12 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-12-28 11:52:12 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-12-28 11:52:14 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-12-28 11:52:14 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-12-28 11:52:14 PM
>> finding nearest gene and calculating distance...		2022-12-28 11:52:15 PM
>> dealing with gene strand ...		2022-12-28 11:52:15 PM
>> merging all info together ...		2022-12-28 11:52:15 PM
>> done		2022-12-28 11:52:15 PM
>> checking seqlevels match...		2022-12-28 11:52:15 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-12-28 11:52:15 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-12-28 11:52:15 PM
>> finding nearest gene and calculating distance...		2022-12-28 11:52:16 PM
>> dealing with gene strand ...		2022-12-28 11:52:16 PM
>> merging all info together ...		2022-12-28 11:52:16 PM
>> done		2022-12-28 11:52:16 PM
>> checking seqlevels match...		2022-12-28 11:52:17 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-12-28 11:52:17 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-12-28 11:52:17 PM
>> finding nearest gene and calculating distance...		2022-12-28 11:52:18 PM
>> dealing with gene strand ...		2022-12-28 11:52:18 PM
>> merging all info together ...		2022-12-28 11:52:18 PM
>> done		2022-12-28 11:52:18 PM
>> checking seqlevels match...		2022-12-28 11:52:18 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-12-28 11:52:18 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-12-28 11:52:19 PM
>> finding nearest gene and calculating distance...		2022-12-28 11:52:19 PM
>> dealing with gene strand ...		2022-12-28 11:52:19 PM
>> merging all info together ...		2022-12-28 11:52:19 PM
>> done		2022-12-28 11:52:19 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-12-28 11:52:20 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-12-28 11:52:20 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-12-28 11:52:20 PM
>> finding nearest gene and calculating distance...		2022-12-28 11:52:21 PM
>> dealing with gene strand ...		2022-12-28 11:52:21 PM
>> merging all info together ...		2022-12-28 11:52:21 PM
>> done		2022-12-28 11:52:21 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-12-28 11:52:21 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-12-28 11:52:22 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:23 PM
>> checking seqlevels match...		2022-12-28 11:52:23 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:25 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-12-28 11:52:26 PM
>> merging all info together...		2022-12-28 11:52:26 PM
>> done		2022-12-28 11:52:26 PM
>> checking seqlevels match...		2022-12-28 11:52:26 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene...		2022-12-28 11:52:26 PM
>> checking seqlevels match...		2022-12-28 11:52:26 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:27 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-12-28 11:52:27 PM
>> checking seqlevels match...		2022-12-28 11:52:27 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:28 PM
>> calculating cor and pvalue, which may be time consuming...		2022-12-28 11:52:28 PM
>> merging all info together...		2022-12-28 11:52:28 PM
>> done		2022-12-28 11:52:28 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-12-28 11:52:28 PM
>> merging all info together...		2022-12-28 11:52:28 PM
>> done		2022-12-28 11:52:28 PM
>> checking seqlevels match...		2022-12-28 11:52:29 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-12-28 11:52:29 PM
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:29 PM
>> finding overlap peak in gene scan region...		2022-12-28 11:52:29 PM
>> dealing with left peak not your gene scan region...		2022-12-28 11:52:29 PM
>> merging two set peaks...		2022-12-28 11:52:29 PM
>> calculating distance and dealing with gene strand...		2022-12-28 11:52:30 PM
>> merging all info together ...		2022-12-28 11:52:30 PM
>> done		2022-12-28 11:52:30 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-12-28 11:52:31 PM
>> merging all info together...		2022-12-28 11:52:31 PM
>> done		2022-12-28 11:52:31 PM
>> checking seqlevels match...		2022-12-28 11:52:31 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene...		2022-12-28 11:52:31 PM
>> checking seqlevels match...		2022-12-28 11:52:31 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:32 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-12-28 11:52:32 PM
>> checking seqlevels match...		2022-12-28 11:52:32 PM
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-12-28 11:52:33 PM
>> calculating cor and pvalue, which may be time consuming...		2022-12-28 11:52:33 PM
>> merging all info together...		2022-12-28 11:52:33 PM
>> done		2022-12-28 11:52:33 PM
Joining, by = "feature_id"
Joining, by = "feature_id"
`geom_smooth()` using formula = 'y ~ x'
Joining, by = "feature_id"
Joining, by = "feature_id"
`geom_smooth()` using formula = 'y ~ x'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ]
> 
> proc.time()
   user  system elapsed 
  53.96    2.00   55.96

name	user	system	elapsed
TF_target_database	0	0	0
calcRP_TFHit	3.23	0.11	3.41
calcRP_coverage	0.03	0.01	0.05
calcRP_region	5.27	0.22	5.49
enhancerPromoterCor	2.53	0.10	2.62
findIT_MARA	0.37	0.01	0.39
findIT_TFHit	0.72	0.06	0.78
findIT_TTPair	0.10	0.08	0.17
findIT_enrichFisher	0.11	0.03	0.15
findIT_enrichWilcox	0.17	0.00	0.17
findIT_regionRP	5.87	0.27	6.14
getAssocPairNumber	0.92	0.03	0.95
integrate_ChIP_RNA	1.61	0.06	1.67
integrate_replicates	0	0	0
jaccard_findIT_TTpair	0.14	0.08	0.22
jaccard_findIT_enrichFisher	0.19	0.00	0.19
loadPeakFile	0.05	0.00	0.05
mm_geneBound	0.90	0.14	1.04
mm_geneScan	0.94	0.06	1.00
mm_nearestGene	0.94	0.07	1.00
peakGeneCor	2.05	0.12	2.17
plot_annoDistance	1.14	0.00	1.15
plot_peakGeneAlias_summary	1.66	0.08	1.74
plot_peakGeneCor	2.64	0.16	2.79
test_geneSet	0	0	0

CHECK results for FindIT2 on palomino5

Summary

Command output

Installation output

Tests output

Example timings