Back to Multiple platform build/check report for BioC 3.15
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-24 11:07:19 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for FindIT2 on riesling1


To the developers/maintainers of the FindIT2 package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 640/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.1.3  (landing page)
Guandong Shang
Snapshot Date: 2022-01-23 13:55:15 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: master
git_last_commit: 4c4fab3
git_last_commit_date: 2021-12-28 22:18:58 -0500 (Tue, 28 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FindIT2
Version: 1.1.3
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FindIT2_1.1.3.tar.gz
StartedAt: 2022-01-23 18:55:41 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 19:00:20 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 279.4 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FindIT2_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/FindIT2.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FindIT2/DESCRIPTION' ... OK
* this is package 'FindIT2' version '1.1.3'
* 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
* 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


Installation output

FindIT2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'FindIT2'
    finding HTML links ... done
    ATAC_normCount                          html  
    RNADiff_LEC2_GR                         html  
    RNA_normCount                           html  
    TF_target_database                      html  
    calcRP_TFHit                            html  
    calcRP_coverage                         html  
    calcRP_region                           html  
    enhancerPromoterCor                     html  
    findIT_MARA                             html  
    findIT_TFHit                            html  
    findIT_TTPair                           html  
    findIT_enrichFisher                     html  
    findIT_enrichWilcox                     html  
    findIT_regionRP                         html  
    getAssocPairNumber                      html  
    integrate_ChIP_RNA                      html  
    integrate_replicates                    html  
    jaccard_findIT_TTpair                   html  
    jaccard_findIT_enrichFisher             html  
    loadPeakFile                            html  
    mm_geneBound                            html  
    mm_geneScan                             html  
    mm_nearestGene                          html  
    peakGeneCor                             html  
    plot_annoDistance                       html  
    plot_peakGeneAlias_summary              html  
    plot_peakGeneCor                        html  
    test_featureSet                         html  
    test_geneSet                            html  
** 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)
Making 'packages.html' ... done

Tests output

FindIT2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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, 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...		2022-01-23 6:59:24 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...		2022-01-23 6:59:24 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 6:59:26 PM
>> finding overlap peak in gene scan region...		2022-01-23 6:59:26 PM
>> dealing with left peak not your gene scan region...		2022-01-23 6:59:26 PM
>> merging two set peaks...		2022-01-23 6:59:26 PM
>> calculating distance and dealing with gene strand...		2022-01-23 6:59:26 PM
>> merging all info together ...		2022-01-23 6:59:26 PM
>> done		2022-01-23 6:59:26 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 6:59:26 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 6:59:27 PM
>> calculating RP using centerToTSS and peak score2022-01-23 6:59:27 PM
>> merging all info together		2022-01-23 6:59:29 PM
>> done		2022-01-23 6:59:30 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 6:59:30 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 6:59:31 PM
>> calculating RP using centerToTSS and peak score2022-01-23 6:59:31 PM
>> merging all info together		2022-01-23 6:59:33 PM
>> done		2022-01-23 6:59:34 PM
>> checking seqlevels match...		2022-01-23 6:59:34 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...		2022-01-23 6:59:34 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 6:59:34 PM
>> finding overlap peak in gene scan region...		2022-01-23 6:59:34 PM
>> dealing with left peak not your gene scan region...		2022-01-23 6:59:34 PM
>> merging two set peaks...		2022-01-23 6:59:35 PM
>> calculating distance and dealing with gene strand...		2022-01-23 6:59:35 PM
>> merging all info together ...		2022-01-23 6:59:35 PM
>> done		2022-01-23 6:59:35 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 6:59:35 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 6:59:35 PM
>> merging all info together		2022-01-23 6:59:35 PM
>> done		2022-01-23 6:59:35 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 6:59:35 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 6:59:36 PM
>> merging all info together		2022-01-23 6:59:36 PM
>> done		2022-01-23 6:59:36 PM
>> checking seqlevels match...		2022-01-23 6:59:37 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...		2022-01-23 6:59:37 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 6:59:38 PM
>> finding overlap peak in gene scan region...		2022-01-23 6:59:38 PM
>> dealing with left peak not your gene scan region...		2022-01-23 6:59:38 PM
>> merging two set peaks...		2022-01-23 6:59:38 PM
>> calculating distance and dealing with gene strand...		2022-01-23 6:59:38 PM
>> merging all info together ...		2022-01-23 6:59:38 PM
>> done		2022-01-23 6:59:38 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 6:59:38 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 6:59:39 PM
>> calculating RP using centerToTSS and peak score2022-01-23 6:59:39 PM
>> merging all info together		2022-01-23 6:59:41 PM
>> done		2022-01-23 6:59:41 PM
>> extracting RP info from regionRP...		2022-01-23 6:59:42 PM
>> dealing with TF_GR_databse...		2022-01-23 6:59:42 PM
>> calculating percent and p-value...		2022-01-23 6:59:42 PM
>> dealing withE5_0h_R1...		2022-01-23 6:59:42 PM
>> dealing withE5_0h_R2...		2022-01-23 6:59:42 PM
>> dealing withE5_4h_R1...		2022-01-23 6:59:42 PM
>> dealing withE5_4h_R2...		2022-01-23 6:59:42 PM
>> dealing withE5_8h_R1...		2022-01-23 6:59:42 PM
>> dealing withE5_8h_R2...		2022-01-23 6:59:42 PM
>> dealing withE5_16h_R1...		2022-01-23 6:59:42 PM
>> dealing withE5_16h_R2...		2022-01-23 6:59:42 PM
>> dealing withE5_24h_R1...		2022-01-23 6:59:42 PM
>> dealing withE5_24h_R2...		2022-01-23 6:59:42 PM
>> dealing withE5_48h_R1...		2022-01-23 6:59:43 PM
>> dealing withE5_48h_R2...		2022-01-23 6:59:43 PM
>> dealing withE5_48h_R3...		2022-01-23 6:59:43 PM
>> dealing withE5_72h_R1...		2022-01-23 6:59:43 PM
>> dealing withE5_72h_R2...		2022-01-23 6:59:43 PM
>> dealing withE5_72h_R3...		2022-01-23 6:59:43 PM
>> merging all info together...		2022-01-23 6:59:43 PM
>> done		2022-01-23 6:59:43 PM
>> preparing gene features information...		2022-01-23 6:59:43 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 6:59:44 PM
>> calculating p-value for each TF, which may be time consuming...		2022-01-23 6:59:44 PM
>> merging all info together...		2022-01-23 6:59:44 PM
>> done		2022-01-23 6:59:44 PM
>> dealing with TF_GR_database...		2022-01-23 6:59:44 PM
>> calculating coef and converting into z-score using INT...		2022-01-23 6:59:44 PM
>> dealing withE5_0h_R1...		2022-01-23 6:59:44 PM
>> dealing withE5_0h_R2...		2022-01-23 6:59:44 PM
>> dealing withE5_4h_R1...		2022-01-23 6:59:44 PM
>> dealing withE5_4h_R2...		2022-01-23 6:59:44 PM
>> dealing withE5_8h_R1...		2022-01-23 6:59:44 PM
>> dealing withE5_8h_R2...		2022-01-23 6:59:45 PM
>> dealing withE5_16h_R1...		2022-01-23 6:59:45 PM
>> dealing withE5_16h_R2...		2022-01-23 6:59:45 PM
>> dealing withE5_24h_R1...		2022-01-23 6:59:45 PM
>> dealing withE5_24h_R2...		2022-01-23 6:59:45 PM
>> dealing withE5_48h_R1...		2022-01-23 6:59:45 PM
>> dealing withE5_48h_R2...		2022-01-23 6:59:45 PM
>> dealing withE5_48h_R3...		2022-01-23 6:59:45 PM
>> dealing withE5_72h_R1...		2022-01-23 6:59:45 PM
>> dealing withE5_72h_R2...		2022-01-23 6:59:45 PM
>> dealing withE5_72h_R3...		2022-01-23 6:59:45 PM
>> merging all info together...		2022-01-23 6:59:45 PM
>> done		2022-01-23 6:59:45 PM
>> checking seqlevels match...		2022-01-23 6:59:46 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...		2022-01-23 6:59:46 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 6:59:46 PM
>> finding overlap peak in gene scan region...		2022-01-23 6:59:46 PM
>> dealing with left peak not your gene scan region...		2022-01-23 6:59:46 PM
>> merging two set peaks...		2022-01-23 6:59:47 PM
>> calculating distance and dealing with gene strand...		2022-01-23 6:59:47 PM
>> merging all info together ...		2022-01-23 6:59:47 PM
>> done		2022-01-23 6:59:47 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 6:59:47 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 6:59:47 PM
>> merging all info together		2022-01-23 6:59:47 PM
>> done		2022-01-23 6:59:47 PM
>> checking seqlevels match...		2022-01-23 6:59:48 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 6:59:48 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 6:59:50 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...		2022-01-23 6:59:50 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...		2022-01-23 6:59:50 PM
>> finding nearest gene and calculating distance...		2022-01-23 6:59:51 PM
>> dealing with gene strand ...		2022-01-23 6:59:51 PM
>> merging all info together ...		2022-01-23 6:59:51 PM
>> done		2022-01-23 6:59:51 PM
>> checking seqlevels match...		2022-01-23 6:59:51 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...		2022-01-23 6:59:51 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...		2022-01-23 6:59:51 PM
>> finding nearest gene and calculating distance...		2022-01-23 6:59:52 PM
>> dealing with gene strand ...		2022-01-23 6:59:52 PM
>> merging all info together ...		2022-01-23 6:59:52 PM
>> done		2022-01-23 6:59:52 PM
>> checking seqlevels match...		2022-01-23 6:59:53 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...		2022-01-23 6:59:53 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...		2022-01-23 6:59:53 PM
>> finding nearest gene and calculating distance...		2022-01-23 6:59:54 PM
>> dealing with gene strand ...		2022-01-23 6:59:55 PM
>> merging all info together ...		2022-01-23 6:59:55 PM
>> done		2022-01-23 6:59:55 PM
>> checking seqlevels match...		2022-01-23 6:59:55 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...		2022-01-23 6:59:55 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...		2022-01-23 6:59:55 PM
>> finding nearest gene and calculating distance...		2022-01-23 6:59:56 PM
>> dealing with gene strand ...		2022-01-23 6:59:56 PM
>> merging all info together ...		2022-01-23 6:59:56 PM
>> done		2022-01-23 6:59:56 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 6:59:57 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...		2022-01-23 6:59:57 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...		2022-01-23 6:59:57 PM
>> finding nearest gene and calculating distance...		2022-01-23 6:59:58 PM
>> dealing with gene strand ...		2022-01-23 6:59:58 PM
>> merging all info together ...		2022-01-23 6:59:58 PM
>> done		2022-01-23 6:59:58 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 6:59:59 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...		2022-01-23 7:00:00 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...		2022-01-23 7:00:01 PM
>> checking seqlevels match...		2022-01-23 7:00:02 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...		2022-01-23 7:00:02 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:00:03 PM
>> merging all info together...		2022-01-23 7:00:03 PM
>> done		2022-01-23 7:00:03 PM
>> checking seqlevels match...		2022-01-23 7:00:03 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...		2022-01-23 7:00:04 PM
>> checking seqlevels match...		2022-01-23 7:00:04 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...		2022-01-23 7:00:04 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 7:00:05 PM
>> checking seqlevels match...		2022-01-23 7:00:05 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...		2022-01-23 7:00:06 PM
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:00:06 PM
>> merging all info together...		2022-01-23 7:00:06 PM
>> done		2022-01-23 7:00:06 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:00:06 PM
>> merging all info together...		2022-01-23 7:00:06 PM
>> done		2022-01-23 7:00:06 PM
>> checking seqlevels match...		2022-01-23 7:00:06 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...		2022-01-23 7:00:06 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:00:07 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:00:07 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:00:07 PM
>> merging two set peaks...		2022-01-23 7:00:07 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:00:07 PM
>> merging all info together ...		2022-01-23 7:00:07 PM
>> done		2022-01-23 7:00:07 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:00:08 PM
>> merging all info together...		2022-01-23 7:00:08 PM
>> done		2022-01-23 7:00:08 PM
>> checking seqlevels match...		2022-01-23 7:00:08 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...		2022-01-23 7:00:08 PM
>> checking seqlevels match...		2022-01-23 7:00:08 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...		2022-01-23 7:00:09 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 7:00:09 PM
>> checking seqlevels match...		2022-01-23 7:00:09 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:00:10 PM
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:00:10 PM
>> merging all info together...		2022-01-23 7:00:10 PM
>> done		2022-01-23 7:00:10 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 
  53.76    2.46   56.20 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit3.910.164.06
calcRP_coverage0.060.030.09
calcRP_region4.710.154.91
enhancerPromoterCor2.770.112.88
findIT_MARA0.310.060.37
findIT_TFHit0.830.150.97
findIT_TTPair0.110.030.14
findIT_enrichFisher0.120.000.13
findIT_enrichWilcox0.140.000.14
findIT_regionRP4.490.144.62
getAssocPairNumber0.940.040.99
integrate_ChIP_RNA1.680.071.75
integrate_replicates000
jaccard_findIT_TTpair0.070.060.12
jaccard_findIT_enrichFisher0.140.010.16
loadPeakFile0.030.000.03
mm_geneBound1.060.021.08
mm_geneScan0.980.000.99
mm_nearestGene0.910.020.92
peakGeneCor2.310.112.42
plot_annoDistance1.060.041.11
plot_peakGeneAlias_summary0.970.020.98
plot_peakGeneCor2.060.012.08
test_geneSet000