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HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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CHECK results for FindIT2 on tokay2


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.
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raw results

Package 642/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.0.3  (landing page)
Guandong Shang
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: RELEASE_3_14
git_last_commit: e395076
git_last_commit_date: 2021-12-28 22:21:52 -0500 (Tue, 28 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FindIT2
Version: 1.0.3
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FindIT2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FindIT2_1.0.3.tar.gz
StartedAt: 2022-01-23 19:12:34 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 19:25:00 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 745.9 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FindIT2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FindIT2_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/FindIT2.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.0.3'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
calcRP_region    5.37   0.45    5.87
findIT_regionRP  5.69   0.02    5.71
calcRP_TFHit     4.45   0.55  165.67
plot_peakGeneCor 2.85   0.00   25.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
findIT_regionRP 5.50   0.02    5.51
calcRP_region   4.98   0.05    5.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/FindIT2_1.0.3.tar.gz && rm -rf FindIT2.buildbin-libdir && mkdir FindIT2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FindIT2.buildbin-libdir FindIT2_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FindIT2_1.0.3.zip && rm FindIT2_1.0.3.tar.gz FindIT2_1.0.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 88  798k   88  702k    0     0  1468k      0 --:--:-- --:--:-- --:--:-- 1466k
100  798k  100  798k    0     0  1540k      0 --:--:-- --:--:-- --:--:-- 1540k

install for i386

* 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

install for x64

* installing *source* package 'FindIT2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FindIT2' as FindIT2_1.0.3.zip
* DONE (FindIT2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'FindIT2' successfully unpacked and MD5 sums checked

Tests output

FindIT2.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 7:22:19 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 7:22:19 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:22:20 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:22:20 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:22:20 PM
>> merging two set peaks...		2022-01-23 7:22:21 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:22:22 PM
>> merging all info together ...		2022-01-23 7:22:22 PM
>> done		2022-01-23 7:22:22 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:22:22 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 7:22:23 PM
>> calculating RP using centerToTSS and peak score2022-01-23 7:22:23 PM
>> merging all info together		2022-01-23 7:22:25 PM
>> done		2022-01-23 7:22:26 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:22:26 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 7:22:27 PM
>> calculating RP using centerToTSS and peak score2022-01-23 7:22:27 PM
>> merging all info together		2022-01-23 7:22:30 PM
>> done		2022-01-23 7:22:30 PM
>> checking seqlevels match...		2022-01-23 7:22:30 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 7:22:30 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:22:34 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:22:34 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:22:34 PM
>> merging two set peaks...		2022-01-23 7:22:35 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:22:35 PM
>> merging all info together ...		2022-01-23 7:22:35 PM
>> done		2022-01-23 7:22:35 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:22:35 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 7:22:35 PM
>> merging all info together		2022-01-23 7:22:35 PM
>> done		2022-01-23 7:22:35 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:22:35 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 7:22:36 PM
>> merging all info together		2022-01-23 7:22:36 PM
>> done		2022-01-23 7:22:36 PM
>> checking seqlevels match...		2022-01-23 7:22:50 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-23 7:22:50 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:22:51 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:22:51 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:22:51 PM
>> merging two set peaks...		2022-01-23 7:22:51 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:22:51 PM
>> merging all info together ...		2022-01-23 7:22:51 PM
>> done		2022-01-23 7:22:51 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:22:51 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 7:23:07 PM
>> calculating RP using centerToTSS and peak score2022-01-23 7:23:07 PM
>> merging all info together		2022-01-23 7:23:09 PM
>> done		2022-01-23 7:23:10 PM
>> extracting RP info from regionRP...		2022-01-23 7:23:14 PM
>> dealing with TF_GR_databse...		2022-01-23 7:23:14 PM
>> calculating percent and p-value...		2022-01-23 7:23:15 PM
>> dealing withE5_0h_R1...		2022-01-23 7:23:15 PM
>> dealing withE5_0h_R2...		2022-01-23 7:23:15 PM
>> dealing withE5_4h_R1...		2022-01-23 7:23:15 PM
>> dealing withE5_4h_R2...		2022-01-23 7:23:15 PM
>> dealing withE5_8h_R1...		2022-01-23 7:23:15 PM
>> dealing withE5_8h_R2...		2022-01-23 7:23:15 PM
>> dealing withE5_16h_R1...		2022-01-23 7:23:15 PM
>> dealing withE5_16h_R2...		2022-01-23 7:23:15 PM
>> dealing withE5_24h_R1...		2022-01-23 7:23:15 PM
>> dealing withE5_24h_R2...		2022-01-23 7:23:15 PM
>> dealing withE5_48h_R1...		2022-01-23 7:23:15 PM
>> dealing withE5_48h_R2...		2022-01-23 7:23:15 PM
>> dealing withE5_48h_R3...		2022-01-23 7:23:15 PM
>> dealing withE5_72h_R1...		2022-01-23 7:23:15 PM
>> dealing withE5_72h_R2...		2022-01-23 7:23:15 PM
>> dealing withE5_72h_R3...		2022-01-23 7:23:15 PM
>> merging all info together...		2022-01-23 7:23:15 PM
>> done		2022-01-23 7:23:15 PM
>> preparing gene features information...		2022-01-23 7:23:16 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:23:17 PM
>> calculating p-value for each TF, which may be time consuming...		2022-01-23 7:23:17 PM
>> merging all info together...		2022-01-23 7:23:17 PM
>> done		2022-01-23 7:23:17 PM
>> dealing with TF_GR_database...		2022-01-23 7:23:17 PM
>> calculating coef and converting into z-score using INT...		2022-01-23 7:23:18 PM
>> dealing withE5_0h_R1...		2022-01-23 7:23:18 PM
>> dealing withE5_0h_R2...		2022-01-23 7:23:18 PM
>> dealing withE5_4h_R1...		2022-01-23 7:23:18 PM
>> dealing withE5_4h_R2...		2022-01-23 7:23:18 PM
>> dealing withE5_8h_R1...		2022-01-23 7:23:18 PM
>> dealing withE5_8h_R2...		2022-01-23 7:23:18 PM
>> dealing withE5_16h_R1...		2022-01-23 7:23:18 PM
>> dealing withE5_16h_R2...		2022-01-23 7:23:18 PM
>> dealing withE5_24h_R1...		2022-01-23 7:23:18 PM
>> dealing withE5_24h_R2...		2022-01-23 7:23:18 PM
>> dealing withE5_48h_R1...		2022-01-23 7:23:18 PM
>> dealing withE5_48h_R2...		2022-01-23 7:23:19 PM
>> dealing withE5_48h_R3...		2022-01-23 7:23:19 PM
>> dealing withE5_72h_R1...		2022-01-23 7:23:19 PM
>> dealing withE5_72h_R2...		2022-01-23 7:23:19 PM
>> dealing withE5_72h_R3...		2022-01-23 7:23:19 PM
>> merging all info together...		2022-01-23 7:23:19 PM
>> done		2022-01-23 7:23:19 PM
>> checking seqlevels match...		2022-01-23 7:23:19 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 7:23:19 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:23:20 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:23:20 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:23:20 PM
>> merging two set peaks...		2022-01-23 7:23:20 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:23:20 PM
>> merging all info together ...		2022-01-23 7:23:20 PM
>> done		2022-01-23 7:23:20 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:23:20 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 7:23:21 PM
>> merging all info together		2022-01-23 7:23:21 PM
>> done		2022-01-23 7:23:21 PM
>> checking seqlevels match...		2022-01-23 7:23:21 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 7:23:21 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 7:23:25 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 7:23:25 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 7:23:25 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:23:26 PM
>> dealing with gene strand ...		2022-01-23 7:23:26 PM
>> merging all info together ...		2022-01-23 7:23:26 PM
>> done		2022-01-23 7:23:26 PM
>> checking seqlevels match...		2022-01-23 7:23:26 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
>> checking seqlevels match...		2022-01-23 7:23:26 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 7:23:26 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:23:27 PM
>> dealing with gene strand ...		2022-01-23 7:23:27 PM
>> merging all info together ...		2022-01-23 7:23:27 PM
>> done		2022-01-23 7:23:27 PM
>> checking seqlevels match...		2022-01-23 7:23:28 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 7:23:28 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 7:23:28 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:23:28 PM
>> dealing with gene strand ...		2022-01-23 7:23:28 PM
>> merging all info together ...		2022-01-23 7:23:28 PM
>> done		2022-01-23 7:23:28 PM
>> checking seqlevels match...		2022-01-23 7:23:29 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
>> checking seqlevels match...		2022-01-23 7:23:29 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 7:23:29 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:23:30 PM
>> dealing with gene strand ...		2022-01-23 7:23:30 PM
>> merging all info together ...		2022-01-23 7:23:30 PM
>> done		2022-01-23 7:23:30 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 7:23:31 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
>> checking seqlevels match...		2022-01-23 7:23:31 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 7:23:31 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:23:32 PM
>> dealing with gene strand ...		2022-01-23 7:23:32 PM
>> merging all info together ...		2022-01-23 7:23:32 PM
>> done		2022-01-23 7:23:32 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 7:23:33 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 7:23:34 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:23:34 PM
>> checking seqlevels match...		2022-01-23 7:23:35 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 7:23:36 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:23:37 PM
>> merging all info together...		2022-01-23 7:23:37 PM
>> done		2022-01-23 7:23:37 PM
>> checking seqlevels match...		2022-01-23 7:23:37 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
>> using scanPromoter parameter to scan promoter for each gene...		2022-01-23 7:23:37 PM
>> checking seqlevels match...		2022-01-23 7:23:37 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:23:39 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 7:23:39 PM
>> checking seqlevels match...		2022-01-23 7:23:39 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 7:23:40 PM
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:23:40 PM
>> merging all info together...		2022-01-23 7:23:40 PM
>> done		2022-01-23 7:23:40 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:23:40 PM
>> merging all info together...		2022-01-23 7:23:40 PM
>> done		2022-01-23 7:23:40 PM
>> checking seqlevels match...		2022-01-23 7:23:40 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 7:23:40 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:23:41 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:23:41 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:23:41 PM
>> merging two set peaks...		2022-01-23 7:23:41 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:23:41 PM
>> merging all info together ...		2022-01-23 7:23:41 PM
>> done		2022-01-23 7:23:41 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:23:42 PM
>> merging all info together...		2022-01-23 7:23:42 PM
>> done		2022-01-23 7:23:42 PM
>> checking seqlevels match...		2022-01-23 7:23:42 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 7:23:42 PM
>> checking seqlevels match...		2022-01-23 7:23:42 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 7:23:43 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 7:23:43 PM
>> checking seqlevels match...		2022-01-23 7:23:44 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 7:23:45 PM
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:23:45 PM
>> merging all info together...		2022-01-23 7:23:45 PM
>> done		2022-01-23 7:23:45 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 
  60.62    1.65   97.75 

FindIT2.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 7:23:59 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-23 7:23:59 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:24:00 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:24:00 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:24:00 PM
>> merging two set peaks...		2022-01-23 7:24:01 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:24:01 PM
>> merging all info together ...		2022-01-23 7:24:01 PM
>> done		2022-01-23 7:24:01 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:24:01 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 7:24:02 PM
>> calculating RP using centerToTSS and peak score2022-01-23 7:24:02 PM
>> merging all info together		2022-01-23 7:24:04 PM
>> done		2022-01-23 7:24:05 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:24:05 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 7:24:06 PM
>> calculating RP using centerToTSS and peak score2022-01-23 7:24:06 PM
>> merging all info together		2022-01-23 7:24:09 PM
>> done		2022-01-23 7:24:10 PM
>> checking seqlevels match...		2022-01-23 7:24:10 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 7:24:10 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:24:11 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:24:11 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:24:11 PM
>> merging two set peaks...		2022-01-23 7:24:11 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:24:12 PM
>> merging all info together ...		2022-01-23 7:24:12 PM
>> done		2022-01-23 7:24:12 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:24:12 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 7:24:12 PM
>> merging all info together		2022-01-23 7:24:13 PM
>> done		2022-01-23 7:24:13 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:24:13 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 7:24:13 PM
>> merging all info together		2022-01-23 7:24:13 PM
>> done		2022-01-23 7:24:13 PM
>> checking seqlevels match...		2022-01-23 7:24:14 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-23 7:24:14 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:24:15 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:24:15 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:24:15 PM
>> merging two set peaks...		2022-01-23 7:24:15 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:24:16 PM
>> merging all info together ...		2022-01-23 7:24:16 PM
>> done		2022-01-23 7:24:16 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:24:16 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-23 7:24:16 PM
>> calculating RP using centerToTSS and peak score2022-01-23 7:24:16 PM
>> merging all info together		2022-01-23 7:24:18 PM
>> done		2022-01-23 7:24:18 PM
>> extracting RP info from regionRP...		2022-01-23 7:24:20 PM
>> dealing with TF_GR_databse...		2022-01-23 7:24:20 PM
>> calculating percent and p-value...		2022-01-23 7:24:20 PM
>> dealing withE5_0h_R1...		2022-01-23 7:24:20 PM
>> dealing withE5_0h_R2...		2022-01-23 7:24:20 PM
>> dealing withE5_4h_R1...		2022-01-23 7:24:20 PM
>> dealing withE5_4h_R2...		2022-01-23 7:24:20 PM
>> dealing withE5_8h_R1...		2022-01-23 7:24:20 PM
>> dealing withE5_8h_R2...		2022-01-23 7:24:20 PM
>> dealing withE5_16h_R1...		2022-01-23 7:24:20 PM
>> dealing withE5_16h_R2...		2022-01-23 7:24:20 PM
>> dealing withE5_24h_R1...		2022-01-23 7:24:20 PM
>> dealing withE5_24h_R2...		2022-01-23 7:24:20 PM
>> dealing withE5_48h_R1...		2022-01-23 7:24:20 PM
>> dealing withE5_48h_R2...		2022-01-23 7:24:20 PM
>> dealing withE5_48h_R3...		2022-01-23 7:24:20 PM
>> dealing withE5_72h_R1...		2022-01-23 7:24:20 PM
>> dealing withE5_72h_R2...		2022-01-23 7:24:20 PM
>> dealing withE5_72h_R3...		2022-01-23 7:24:20 PM
>> merging all info together...		2022-01-23 7:24:20 PM
>> done		2022-01-23 7:24:21 PM
>> preparing gene features information...		2022-01-23 7:24:21 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:24:21 PM
>> calculating p-value for each TF, which may be time consuming...		2022-01-23 7:24:21 PM
>> merging all info together...		2022-01-23 7:24:22 PM
>> done		2022-01-23 7:24:22 PM
>> dealing with TF_GR_database...		2022-01-23 7:24:22 PM
>> calculating coef and converting into z-score using INT...		2022-01-23 7:24:22 PM
>> dealing withE5_0h_R1...		2022-01-23 7:24:22 PM
>> dealing withE5_0h_R2...		2022-01-23 7:24:22 PM
>> dealing withE5_4h_R1...		2022-01-23 7:24:22 PM
>> dealing withE5_4h_R2...		2022-01-23 7:24:22 PM
>> dealing withE5_8h_R1...		2022-01-23 7:24:22 PM
>> dealing withE5_8h_R2...		2022-01-23 7:24:22 PM
>> dealing withE5_16h_R1...		2022-01-23 7:24:22 PM
>> dealing withE5_16h_R2...		2022-01-23 7:24:23 PM
>> dealing withE5_24h_R1...		2022-01-23 7:24:23 PM
>> dealing withE5_24h_R2...		2022-01-23 7:24:23 PM
>> dealing withE5_48h_R1...		2022-01-23 7:24:23 PM
>> dealing withE5_48h_R2...		2022-01-23 7:24:23 PM
>> dealing withE5_48h_R3...		2022-01-23 7:24:23 PM
>> dealing withE5_72h_R1...		2022-01-23 7:24:23 PM
>> dealing withE5_72h_R2...		2022-01-23 7:24:23 PM
>> dealing withE5_72h_R3...		2022-01-23 7:24:23 PM
>> merging all info together...		2022-01-23 7:24:23 PM
>> done		2022-01-23 7:24:23 PM
>> checking seqlevels match...		2022-01-23 7:24:23 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-23 7:24:23 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:24:24 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:24:24 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:24:24 PM
>> merging two set peaks...		2022-01-23 7:24:24 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:24:24 PM
>> merging all info together ...		2022-01-23 7:24:24 PM
>> done		2022-01-23 7:24:24 PM
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-23 7:24:24 PM
>> calculating RP using centerToTSS and TF hit		2022-01-23 7:24:25 PM
>> merging all info together		2022-01-23 7:24:25 PM
>> done		2022-01-23 7:24:25 PM
>> checking seqlevels match...		2022-01-23 7:24:26 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 7:24:26 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-23 7:24:29 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
>> checking seqlevels match...		2022-01-23 7:24:29 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 7:24:29 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:24:30 PM
>> dealing with gene strand ...		2022-01-23 7:24:30 PM
>> merging all info together ...		2022-01-23 7:24:30 PM
>> done		2022-01-23 7:24:30 PM
>> checking seqlevels match...		2022-01-23 7:24:30 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 7:24:30 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 7:24:30 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:24:31 PM
>> dealing with gene strand ...		2022-01-23 7:24:31 PM
>> merging all info together ...		2022-01-23 7:24:31 PM
>> done		2022-01-23 7:24:31 PM
>> checking seqlevels match...		2022-01-23 7:24:33 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 7:24:33 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 7:24:33 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:24:33 PM
>> dealing with gene strand ...		2022-01-23 7:24:33 PM
>> merging all info together ...		2022-01-23 7:24:33 PM
>> done		2022-01-23 7:24:33 PM
>> checking seqlevels match...		2022-01-23 7:24:34 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
>> checking seqlevels match...		2022-01-23 7:24:34 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-23 7:24:34 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:24:35 PM
>> dealing with gene strand ...		2022-01-23 7:24:35 PM
>> merging all info together ...		2022-01-23 7:24:35 PM
>> done		2022-01-23 7:24:35 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 7:24:36 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 7:24:36 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 7:24:36 PM
>> finding nearest gene and calculating distance...		2022-01-23 7:24:37 PM
>> dealing with gene strand ...		2022-01-23 7:24:37 PM
>> merging all info together ...		2022-01-23 7:24:37 PM
>> done		2022-01-23 7:24:37 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-23 7:24:38 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 7:24:39 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 7:24:40 PM
>> checking seqlevels match...		2022-01-23 7:24:41 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 7:24:41 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:24:42 PM
>> merging all info together...		2022-01-23 7:24:42 PM
>> done		2022-01-23 7:24:42 PM
>> checking seqlevels match...		2022-01-23 7:24:42 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 7:24:42 PM
>> checking seqlevels match...		2022-01-23 7:24:43 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 7:24:43 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 7:24:44 PM
>> checking seqlevels match...		2022-01-23 7:24:44 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 7:24:44 PM
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:24:45 PM
>> merging all info together...		2022-01-23 7:24:45 PM
>> done		2022-01-23 7:24:45 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:24:45 PM
>> merging all info together...		2022-01-23 7:24:45 PM
>> done		2022-01-23 7:24:45 PM
>> checking seqlevels match...		2022-01-23 7:24:45 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 7:24:45 PM
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:24:46 PM
>> finding overlap peak in gene scan region...		2022-01-23 7:24:46 PM
>> dealing with left peak not your gene scan region...		2022-01-23 7:24:46 PM
>> merging two set peaks...		2022-01-23 7:24:46 PM
>> calculating distance and dealing with gene strand...		2022-01-23 7:24:46 PM
>> merging all info together ...		2022-01-23 7:24:46 PM
>> done		2022-01-23 7:24:46 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:24:47 PM
>> merging all info together...		2022-01-23 7:24:47 PM
>> done		2022-01-23 7:24:47 PM
>> checking seqlevels match...		2022-01-23 7:24:47 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 7:24:47 PM
>> checking seqlevels match...		2022-01-23 7:24:47 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 7:24:48 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-23 7:24:48 PM
>> checking seqlevels match...		2022-01-23 7:24:48 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
>> some scan range may cross Chr bound, trimming...		2022-01-23 7:24:49 PM
>> calculating cor and pvalue, which may be time consuming...		2022-01-23 7:24:49 PM
>> merging all info together...		2022-01-23 7:24:50 PM
>> done		2022-01-23 7:24:50 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 
  61.46    0.82   62.26 

Example timings

FindIT2.Rcheck/examples_i386/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit 4.45 0.55165.67
calcRP_coverage0.030.030.07
calcRP_region5.370.455.87
enhancerPromoterCor2.610.192.80
findIT_MARA0.300.000.29
findIT_TFHit1.000.031.04
findIT_TTPair0.090.030.12
findIT_enrichFisher0.180.000.17
findIT_enrichWilcox0.170.000.17
findIT_regionRP5.690.025.71
getAssocPairNumber1.280.011.29
integrate_ChIP_RNA2.040.052.10
integrate_replicates000
jaccard_findIT_TTpair0.070.060.12
jaccard_findIT_enrichFisher0.180.000.19
loadPeakFile0.070.000.06
mm_geneBound1.150.001.16
mm_geneScan1.130.021.14
mm_nearestGene1.620.001.62
peakGeneCor1.960.052.00
plot_annoDistance1.350.001.34
plot_peakGeneAlias_summary1.250.011.27
plot_peakGeneCor 2.85 0.0025.50
test_geneSet000

FindIT2.Rcheck/examples_x64/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit3.350.063.40
calcRP_coverage0.050.000.04
calcRP_region4.980.055.04
enhancerPromoterCor3.430.033.45
findIT_MARA0.280.030.31
findIT_TFHit0.920.060.98
findIT_TTPair0.080.030.11
findIT_enrichFisher0.170.000.17
findIT_enrichWilcox0.360.000.36
findIT_regionRP5.500.025.51
getAssocPairNumber1.080.031.11
integrate_ChIP_RNA2.530.032.56
integrate_replicates000
jaccard_findIT_TTpair0.080.030.11
jaccard_findIT_enrichFisher0.190.000.18
loadPeakFile0.060.000.07
mm_geneBound1.100.051.14
mm_geneScan1.120.021.14
mm_nearestGene1.560.011.58
peakGeneCor2.140.022.16
plot_annoDistance1.800.001.79
plot_peakGeneAlias_summary1.450.001.46
plot_peakGeneCor3.390.013.40
test_geneSet000