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This page was generated on 2022-01-21 11:05:53 -0500 (Fri, 21 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
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CHECK results for FindIT2 on nebbiolo1


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 640/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.1.3  (landing page)
Guandong Shang
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings FindIT2_1.1.3.tar.gz
StartedAt: 2022-01-20 19:09:57 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:15:04 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 307.1 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FindIT2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
findIT_regionRP 5.164  0.012   5.176
calcRP_coverage 4.013  1.156   5.169
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FindIT2)

Tests output

FindIT2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) {
+     stop("unable to load TxDb.Athaliana.BioMart.plantsmart28")
+ }
Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28
> 
> test_check("FindIT2")
>> preparing gene features information...		2022-01-20 19:14:09
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:10
>> preparing weight info...		2022-01-20 19:14:10
>> loading E50h_sampleChr5.bw info...		2022-01-20 19:14:10
------------
>> extracting and calcluating Chr5 signal...		2022-01-20 19:14:10
>> dealing with Chr5 left gene signal...		2022-01-20 19:14:15
>> norming Chr5RP accoring to the whole Chr RP...		2022-01-20 19:14:15
>> merging all Chr RP together...		2022-01-20 19:14:15
>> done		2022-01-20 19:14:15
>> checking seqlevels match...		2022-01-20 19:14:15
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-20 19:14:15
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:16
>> finding overlap peak in gene scan region...		2022-01-20 19:14:16
>> dealing with left peak not your gene scan region...		2022-01-20 19:14:16
>> merging two set peaks...		2022-01-20 19:14:16
>> calculating distance and dealing with gene strand...		2022-01-20 19:14:16
>> merging all info together ...		2022-01-20 19:14:16
>> done		2022-01-20 19:14:16
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-20 19:14:16
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-20 19:14:17
>> calculating RP using centerToTSS and peak score2022-01-20 19:14:17
>> merging all info together		2022-01-20 19:14:19
>> done		2022-01-20 19:14:20
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-20 19:14:20
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-20 19:14:20
>> calculating RP using centerToTSS and peak score2022-01-20 19:14:20
>> merging all info together		2022-01-20 19:14:23
>> done		2022-01-20 19:14:23
>> checking seqlevels match...		2022-01-20 19:14:23
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-20 19:14:23
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:24
>> finding overlap peak in gene scan region...		2022-01-20 19:14:24
>> dealing with left peak not your gene scan region...		2022-01-20 19:14:24
>> merging two set peaks...		2022-01-20 19:14:24
>> calculating distance and dealing with gene strand...		2022-01-20 19:14:24
>> merging all info together ...		2022-01-20 19:14:24
>> done		2022-01-20 19:14:24
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-20 19:14:24
>> calculating RP using centerToTSS and TF hit		2022-01-20 19:14:25
>> merging all info together		2022-01-20 19:14:25
>> done		2022-01-20 19:14:25
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-20 19:14:25
>> calculating RP using centerToTSS and TF hit		2022-01-20 19:14:26
>> merging all info together		2022-01-20 19:14:26
>> done		2022-01-20 19:14:26
>> checking seqlevels match...		2022-01-20 19:14:26
>> 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...		2022-01-20 19:14:26
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:27
>> finding overlap peak in gene scan region...		2022-01-20 19:14:27
>> dealing with left peak not your gene scan region...		2022-01-20 19:14:27
>> merging two set peaks...		2022-01-20 19:14:27
>> calculating distance and dealing with gene strand...		2022-01-20 19:14:27
>> merging all info together ...		2022-01-20 19:14:27
>> done		2022-01-20 19:14:27
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-20 19:14:27
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2022-01-20 19:14:28
>> calculating RP using centerToTSS and peak score2022-01-20 19:14:28
>> merging all info together		2022-01-20 19:14:30
>> done		2022-01-20 19:14:30
>> extracting RP info from regionRP...		2022-01-20 19:14:31
>> dealing with TF_GR_databse...		2022-01-20 19:14:31
>> calculating percent and p-value...		2022-01-20 19:14:31
>> dealing withE5_0h_R1...		2022-01-20 19:14:31
>> dealing withE5_0h_R2...		2022-01-20 19:14:31
>> dealing withE5_4h_R1...		2022-01-20 19:14:31
>> dealing withE5_4h_R2...		2022-01-20 19:14:31
>> dealing withE5_8h_R1...		2022-01-20 19:14:31
>> dealing withE5_8h_R2...		2022-01-20 19:14:31
>> dealing withE5_16h_R1...		2022-01-20 19:14:31
>> dealing withE5_16h_R2...		2022-01-20 19:14:31
>> dealing withE5_24h_R1...		2022-01-20 19:14:31
>> dealing withE5_24h_R2...		2022-01-20 19:14:31
>> dealing withE5_48h_R1...		2022-01-20 19:14:31
>> dealing withE5_48h_R2...		2022-01-20 19:14:31
>> dealing withE5_48h_R3...		2022-01-20 19:14:31
>> dealing withE5_72h_R1...		2022-01-20 19:14:31
>> dealing withE5_72h_R2...		2022-01-20 19:14:31
>> dealing withE5_72h_R3...		2022-01-20 19:14:31
>> merging all info together...		2022-01-20 19:14:31
>> done		2022-01-20 19:14:32
>> preparing gene features information...		2022-01-20 19:14:32
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:32
>> calculating p-value for each TF, which may be time consuming...		2022-01-20 19:14:32
>> merging all info together...		2022-01-20 19:14:32
>> done		2022-01-20 19:14:32
>> dealing with TF_GR_database...		2022-01-20 19:14:33
>> calculating coef and converting into z-score using INT...		2022-01-20 19:14:33
>> dealing withE5_0h_R1...		2022-01-20 19:14:33
>> dealing withE5_0h_R2...		2022-01-20 19:14:33
>> dealing withE5_4h_R1...		2022-01-20 19:14:33
>> dealing withE5_4h_R2...		2022-01-20 19:14:33
>> dealing withE5_8h_R1...		2022-01-20 19:14:33
>> dealing withE5_8h_R2...		2022-01-20 19:14:33
>> dealing withE5_16h_R1...		2022-01-20 19:14:33
>> dealing withE5_16h_R2...		2022-01-20 19:14:33
>> dealing withE5_24h_R1...		2022-01-20 19:14:33
>> dealing withE5_24h_R2...		2022-01-20 19:14:34
>> dealing withE5_48h_R1...		2022-01-20 19:14:34
>> dealing withE5_48h_R2...		2022-01-20 19:14:34
>> dealing withE5_48h_R3...		2022-01-20 19:14:34
>> dealing withE5_72h_R1...		2022-01-20 19:14:34
>> dealing withE5_72h_R2...		2022-01-20 19:14:34
>> dealing withE5_72h_R3...		2022-01-20 19:14:34
>> merging all info together...		2022-01-20 19:14:34
>> done		2022-01-20 19:14:34
>> checking seqlevels match...		2022-01-20 19:14:34
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2022-01-20 19:14:34
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:35
>> finding overlap peak in gene scan region...		2022-01-20 19:14:35
>> dealing with left peak not your gene scan region...		2022-01-20 19:14:35
>> merging two set peaks...		2022-01-20 19:14:35
>> calculating distance and dealing with gene strand...		2022-01-20 19:14:35
>> merging all info together ...		2022-01-20 19:14:35
>> done		2022-01-20 19:14:35
>> calculating peakCenter to TSS using peak-gene pair...		2022-01-20 19:14:35
>> calculating RP using centerToTSS and TF hit		2022-01-20 19:14:37
>> merging all info together		2022-01-20 19:14:37
>> done		2022-01-20 19:14:37
>> checking seqlevels match...		2022-01-20 19:14:38
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-20 19:14:38
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2022-01-20 19:14:40
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-01-20 19:14:40
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-20 19:14:41
>> finding nearest gene and calculating distance...		2022-01-20 19:14:41
>> dealing with gene strand ...		2022-01-20 19:14:41
>> merging all info together ...		2022-01-20 19:14:41
>> done		2022-01-20 19:14:41
>> checking seqlevels match...		2022-01-20 19:14:41
>> 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...		2022-01-20 19:14:41
>> 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...		2022-01-20 19:14:41
>> finding nearest gene and calculating distance...		2022-01-20 19:14:42
>> dealing with gene strand ...		2022-01-20 19:14:42
>> merging all info together ...		2022-01-20 19:14:42
>> done		2022-01-20 19:14:42
>> checking seqlevels match...		2022-01-20 19:14:43
>> 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...		2022-01-20 19:14:43
>> 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...		2022-01-20 19:14:43
>> finding nearest gene and calculating distance...		2022-01-20 19:14:44
>> dealing with gene strand ...		2022-01-20 19:14:44
>> merging all info together ...		2022-01-20 19:14:44
>> done		2022-01-20 19:14:44
>> checking seqlevels match...		2022-01-20 19:14:45
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2022-01-20 19:14:45
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2022-01-20 19:14:45
>> finding nearest gene and calculating distance...		2022-01-20 19:14:45
>> dealing with gene strand ...		2022-01-20 19:14:46
>> merging all info together ...		2022-01-20 19:14:46
>> done		2022-01-20 19:14:46
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-20 19:14:46
>> 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...		2022-01-20 19:14:47
>> 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...		2022-01-20 19:14:47
>> finding nearest gene and calculating distance...		2022-01-20 19:14:47
>> dealing with gene strand ...		2022-01-20 19:14:47
>> merging all info together ...		2022-01-20 19:14:47
>> done		2022-01-20 19:14:47
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2022-01-20 19:14:48
>> 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...		2022-01-20 19:14:49
>> 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...		2022-01-20 19:14:50
>> checking seqlevels match...		2022-01-20 19:14:50
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:51
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-20 19:14:52
>> merging all info together...		2022-01-20 19:14:52
>> done		2022-01-20 19:14:52
>> checking seqlevels match...		2022-01-20 19:14:52
>> 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...		2022-01-20 19:14:52
>> checking seqlevels match...		2022-01-20 19:14:53
>> 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...		2022-01-20 19:14:53
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-20 19:14:54
>> checking seqlevels match...		2022-01-20 19:14:54
>> 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...		2022-01-20 19:14:54
>> calculating cor and pvalue, which may be time consuming...		2022-01-20 19:14:54
>> merging all info together...		2022-01-20 19:14:55
>> done		2022-01-20 19:14:55
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-20 19:14:55
>> merging all info together...		2022-01-20 19:14:55
>> done		2022-01-20 19:14:55
>> checking seqlevels match...		2022-01-20 19:14:55
>> 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...		2022-01-20 19:14:55
>> some scan range may cross Chr bound, trimming...		2022-01-20 19:14:56
>> finding overlap peak in gene scan region...		2022-01-20 19:14:56
>> dealing with left peak not your gene scan region...		2022-01-20 19:14:56
>> merging two set peaks...		2022-01-20 19:14:56
>> calculating distance and dealing with gene strand...		2022-01-20 19:14:56
>> merging all info together ...		2022-01-20 19:14:56
>> done		2022-01-20 19:14:56
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2022-01-20 19:14:57
>> merging all info together...		2022-01-20 19:14:57
>> done		2022-01-20 19:14:57
>> checking seqlevels match...		2022-01-20 19:14:57
>> 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...		2022-01-20 19:14:57
>> checking seqlevels match...		2022-01-20 19:14:57
>> 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...		2022-01-20 19:14:58
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2022-01-20 19:14:58
>> checking seqlevels match...		2022-01-20 19:14:58
>> 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...		2022-01-20 19:14:59
>> calculating cor and pvalue, which may be time consuming...		2022-01-20 19:15:00
>> merging all info together...		2022-01-20 19:15:00
>> done		2022-01-20 19:15:00
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 65 ]
> 
> proc.time()
   user  system elapsed 
 60.803   2.768  63.561 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database000
calcRP_TFHit3.6090.1473.785
calcRP_coverage4.0131.1565.169
calcRP_region4.1250.0804.206
enhancerPromoterCor2.3600.0282.388
findIT_MARA0.2720.0000.272
findIT_TFHit1.0140.0201.034
findIT_TTPair0.0650.0040.069
findIT_enrichFisher0.1920.0000.192
findIT_enrichWilcox0.1480.0040.151
findIT_regionRP5.1640.0125.176
getAssocPairNumber1.1990.0161.216
integrate_ChIP_RNA1.9050.0001.905
integrate_replicates0.0010.0020.002
jaccard_findIT_TTpair0.0790.0060.084
jaccard_findIT_enrichFisher0.1750.0000.175
loadPeakFile0.0500.0040.054
mm_geneBound1.1180.0121.130
mm_geneScan1.1050.0061.111
mm_nearestGene1.0580.0121.070
peakGeneCor1.9620.0121.974
plot_annoDistance1.3360.0081.344
plot_peakGeneAlias_summary2.0630.0162.079
plot_peakGeneCor2.3050.0102.315
test_geneSet0.0010.0000.001