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HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
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CHECK results for FindIT2 on merida1


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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindIT2.git to
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raw results

Package 668/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.5.0  (landing page)
Guandong Shang
Snapshot Date: 2023-01-26 14:00:20 -0500 (Thu, 26 Jan 2023)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: master
git_last_commit: db4c20d
git_last_commit_date: 2022-11-01 11:25:15 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FindIT2
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.5.0.tar.gz
StartedAt: 2023-01-27 01:21:01 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 01:35:42 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 881.6 seconds
RetCode: 0
Status:   OK  
CheckDir: FindIT2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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     13.032  0.189  19.042
calcRP_region       10.133  0.188  14.611
calcRP_coverage      6.394  0.543   9.510
calcRP_TFHit         6.497  0.161   9.399
plot_peakGeneCor     6.493  0.049   9.243
enhancerPromoterCor  5.601  0.059   7.476
peakGeneCor          5.172  0.050   7.266
integrate_ChIP_RNA   4.090  0.039   5.875
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘FindIT2’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FindIT2)

Tests output

FindIT2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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

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

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

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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) {
+     stop("unable to load TxDb.Athaliana.BioMart.plantsmart28")
+ }
Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28
> 
> test_check("FindIT2")
>> preparing gene features information...		2023-01-27 01:32:55
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:32:59
>> preparing weight info...		2023-01-27 01:32:59
>> loading E50h_sampleChr5.bw info...		2023-01-27 01:32:59
------------
>> extracting and calcluating Chr5 signal...		2023-01-27 01:33:00
>> dealing with Chr5 left gene signal...		2023-01-27 01:33:07
>> norming Chr5RP accoring to the whole Chr RP...		2023-01-27 01:33:08
>> merging all Chr RP together...		2023-01-27 01:33:08
>> done		2023-01-27 01:33:08
>> checking seqlevels match...		2023-01-27 01:33:08
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-01-27 01:33:08
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:33:11
>> finding overlap peak in gene scan region...		2023-01-27 01:33:11
>> dealing with left peak not your gene scan region...		2023-01-27 01:33:11
>> merging two set peaks...		2023-01-27 01:33:11
>> calculating distance and dealing with gene strand...		2023-01-27 01:33:12
>> merging all info together ...		2023-01-27 01:33:12
>> done		2023-01-27 01:33:12
>> calculating peakCenter to TSS using peak-gene pair...		2023-01-27 01:33:12
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-01-27 01:33:14
>> calculating RP using centerToTSS and peak score2023-01-27 01:33:14
>> merging all info together		2023-01-27 01:33:20
>> done		2023-01-27 01:33:22
>> calculating peakCenter to TSS using peak-gene pair...		2023-01-27 01:33:23
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-01-27 01:33:25
>> calculating RP using centerToTSS and peak score2023-01-27 01:33:25
>> merging all info together		2023-01-27 01:33:33
>> done		2023-01-27 01:33:34
>> checking seqlevels match...		2023-01-27 01:33:34
>> 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...		2023-01-27 01:33:35
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:33:37
>> finding overlap peak in gene scan region...		2023-01-27 01:33:37
>> dealing with left peak not your gene scan region...		2023-01-27 01:33:37
>> merging two set peaks...		2023-01-27 01:33:37
>> calculating distance and dealing with gene strand...		2023-01-27 01:33:37
>> merging all info together ...		2023-01-27 01:33:38
>> done		2023-01-27 01:33:38
>> calculating peakCenter to TSS using peak-gene pair...		2023-01-27 01:33:38
>> calculating RP using centerToTSS and TF hit		2023-01-27 01:33:39
>> merging all info together		2023-01-27 01:33:39
>> done		2023-01-27 01:33:40
>> calculating peakCenter to TSS using peak-gene pair...		2023-01-27 01:33:40
>> calculating RP using centerToTSS and TF hit		2023-01-27 01:33:42
>> merging all info together		2023-01-27 01:33:42
>> done		2023-01-27 01:33:42
>> checking seqlevels match...		2023-01-27 01:33:45
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-01-27 01:33:45
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:33:47
>> finding overlap peak in gene scan region...		2023-01-27 01:33:47
>> dealing with left peak not your gene scan region...		2023-01-27 01:33:47
>> merging two set peaks...		2023-01-27 01:33:47
>> calculating distance and dealing with gene strand...		2023-01-27 01:33:48
>> merging all info together ...		2023-01-27 01:33:48
>> done		2023-01-27 01:33:48
>> calculating peakCenter to TSS using peak-gene pair...		2023-01-27 01:33:48
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2023-01-27 01:33:50
>> calculating RP using centerToTSS and peak score2023-01-27 01:33:50
>> merging all info together		2023-01-27 01:33:56
>> done		2023-01-27 01:33:57
>> extracting RP info from regionRP...		2023-01-27 01:34:00
>> dealing with TF_GR_databse...		2023-01-27 01:34:00
>> calculating percent and p-value...		2023-01-27 01:34:01
>> dealing withE5_0h_R1...		2023-01-27 01:34:01
>> dealing withE5_0h_R2...		2023-01-27 01:34:01
>> dealing withE5_4h_R1...		2023-01-27 01:34:01
>> dealing withE5_4h_R2...		2023-01-27 01:34:01
>> dealing withE5_8h_R1...		2023-01-27 01:34:01
>> dealing withE5_8h_R2...		2023-01-27 01:34:01
>> dealing withE5_16h_R1...		2023-01-27 01:34:01
>> dealing withE5_16h_R2...		2023-01-27 01:34:01
>> dealing withE5_24h_R1...		2023-01-27 01:34:02
>> dealing withE5_24h_R2...		2023-01-27 01:34:02
>> dealing withE5_48h_R1...		2023-01-27 01:34:02
>> dealing withE5_48h_R2...		2023-01-27 01:34:02
>> dealing withE5_48h_R3...		2023-01-27 01:34:02
>> dealing withE5_72h_R1...		2023-01-27 01:34:02
>> dealing withE5_72h_R2...		2023-01-27 01:34:02
>> dealing withE5_72h_R3...		2023-01-27 01:34:02
>> merging all info together...		2023-01-27 01:34:02
>> done		2023-01-27 01:34:03
>> preparing gene features information...		2023-01-27 01:34:03
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:34:05
>> calculating p-value for each TF, which may be time consuming...		2023-01-27 01:34:05
>> merging all info together...		2023-01-27 01:34:05
>> done		2023-01-27 01:34:05
>> dealing with TF_GR_database...		2023-01-27 01:34:06
>> calculating coef and converting into z-score using INT...		2023-01-27 01:34:07
>> dealing with E5_0h_R1...		2023-01-27 01:34:07
>> dealing with E5_0h_R2...		2023-01-27 01:34:07
>> dealing with E5_4h_R1...		2023-01-27 01:34:07
>> dealing with E5_4h_R2...		2023-01-27 01:34:08
>> dealing with E5_8h_R1...		2023-01-27 01:34:08
>> dealing with E5_8h_R2...		2023-01-27 01:34:08
>> dealing with E5_16h_R1...		2023-01-27 01:34:08
>> dealing with E5_16h_R2...		2023-01-27 01:34:08
>> dealing with E5_24h_R1...		2023-01-27 01:34:09
>> dealing with E5_24h_R2...		2023-01-27 01:34:09
>> dealing with E5_48h_R1...		2023-01-27 01:34:09
>> dealing with E5_48h_R2...		2023-01-27 01:34:09
>> dealing with E5_48h_R3...		2023-01-27 01:34:10
>> dealing with E5_72h_R1...		2023-01-27 01:34:10
>> dealing with E5_72h_R2...		2023-01-27 01:34:10
>> dealing with E5_72h_R3...		2023-01-27 01:34:10
>> merging all info together...		2023-01-27 01:34:11
>> done		2023-01-27 01:34:11
>> checking seqlevels match...		2023-01-27 01:34:11
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-01-27 01:34:12
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:34:14
>> finding overlap peak in gene scan region...		2023-01-27 01:34:14
>> dealing with left peak not your gene scan region...		2023-01-27 01:34:14
>> merging two set peaks...		2023-01-27 01:34:14
>> calculating distance and dealing with gene strand...		2023-01-27 01:34:14
>> merging all info together ...		2023-01-27 01:34:14
>> done		2023-01-27 01:34:14
>> calculating peakCenter to TSS using peak-gene pair...		2023-01-27 01:34:14
>> calculating RP using centerToTSS and TF hit		2023-01-27 01:34:16
>> merging all info together		2023-01-27 01:34:16
>> done		2023-01-27 01:34:17
>> checking seqlevels match...		2023-01-27 01:34:18
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-01-27 01:34:18
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2023-01-27 01:34:27
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2023-01-27 01:34:27
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-01-27 01:34:27
>> finding nearest gene and calculating distance...		2023-01-27 01:34:29
>> dealing with gene strand ...		2023-01-27 01:34:29
>> merging all info together ...		2023-01-27 01:34:29
>> done		2023-01-27 01:34:29
>> checking seqlevels match...		2023-01-27 01:34:29
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2023-01-27 01:34:30
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-01-27 01:34:30
>> finding nearest gene and calculating distance...		2023-01-27 01:34:32
>> dealing with gene strand ...		2023-01-27 01:34:32
>> merging all info together ...		2023-01-27 01:34:32
>> done		2023-01-27 01:34:32
>> checking seqlevels match...		2023-01-27 01:34:34
>> 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
>> checking seqlevels match...		2023-01-27 01:34:34
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2023-01-27 01:34:35
>> finding nearest gene and calculating distance...		2023-01-27 01:34:36
>> dealing with gene strand ...		2023-01-27 01:34:37
>> merging all info together ...		2023-01-27 01:34:37
>> done		2023-01-27 01:34:37
>> checking seqlevels match...		2023-01-27 01:34:39
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2023-01-27 01:34:40
>> 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...		2023-01-27 01:34:40
>> finding nearest gene and calculating distance...		2023-01-27 01:34:42
>> dealing with gene strand ...		2023-01-27 01:34:42
>> merging all info together ...		2023-01-27 01:34:42
>> done		2023-01-27 01:34:42
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-01-27 01:34:45
>> 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...		2023-01-27 01:34:45
>> 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...		2023-01-27 01:34:45
>> finding nearest gene and calculating distance...		2023-01-27 01:34:47
>> dealing with gene strand ...		2023-01-27 01:34:48
>> merging all info together ...		2023-01-27 01:34:48
>> done		2023-01-27 01:34:48
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2023-01-27 01:34:50
>> 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
>> checking seqlevels match...		2023-01-27 01:34:53
>> 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...		2023-01-27 01:34:55
>> checking seqlevels match...		2023-01-27 01:34:57
>> 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...		2023-01-27 01:35:00
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-01-27 01:35:04
>> merging all info together...		2023-01-27 01:35:04
>> done		2023-01-27 01:35:04
>> checking seqlevels match...		2023-01-27 01:35:04
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene...		2023-01-27 01:35:05
>> checking seqlevels match...		2023-01-27 01:35:05
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:35:07
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-01-27 01:35:08
>> checking seqlevels match...		2023-01-27 01:35:08
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:35:10
>> calculating cor and pvalue, which may be time consuming...		2023-01-27 01:35:10
>> merging all info together...		2023-01-27 01:35:11
>> done		2023-01-27 01:35:11
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-01-27 01:35:11
>> merging all info together...		2023-01-27 01:35:11
>> done		2023-01-27 01:35:11
>> checking seqlevels match...		2023-01-27 01:35:12
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2023-01-27 01:35:12
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:35:14
>> finding overlap peak in gene scan region...		2023-01-27 01:35:14
>> dealing with left peak not your gene scan region...		2023-01-27 01:35:14
>> merging two set peaks...		2023-01-27 01:35:15
>> calculating distance and dealing with gene strand...		2023-01-27 01:35:15
>> merging all info together ...		2023-01-27 01:35:15
>> done		2023-01-27 01:35:15
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2023-01-27 01:35:19
>> merging all info together...		2023-01-27 01:35:19
>> done		2023-01-27 01:35:19
>> checking seqlevels match...		2023-01-27 01:35:19
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> using scanPromoter parameter to scan promoter for each gene...		2023-01-27 01:35:19
>> checking seqlevels match...		2023-01-27 01:35:19
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:35:22
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2023-01-27 01:35:23
>> checking seqlevels match...		2023-01-27 01:35:23
>> 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
>> some scan range may cross Chr bound, trimming...		2023-01-27 01:35:25
>> calculating cor and pvalue, which may be time consuming...		2023-01-27 01:35:25
>> merging all info together...		2023-01-27 01:35:26
>> done		2023-01-27 01:35:26
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 
129.346   2.540 186.349 

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0000.0000.001
calcRP_TFHit6.4970.1619.399
calcRP_coverage6.3940.5439.510
calcRP_region10.133 0.18814.611
enhancerPromoterCor5.6010.0597.476
findIT_MARA0.9240.0101.155
findIT_TFHit1.9720.0582.715
findIT_TTPair0.2020.0080.292
findIT_enrichFisher0.3440.0050.487
findIT_enrichWilcox0.3940.0060.568
findIT_regionRP13.032 0.18919.042
getAssocPairNumber2.3020.0243.416
integrate_ChIP_RNA4.0900.0395.875
integrate_replicates0.0040.0010.004
jaccard_findIT_TTpair0.2840.0080.410
jaccard_findIT_enrichFisher0.4620.0050.658
loadPeakFile0.1220.0010.175
mm_geneBound2.3250.0193.299
mm_geneScan2.4030.0223.292
mm_nearestGene2.0830.0292.932
peakGeneCor5.1720.0507.266
plot_annoDistance2.8260.0313.896
plot_peakGeneAlias_summary2.7110.0293.701
plot_peakGeneCor6.4930.0499.243
test_geneSet0.0000.0010.001