Guandong Shang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (Tue, 28 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:59 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 642/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.0.3 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FindIT2 |
| Version: 1.0.3 |
| 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_1.0.3.tar.gz |
| StartedAt: 2022-04-12 13:17:45 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 13:26:30 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 524.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.0.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/FindIT2.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 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 12.007 0.126 12.163
calcRP_region 8.707 0.176 8.891
calcRP_coverage 6.215 0.852 7.078
calcRP_TFHit 5.939 0.197 6.219
plot_peakGeneCor 5.331 0.063 5.397
* 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
FindIT2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
FindIT2.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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, 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... 2022-04-12 13:24:45
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:24:47
>> preparing weight info... 2022-04-12 13:24:47
>> loading E50h_sampleChr5.bw info... 2022-04-12 13:24:47
------------
>> extracting and calcluating Chr5 signal... 2022-04-12 13:24:47
>> dealing with Chr5 left gene signal... 2022-04-12 13:24:52
>> norming Chr5RP accoring to the whole Chr RP... 2022-04-12 13:24:53
>> merging all Chr RP together... 2022-04-12 13:24:53
>> done 2022-04-12 13:24:53
>> checking seqlevels match... 2022-04-12 13:24:53
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2022-04-12 13:24:53
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:24:55
>> finding overlap peak in gene scan region... 2022-04-12 13:24:55
>> dealing with left peak not your gene scan region... 2022-04-12 13:24:55
>> merging two set peaks... 2022-04-12 13:24:55
>> calculating distance and dealing with gene strand... 2022-04-12 13:24:55
>> merging all info together ... 2022-04-12 13:24:55
>> done 2022-04-12 13:24:55
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 13:24:55
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 13:24:57
>> calculating RP using centerToTSS and peak score2022-04-12 13:24:57
>> merging all info together 2022-04-12 13:25:00
>> done 2022-04-12 13:25:02
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 13:25:02
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 13:25:03
>> calculating RP using centerToTSS and peak score2022-04-12 13:25:03
>> merging all info together 2022-04-12 13:25:08
>> done 2022-04-12 13:25:09
>> checking seqlevels match... 2022-04-12 13:25:09
>> 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... 2022-04-12 13:25:09
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:25:11
>> finding overlap peak in gene scan region... 2022-04-12 13:25:11
>> dealing with left peak not your gene scan region... 2022-04-12 13:25:11
>> merging two set peaks... 2022-04-12 13:25:11
>> calculating distance and dealing with gene strand... 2022-04-12 13:25:12
>> merging all info together ... 2022-04-12 13:25:12
>> done 2022-04-12 13:25:12
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 13:25:12
>> calculating RP using centerToTSS and TF hit 2022-04-12 13:25:13
>> merging all info together 2022-04-12 13:25:13
>> done 2022-04-12 13:25:13
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 13:25:13
>> calculating RP using centerToTSS and TF hit 2022-04-12 13:25:15
>> merging all info together 2022-04-12 13:25:15
>> done 2022-04-12 13:25:15
>> checking seqlevels match... 2022-04-12 13:25:16
>> 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... 2022-04-12 13:25:16
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:25:18
>> finding overlap peak in gene scan region... 2022-04-12 13:25:18
>> dealing with left peak not your gene scan region... 2022-04-12 13:25:18
>> merging two set peaks... 2022-04-12 13:25:18
>> calculating distance and dealing with gene strand... 2022-04-12 13:25:18
>> merging all info together ... 2022-04-12 13:25:18
>> done 2022-04-12 13:25:18
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 13:25:18
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 13:25:20
>> calculating RP using centerToTSS and peak score2022-04-12 13:25:20
>> merging all info together 2022-04-12 13:25:23
>> done 2022-04-12 13:25:24
>> extracting RP info from regionRP... 2022-04-12 13:25:25
>> dealing with TF_GR_databse... 2022-04-12 13:25:25
>> calculating percent and p-value... 2022-04-12 13:25:25
>> dealing withE5_0h_R1... 2022-04-12 13:25:25
>> dealing withE5_0h_R2... 2022-04-12 13:25:26
>> dealing withE5_4h_R1... 2022-04-12 13:25:26
>> dealing withE5_4h_R2... 2022-04-12 13:25:26
>> dealing withE5_8h_R1... 2022-04-12 13:25:26
>> dealing withE5_8h_R2... 2022-04-12 13:25:26
>> dealing withE5_16h_R1... 2022-04-12 13:25:26
>> dealing withE5_16h_R2... 2022-04-12 13:25:26
>> dealing withE5_24h_R1... 2022-04-12 13:25:26
>> dealing withE5_24h_R2... 2022-04-12 13:25:26
>> dealing withE5_48h_R1... 2022-04-12 13:25:26
>> dealing withE5_48h_R2... 2022-04-12 13:25:26
>> dealing withE5_48h_R3... 2022-04-12 13:25:26
>> dealing withE5_72h_R1... 2022-04-12 13:25:26
>> dealing withE5_72h_R2... 2022-04-12 13:25:26
>> dealing withE5_72h_R3... 2022-04-12 13:25:26
>> merging all info together... 2022-04-12 13:25:26
>> done 2022-04-12 13:25:27
>> preparing gene features information... 2022-04-12 13:25:27
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:25:28
>> calculating p-value for each TF, which may be time consuming... 2022-04-12 13:25:28
>> merging all info together... 2022-04-12 13:25:29
>> done 2022-04-12 13:25:29
>> dealing with TF_GR_database... 2022-04-12 13:25:29
>> calculating coef and converting into z-score using INT... 2022-04-12 13:25:29
>> dealing withE5_0h_R1... 2022-04-12 13:25:29
>> dealing withE5_0h_R2... 2022-04-12 13:25:30
>> dealing withE5_4h_R1... 2022-04-12 13:25:30
>> dealing withE5_4h_R2... 2022-04-12 13:25:30
>> dealing withE5_8h_R1... 2022-04-12 13:25:30
>> dealing withE5_8h_R2... 2022-04-12 13:25:30
>> dealing withE5_16h_R1... 2022-04-12 13:25:31
>> dealing withE5_16h_R2... 2022-04-12 13:25:31
>> dealing withE5_24h_R1... 2022-04-12 13:25:31
>> dealing withE5_24h_R2... 2022-04-12 13:25:31
>> dealing withE5_48h_R1... 2022-04-12 13:25:31
>> dealing withE5_48h_R2... 2022-04-12 13:25:31
>> dealing withE5_48h_R3... 2022-04-12 13:25:32
>> dealing withE5_72h_R1... 2022-04-12 13:25:32
>> dealing withE5_72h_R2... 2022-04-12 13:25:32
>> dealing withE5_72h_R3... 2022-04-12 13:25:32
>> merging all info together... 2022-04-12 13:25:32
>> done 2022-04-12 13:25:32
>> checking seqlevels match... 2022-04-12 13:25:33
>> 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... 2022-04-12 13:25:33
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:25:34
>> finding overlap peak in gene scan region... 2022-04-12 13:25:34
>> dealing with left peak not your gene scan region... 2022-04-12 13:25:34
>> merging two set peaks... 2022-04-12 13:25:34
>> calculating distance and dealing with gene strand... 2022-04-12 13:25:34
>> merging all info together ... 2022-04-12 13:25:34
>> done 2022-04-12 13:25:35
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 13:25:35
>> calculating RP using centerToTSS and TF hit 2022-04-12 13:25:36
>> merging all info together 2022-04-12 13:25:36
>> done 2022-04-12 13:25:36
>> checking seqlevels match... 2022-04-12 13:25:37
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-04-12 13:25:37
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-04-12 13:25:42
>> 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... 2022-04-12 13:25:43
>> 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... 2022-04-12 13:25:43
>> finding nearest gene and calculating distance... 2022-04-12 13:25:44
>> dealing with gene strand ... 2022-04-12 13:25:45
>> merging all info together ... 2022-04-12 13:25:45
>> done 2022-04-12 13:25:45
>> checking seqlevels match... 2022-04-12 13:25:45
>> 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... 2022-04-12 13:25:46
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 13:25:46
>> finding nearest gene and calculating distance... 2022-04-12 13:25:47
>> dealing with gene strand ... 2022-04-12 13:25:47
>> merging all info together ... 2022-04-12 13:25:47
>> done 2022-04-12 13:25:47
>> checking seqlevels match... 2022-04-12 13:25:48
>> 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... 2022-04-12 13:25:48
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 13:25:48
>> finding nearest gene and calculating distance... 2022-04-12 13:25:50
>> dealing with gene strand ... 2022-04-12 13:25:50
>> merging all info together ... 2022-04-12 13:25:50
>> done 2022-04-12 13:25:50
>> checking seqlevels match... 2022-04-12 13:25:51
>> 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... 2022-04-12 13:25:52
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 13:25:52
>> finding nearest gene and calculating distance... 2022-04-12 13:25:53
>> dealing with gene strand ... 2022-04-12 13:25:53
>> merging all info together ... 2022-04-12 13:25:53
>> done 2022-04-12 13:25:53
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-04-12 13:25:54
>> 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
>> checking seqlevels match... 2022-04-12 13:25:55
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 13:25:55
>> finding nearest gene and calculating distance... 2022-04-12 13:25:56
>> dealing with gene strand ... 2022-04-12 13:25:56
>> merging all info together ... 2022-04-12 13:25:56
>> done 2022-04-12 13:25:56
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-04-12 13:25:58
>> 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
>> checking seqlevels match... 2022-04-12 13:25:59
>> 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... 2022-04-12 13:26:00
>> checking seqlevels match... 2022-04-12 13:26:02
>> 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... 2022-04-12 13:26:03
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 13:26:05
>> merging all info together... 2022-04-12 13:26:05
>> done 2022-04-12 13:26:06
>> checking seqlevels match... 2022-04-12 13:26:06
>> 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... 2022-04-12 13:26:06
>> checking seqlevels match... 2022-04-12 13:26:06
>> 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... 2022-04-12 13:26:07
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-04-12 13:26:08
>> checking seqlevels match... 2022-04-12 13:26:08
>> 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... 2022-04-12 13:26:09
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 13:26:10
>> merging all info together... 2022-04-12 13:26:10
>> done 2022-04-12 13:26:10
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 13:26:10
>> merging all info together... 2022-04-12 13:26:10
>> done 2022-04-12 13:26:11
>> checking seqlevels match... 2022-04-12 13:26:11
>> 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... 2022-04-12 13:26:11
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:26:12
>> finding overlap peak in gene scan region... 2022-04-12 13:26:12
>> dealing with left peak not your gene scan region... 2022-04-12 13:26:12
>> merging two set peaks... 2022-04-12 13:26:13
>> calculating distance and dealing with gene strand... 2022-04-12 13:26:13
>> merging all info together ... 2022-04-12 13:26:13
>> done 2022-04-12 13:26:13
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 13:26:15
>> merging all info together... 2022-04-12 13:26:15
>> done 2022-04-12 13:26:15
>> checking seqlevels match... 2022-04-12 13:26:15
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2022-04-12 13:26:15
>> checking seqlevels match... 2022-04-12 13:26:15
>> 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
>> some scan range may cross Chr bound, trimming... 2022-04-12 13:26:17
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-04-12 13:26:17
>> checking seqlevels match... 2022-04-12 13:26:17
>> 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... 2022-04-12 13:26:19
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 13:26:19
>> merging all info together... 2022-04-12 13:26:19
>> done 2022-04-12 13:26:20
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
111.304 2.756 114.183
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0.001 | 0.001 | 0.001 | |
| calcRP_TFHit | 5.939 | 0.197 | 6.219 | |
| calcRP_coverage | 6.215 | 0.852 | 7.078 | |
| calcRP_region | 8.707 | 0.176 | 8.891 | |
| enhancerPromoterCor | 4.919 | 0.050 | 4.975 | |
| findIT_MARA | 0.845 | 0.055 | 0.901 | |
| findIT_TFHit | 1.779 | 0.027 | 1.807 | |
| findIT_TTPair | 0.156 | 0.008 | 0.163 | |
| findIT_enrichFisher | 0.346 | 0.004 | 0.350 | |
| findIT_enrichWilcox | 0.376 | 0.006 | 0.383 | |
| findIT_regionRP | 12.007 | 0.126 | 12.163 | |
| getAssocPairNumber | 2.385 | 0.023 | 2.412 | |
| integrate_ChIP_RNA | 4.785 | 0.046 | 4.839 | |
| integrate_replicates | 0.003 | 0.001 | 0.003 | |
| jaccard_findIT_TTpair | 0.223 | 0.006 | 0.229 | |
| jaccard_findIT_enrichFisher | 0.445 | 0.004 | 0.451 | |
| loadPeakFile | 0.133 | 0.002 | 0.135 | |
| mm_geneBound | 2.056 | 0.029 | 2.087 | |
| mm_geneScan | 2.063 | 0.018 | 2.084 | |
| mm_nearestGene | 1.979 | 0.028 | 2.009 | |
| peakGeneCor | 4.145 | 0.044 | 4.197 | |
| plot_annoDistance | 2.521 | 0.027 | 2.551 | |
| plot_peakGeneAlias_summary | 2.372 | 0.031 | 2.409 | |
| plot_peakGeneCor | 5.331 | 0.063 | 5.397 | |
| test_geneSet | 0.001 | 0.002 | 0.002 | |