Guandong Shang
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_15 |
| git_last_commit: 17dec46 |
| git_last_commit_date: 2022-05-25 06:53:22 -0400 (Wed, 25 May 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:56 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 664/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.2.3 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FindIT2 |
| Version: 1.2.3 |
| 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_1.2.3.tar.gz |
| StartedAt: 2022-10-19 02:25:49 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 02:35:59 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 610.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.2.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/FindIT2.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.2.3’
* 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 11.463 0.097 11.577
calcRP_region 9.601 0.155 9.775
calcRP_coverage 6.181 0.713 6.909
plot_peakGeneCor 6.123 0.084 6.220
calcRP_TFHit 5.984 0.196 6.276
enhancerPromoterCor 5.255 0.062 5.328
peakGeneCor 4.916 0.142 5.067
* 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/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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... 2022-10-19 02:34:05
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:34:08
>> preparing weight info... 2022-10-19 02:34:08
>> loading E50h_sampleChr5.bw info... 2022-10-19 02:34:08
------------
>> extracting and calcluating Chr5 signal... 2022-10-19 02:34:08
>> dealing with Chr5 left gene signal... 2022-10-19 02:34:13
>> norming Chr5RP accoring to the whole Chr RP... 2022-10-19 02:34:13
>> merging all Chr RP together... 2022-10-19 02:34:13
>> done 2022-10-19 02:34:13
>> checking seqlevels match... 2022-10-19 02:34:13
>> 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... 2022-10-19 02:34:13
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:34:16
>> finding overlap peak in gene scan region... 2022-10-19 02:34:16
>> dealing with left peak not your gene scan region... 2022-10-19 02:34:16
>> merging two set peaks... 2022-10-19 02:34:16
>> calculating distance and dealing with gene strand... 2022-10-19 02:34:17
>> merging all info together ... 2022-10-19 02:34:17
>> done 2022-10-19 02:34:17
>> calculating peakCenter to TSS using peak-gene pair... 2022-10-19 02:34:17
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-10-19 02:34:18
>> calculating RP using centerToTSS and peak score2022-10-19 02:34:18
>> merging all info together 2022-10-19 02:34:23
>> done 2022-10-19 02:34:24
>> calculating peakCenter to TSS using peak-gene pair... 2022-10-19 02:34:24
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-10-19 02:34:26
>> calculating RP using centerToTSS and peak score2022-10-19 02:34:26
>> merging all info together 2022-10-19 02:34:31
>> done 2022-10-19 02:34:32
>> checking seqlevels match... 2022-10-19 02:34:33
>> 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... 2022-10-19 02:34:33
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:34:34
>> finding overlap peak in gene scan region... 2022-10-19 02:34:34
>> dealing with left peak not your gene scan region... 2022-10-19 02:34:34
>> merging two set peaks... 2022-10-19 02:34:35
>> calculating distance and dealing with gene strand... 2022-10-19 02:34:35
>> merging all info together ... 2022-10-19 02:34:35
>> done 2022-10-19 02:34:35
>> calculating peakCenter to TSS using peak-gene pair... 2022-10-19 02:34:35
>> calculating RP using centerToTSS and TF hit 2022-10-19 02:34:36
>> merging all info together 2022-10-19 02:34:36
>> done 2022-10-19 02:34:37
>> calculating peakCenter to TSS using peak-gene pair... 2022-10-19 02:34:37
>> calculating RP using centerToTSS and TF hit 2022-10-19 02:34:38
>> merging all info together 2022-10-19 02:34:38
>> done 2022-10-19 02:34:38
>> checking seqlevels match... 2022-10-19 02:34:40
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2022-10-19 02:34:40
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:34:42
>> finding overlap peak in gene scan region... 2022-10-19 02:34:42
>> dealing with left peak not your gene scan region... 2022-10-19 02:34:42
>> merging two set peaks... 2022-10-19 02:34:42
>> calculating distance and dealing with gene strand... 2022-10-19 02:34:42
>> merging all info together ... 2022-10-19 02:34:42
>> done 2022-10-19 02:34:42
>> calculating peakCenter to TSS using peak-gene pair... 2022-10-19 02:34:42
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-10-19 02:34:44
>> calculating RP using centerToTSS and peak score2022-10-19 02:34:44
>> merging all info together 2022-10-19 02:34:48
>> done 2022-10-19 02:34:49
>> extracting RP info from regionRP... 2022-10-19 02:34:51
>> dealing with TF_GR_databse... 2022-10-19 02:34:51
>> calculating percent and p-value... 2022-10-19 02:34:51
>> dealing withE5_0h_R1... 2022-10-19 02:34:51
>> dealing withE5_0h_R2... 2022-10-19 02:34:51
>> dealing withE5_4h_R1... 2022-10-19 02:34:51
>> dealing withE5_4h_R2... 2022-10-19 02:34:51
>> dealing withE5_8h_R1... 2022-10-19 02:34:52
>> dealing withE5_8h_R2... 2022-10-19 02:34:52
>> dealing withE5_16h_R1... 2022-10-19 02:34:52
>> dealing withE5_16h_R2... 2022-10-19 02:34:52
>> dealing withE5_24h_R1... 2022-10-19 02:34:52
>> dealing withE5_24h_R2... 2022-10-19 02:34:52
>> dealing withE5_48h_R1... 2022-10-19 02:34:52
>> dealing withE5_48h_R2... 2022-10-19 02:34:52
>> dealing withE5_48h_R3... 2022-10-19 02:34:52
>> dealing withE5_72h_R1... 2022-10-19 02:34:52
>> dealing withE5_72h_R2... 2022-10-19 02:34:52
>> dealing withE5_72h_R3... 2022-10-19 02:34:52
>> merging all info together... 2022-10-19 02:34:53
>> done 2022-10-19 02:34:53
>> preparing gene features information... 2022-10-19 02:34:53
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:34:55
>> calculating p-value for each TF, which may be time consuming... 2022-10-19 02:34:55
>> merging all info together... 2022-10-19 02:34:55
>> done 2022-10-19 02:34:55
>> dealing with TF_GR_database... 2022-10-19 02:34:55
>> calculating coef and converting into z-score using INT... 2022-10-19 02:34:56
>> dealing with E5_0h_R1... 2022-10-19 02:34:56
>> dealing with E5_0h_R2... 2022-10-19 02:34:56
>> dealing with E5_4h_R1... 2022-10-19 02:34:56
>> dealing with E5_4h_R2... 2022-10-19 02:34:56
>> dealing with E5_8h_R1... 2022-10-19 02:34:57
>> dealing with E5_8h_R2... 2022-10-19 02:34:57
>> dealing with E5_16h_R1... 2022-10-19 02:34:57
>> dealing with E5_16h_R2... 2022-10-19 02:34:57
>> dealing with E5_24h_R1... 2022-10-19 02:34:57
>> dealing with E5_24h_R2... 2022-10-19 02:34:58
>> dealing with E5_48h_R1... 2022-10-19 02:34:58
>> dealing with E5_48h_R2... 2022-10-19 02:34:58
>> dealing with E5_48h_R3... 2022-10-19 02:34:58
>> dealing with E5_72h_R1... 2022-10-19 02:34:58
>> dealing with E5_72h_R2... 2022-10-19 02:34:58
>> dealing with E5_72h_R3... 2022-10-19 02:34:59
>> merging all info together... 2022-10-19 02:34:59
>> done 2022-10-19 02:34:59
>> checking seqlevels match... 2022-10-19 02:34:59
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2022-10-19 02:35:00
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:35:01
>> finding overlap peak in gene scan region... 2022-10-19 02:35:01
>> dealing with left peak not your gene scan region... 2022-10-19 02:35:01
>> merging two set peaks... 2022-10-19 02:35:01
>> calculating distance and dealing with gene strand... 2022-10-19 02:35:01
>> merging all info together ... 2022-10-19 02:35:02
>> done 2022-10-19 02:35:02
>> calculating peakCenter to TSS using peak-gene pair... 2022-10-19 02:35:02
>> calculating RP using centerToTSS and TF hit 2022-10-19 02:35:03
>> merging all info together 2022-10-19 02:35:03
>> done 2022-10-19 02:35:03
>> checking seqlevels match... 2022-10-19 02:35:04
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-10-19 02:35:04
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-10-19 02:35:09
>> 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
>> checking seqlevels match... 2022-10-19 02:35:10
>> 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... 2022-10-19 02:35:10
>> finding nearest gene and calculating distance... 2022-10-19 02:35:12
>> dealing with gene strand ... 2022-10-19 02:35:12
>> merging all info together ... 2022-10-19 02:35:12
>> done 2022-10-19 02:35:12
>> checking seqlevels match... 2022-10-19 02:35:12
>> 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
>> checking seqlevels match... 2022-10-19 02:35:12
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-10-19 02:35:12
>> finding nearest gene and calculating distance... 2022-10-19 02:35:14
>> dealing with gene strand ... 2022-10-19 02:35:14
>> merging all info together ... 2022-10-19 02:35:14
>> done 2022-10-19 02:35:14
>> checking seqlevels match... 2022-10-19 02:35:15
>> 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
>> checking seqlevels match... 2022-10-19 02:35:15
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-10-19 02:35:15
>> finding nearest gene and calculating distance... 2022-10-19 02:35:17
>> dealing with gene strand ... 2022-10-19 02:35:17
>> merging all info together ... 2022-10-19 02:35:17
>> done 2022-10-19 02:35:17
>> checking seqlevels match... 2022-10-19 02:35:18
>> 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... 2022-10-19 02:35:18
>> 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... 2022-10-19 02:35:19
>> finding nearest gene and calculating distance... 2022-10-19 02:35:20
>> dealing with gene strand ... 2022-10-19 02:35:20
>> merging all info together ... 2022-10-19 02:35:20
>> done 2022-10-19 02:35:20
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-10-19 02:35:21
>> 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... 2022-10-19 02:35:22
>> 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... 2022-10-19 02:35:22
>> finding nearest gene and calculating distance... 2022-10-19 02:35:23
>> dealing with gene strand ... 2022-10-19 02:35:23
>> merging all info together ... 2022-10-19 02:35:23
>> done 2022-10-19 02:35:23
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-10-19 02:35:25
>> 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... 2022-10-19 02:35:26
>> 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
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:35:28
>> checking seqlevels match... 2022-10-19 02:35:29
>> 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
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:35:30
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-10-19 02:35:33
>> merging all info together... 2022-10-19 02:35:34
>> done 2022-10-19 02:35:34
>> checking seqlevels match... 2022-10-19 02:35:34
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2022-10-19 02:35:34
>> checking seqlevels match... 2022-10-19 02:35:34
>> 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
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:35:35
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-10-19 02:35:36
>> checking seqlevels match... 2022-10-19 02:35:36
>> 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... 2022-10-19 02:35:37
>> calculating cor and pvalue, which may be time consuming... 2022-10-19 02:35:38
>> merging all info together... 2022-10-19 02:35:38
>> done 2022-10-19 02:35:38
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-10-19 02:35:38
>> merging all info together... 2022-10-19 02:35:38
>> done 2022-10-19 02:35:39
>> checking seqlevels match... 2022-10-19 02:35:39
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2022-10-19 02:35:39
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:35:40
>> finding overlap peak in gene scan region... 2022-10-19 02:35:40
>> dealing with left peak not your gene scan region... 2022-10-19 02:35:40
>> merging two set peaks... 2022-10-19 02:35:41
>> calculating distance and dealing with gene strand... 2022-10-19 02:35:41
>> merging all info together ... 2022-10-19 02:35:41
>> done 2022-10-19 02:35:41
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-10-19 02:35:43
>> merging all info together... 2022-10-19 02:35:43
>> done 2022-10-19 02:35:44
>> checking seqlevels match... 2022-10-19 02:35:44
>> 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... 2022-10-19 02:35:44
>> checking seqlevels match... 2022-10-19 02:35:44
>> 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... 2022-10-19 02:35:45
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-10-19 02:35:46
>> checking seqlevels match... 2022-10-19 02:35:46
>> 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
>> some scan range may cross Chr bound, trimming... 2022-10-19 02:35:47
>> calculating cor and pvalue, which may be time consuming... 2022-10-19 02:35:47
>> merging all info together... 2022-10-19 02:35:48
>> done 2022-10-19 02:35:48
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
123.199 2.711 126.790
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0.000 | 0.000 | 0.001 | |
| calcRP_TFHit | 5.984 | 0.196 | 6.276 | |
| calcRP_coverage | 6.181 | 0.713 | 6.909 | |
| calcRP_region | 9.601 | 0.155 | 9.775 | |
| enhancerPromoterCor | 5.255 | 0.062 | 5.328 | |
| findIT_MARA | 0.906 | 0.014 | 0.922 | |
| findIT_TFHit | 1.702 | 0.022 | 1.726 | |
| findIT_TTPair | 0.167 | 0.007 | 0.174 | |
| findIT_enrichFisher | 0.321 | 0.004 | 0.325 | |
| findIT_enrichWilcox | 0.341 | 0.004 | 0.347 | |
| findIT_regionRP | 11.463 | 0.097 | 11.577 | |
| getAssocPairNumber | 2.391 | 0.026 | 2.451 | |
| integrate_ChIP_RNA | 4.124 | 0.041 | 4.178 | |
| integrate_replicates | 0.004 | 0.001 | 0.005 | |
| jaccard_findIT_TTpair | 0.237 | 0.006 | 0.244 | |
| jaccard_findIT_enrichFisher | 0.433 | 0.004 | 0.438 | |
| loadPeakFile | 0.119 | 0.002 | 0.122 | |
| mm_geneBound | 2.394 | 0.024 | 2.425 | |
| mm_geneScan | 3.210 | 0.026 | 3.241 | |
| mm_nearestGene | 1.986 | 0.025 | 2.014 | |
| peakGeneCor | 4.916 | 0.142 | 5.067 | |
| plot_annoDistance | 2.898 | 0.048 | 3.006 | |
| plot_peakGeneAlias_summary | 2.547 | 0.038 | 2.597 | |
| plot_peakGeneCor | 6.123 | 0.084 | 6.220 | |
| test_geneSet | 0.001 | 0.001 | 0.000 | |