Guandong Shang
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: devel |
| git_last_commit: ad4f102 |
| git_last_commit_date: 2024-02-27 03:41:20 -0400 (Tue, 27 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:43 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 716/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.9.1 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the FindIT2 package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: FindIT2 |
| Version: 1.9.1 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings FindIT2_1.9.1.tar.gz |
| StartedAt: 2024-03-28 05:22:06 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:29:52 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 466.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings FindIT2_1.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.9.1’
* 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 code 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 loading without being on the library search path ... 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
calcRP_coverage 10.714 0.703 11.442
findIT_regionRP 9.656 0.147 9.822
calcRP_region 7.167 0.152 7.334
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
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... 2024-03-28 05:28:29
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:28:31
>> preparing weight info... 2024-03-28 05:28:31
>> loading E50h_sampleChr5.bw info... 2024-03-28 05:28:31
------------
>> extracting and calcluating Chr5 signal... 2024-03-28 05:28:31
>> dealing with Chr5 left gene signal... 2024-03-28 05:28:41
>> norming Chr5RP accoring to the whole Chr RP... 2024-03-28 05:28:41
>> merging all Chr RP together... 2024-03-28 05:28:41
>> done 2024-03-28 05:28:41
>> checking seqlevels match... 2024-03-28 05:28:41
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-03-28 05:28:41
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:28:42
>> finding overlap peak in gene scan region... 2024-03-28 05:28:42
>> dealing with left peak not your gene scan region... 2024-03-28 05:28:43
>> merging two set peaks... 2024-03-28 05:28:43
>> calculating distance and dealing with gene strand... 2024-03-28 05:28:43
>> merging all info together ... 2024-03-28 05:28:43
>> done 2024-03-28 05:28:43
>> calculating peakCenter to TSS using peak-gene pair... 2024-03-28 05:28:43
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-03-28 05:28:44
>> calculating RP using centerToTSS and peak score2024-03-28 05:28:44
>> merging all info together 2024-03-28 05:28:47
>> done 2024-03-28 05:28:48
>> calculating peakCenter to TSS using peak-gene pair... 2024-03-28 05:28:48
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-03-28 05:28:49
>> calculating RP using centerToTSS and peak score2024-03-28 05:28:49
>> merging all info together 2024-03-28 05:28:53
>> done 2024-03-28 05:28:53
>> checking seqlevels match... 2024-03-28 05:28:53
>> 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... 2024-03-28 05:28:54
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:28:55
>> finding overlap peak in gene scan region... 2024-03-28 05:28:55
>> dealing with left peak not your gene scan region... 2024-03-28 05:28:55
>> merging two set peaks... 2024-03-28 05:28:55
>> calculating distance and dealing with gene strand... 2024-03-28 05:28:55
>> merging all info together ... 2024-03-28 05:28:55
>> done 2024-03-28 05:28:55
>> calculating peakCenter to TSS using peak-gene pair... 2024-03-28 05:28:55
>> calculating RP using centerToTSS and TF hit 2024-03-28 05:28:56
>> merging all info together 2024-03-28 05:28:56
>> done 2024-03-28 05:28:56
>> calculating peakCenter to TSS using peak-gene pair... 2024-03-28 05:28:56
>> calculating RP using centerToTSS and TF hit 2024-03-28 05:28:57
>> merging all info together 2024-03-28 05:28:57
>> done 2024-03-28 05:28:57
>> checking seqlevels match... 2024-03-28 05:28:58
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-03-28 05:28:58
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:28:59
>> finding overlap peak in gene scan region... 2024-03-28 05:28:59
>> dealing with left peak not your gene scan region... 2024-03-28 05:29:00
>> merging two set peaks... 2024-03-28 05:29:00
>> calculating distance and dealing with gene strand... 2024-03-28 05:29:00
>> merging all info together ... 2024-03-28 05:29:00
>> done 2024-03-28 05:29:00
>> calculating peakCenter to TSS using peak-gene pair... 2024-03-28 05:29:00
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-03-28 05:29:01
>> calculating RP using centerToTSS and peak score2024-03-28 05:29:01
>> merging all info together 2024-03-28 05:29:04
>> done 2024-03-28 05:29:04
>> extracting RP info from regionRP... 2024-03-28 05:29:05
>> dealing with TF_GR_databse... 2024-03-28 05:29:05
>> calculating percent and p-value... 2024-03-28 05:29:05
>> dealing withE5_0h_R1... 2024-03-28 05:29:05
>> dealing withE5_0h_R2... 2024-03-28 05:29:05
>> dealing withE5_4h_R1... 2024-03-28 05:29:05
>> dealing withE5_4h_R2... 2024-03-28 05:29:06
>> dealing withE5_8h_R1... 2024-03-28 05:29:06
>> dealing withE5_8h_R2... 2024-03-28 05:29:06
>> dealing withE5_16h_R1... 2024-03-28 05:29:06
>> dealing withE5_16h_R2... 2024-03-28 05:29:06
>> dealing withE5_24h_R1... 2024-03-28 05:29:06
>> dealing withE5_24h_R2... 2024-03-28 05:29:06
>> dealing withE5_48h_R1... 2024-03-28 05:29:06
>> dealing withE5_48h_R2... 2024-03-28 05:29:06
>> dealing withE5_48h_R3... 2024-03-28 05:29:06
>> dealing withE5_72h_R1... 2024-03-28 05:29:06
>> dealing withE5_72h_R2... 2024-03-28 05:29:06
>> dealing withE5_72h_R3... 2024-03-28 05:29:06
>> merging all info together... 2024-03-28 05:29:06
>> done 2024-03-28 05:29:07
>> preparing gene features information... 2024-03-28 05:29:07
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:29:08
>> calculating p-value for each TF, which may be time consuming... 2024-03-28 05:29:08
>> merging all info together... 2024-03-28 05:29:08
>> done 2024-03-28 05:29:08
>> dealing with TF_GR_database... 2024-03-28 05:29:08
>> calculating coef and converting into z-score using INT... 2024-03-28 05:29:08
>> dealing with E5_0h_R1... 2024-03-28 05:29:08
>> dealing with E5_0h_R2... 2024-03-28 05:29:08
>> dealing with E5_4h_R1... 2024-03-28 05:29:09
>> dealing with E5_4h_R2... 2024-03-28 05:29:09
>> dealing with E5_8h_R1... 2024-03-28 05:29:09
>> dealing with E5_8h_R2... 2024-03-28 05:29:09
>> dealing with E5_16h_R1... 2024-03-28 05:29:09
>> dealing with E5_16h_R2... 2024-03-28 05:29:09
>> dealing with E5_24h_R1... 2024-03-28 05:29:09
>> dealing with E5_24h_R2... 2024-03-28 05:29:09
>> dealing with E5_48h_R1... 2024-03-28 05:29:09
>> dealing with E5_48h_R2... 2024-03-28 05:29:10
>> dealing with E5_48h_R3... 2024-03-28 05:29:10
>> dealing with E5_72h_R1... 2024-03-28 05:29:10
>> dealing with E5_72h_R2... 2024-03-28 05:29:10
>> dealing with E5_72h_R3... 2024-03-28 05:29:10
>> merging all info together... 2024-03-28 05:29:10
>> done 2024-03-28 05:29:10
>> checking seqlevels match... 2024-03-28 05:29:10
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-03-28 05:29:11
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:29:12
>> finding overlap peak in gene scan region... 2024-03-28 05:29:12
>> dealing with left peak not your gene scan region... 2024-03-28 05:29:12
>> merging two set peaks... 2024-03-28 05:29:12
>> calculating distance and dealing with gene strand... 2024-03-28 05:29:12
>> merging all info together ... 2024-03-28 05:29:12
>> done 2024-03-28 05:29:12
>> calculating peakCenter to TSS using peak-gene pair... 2024-03-28 05:29:12
>> calculating RP using centerToTSS and TF hit 2024-03-28 05:29:13
>> merging all info together 2024-03-28 05:29:13
>> done 2024-03-28 05:29:13
>> checking seqlevels match... 2024-03-28 05:29:14
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2024-03-28 05:29:14
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2024-03-28 05:29:18
>> 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... 2024-03-28 05:29:18
>> 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... 2024-03-28 05:29:18
>> finding nearest gene and calculating distance... 2024-03-28 05:29:19
>> dealing with gene strand ... 2024-03-28 05:29:19
>> merging all info together ... 2024-03-28 05:29:19
>> done 2024-03-28 05:29:19
>> checking seqlevels match... 2024-03-28 05:29:20
>> 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... 2024-03-28 05:29:20
>> 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... 2024-03-28 05:29:20
>> finding nearest gene and calculating distance... 2024-03-28 05:29:21
>> dealing with gene strand ... 2024-03-28 05:29:21
>> merging all info together ... 2024-03-28 05:29:21
>> done 2024-03-28 05:29:21
>> checking seqlevels match... 2024-03-28 05:29:22
>> 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
>> checking seqlevels match... 2024-03-28 05:29:22
>> 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... 2024-03-28 05:29:22
>> finding nearest gene and calculating distance... 2024-03-28 05:29:23
>> dealing with gene strand ... 2024-03-28 05:29:23
>> merging all info together ... 2024-03-28 05:29:23
>> done 2024-03-28 05:29:23
>> checking seqlevels match... 2024-03-28 05:29:25
>> 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... 2024-03-28 05:29:25
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-03-28 05:29:25
>> finding nearest gene and calculating distance... 2024-03-28 05:29:27
>> dealing with gene strand ... 2024-03-28 05:29:27
>> merging all info together ... 2024-03-28 05:29:27
>> done 2024-03-28 05:29:27
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2024-03-28 05:29:28
>> 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... 2024-03-28 05:29:28
>> 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... 2024-03-28 05:29:28
>> finding nearest gene and calculating distance... 2024-03-28 05:29:29
>> dealing with gene strand ... 2024-03-28 05:29:29
>> merging all info together ... 2024-03-28 05:29:30
>> done 2024-03-28 05:29:30
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2024-03-28 05:29:31
>> 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... 2024-03-28 05:29:32
>> 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... 2024-03-28 05:29:33
>> checking seqlevels match... 2024-03-28 05:29:34
>> 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... 2024-03-28 05:29:35
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-03-28 05:29:37
>> merging all info together... 2024-03-28 05:29:37
>> done 2024-03-28 05:29:37
>> checking seqlevels match... 2024-03-28 05:29:37
>> 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... 2024-03-28 05:29:37
>> checking seqlevels match... 2024-03-28 05:29:37
>> 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... 2024-03-28 05:29:38
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2024-03-28 05:29:39
>> checking seqlevels match... 2024-03-28 05:29:39
>> 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
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:29:40
>> calculating cor and pvalue, which may be time consuming... 2024-03-28 05:29:40
>> merging all info together... 2024-03-28 05:29:40
>> done 2024-03-28 05:29:40
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-03-28 05:29:40
>> merging all info together... 2024-03-28 05:29:41
>> done 2024-03-28 05:29:41
>> checking seqlevels match... 2024-03-28 05:29:41
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-03-28 05:29:41
>> some scan range may cross Chr bound, trimming... 2024-03-28 05:29:42
>> finding overlap peak in gene scan region... 2024-03-28 05:29:42
>> dealing with left peak not your gene scan region... 2024-03-28 05:29:42
>> merging two set peaks... 2024-03-28 05:29:42
>> calculating distance and dealing with gene strand... 2024-03-28 05:29:42
>> merging all info together ... 2024-03-28 05:29:42
>> done 2024-03-28 05:29:42
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-03-28 05:29:44
>> merging all info together... 2024-03-28 05:29:44
>> done 2024-03-28 05:29:44
>> checking seqlevels match... 2024-03-28 05:29:44
>> 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... 2024-03-28 05:29:44
>> checking seqlevels match... 2024-03-28 05:29:44
>> 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... 2024-03-28 05:29:45
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2024-03-28 05:29:46
>> checking seqlevels match... 2024-03-28 05:29:46
>> 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... 2024-03-28 05:29:47
>> calculating cor and pvalue, which may be time consuming... 2024-03-28 05:29:47
>> merging all info together... 2024-03-28 05:29:47
>> done 2024-03-28 05:29:47
Joining with `by = join_by(feature_id)`
Joining with `by = join_by(feature_id)`
`geom_smooth()` using formula = 'y ~ x'
Joining with `by = join_by(feature_id)`
Joining with `by = join_by(feature_id)`
`geom_smooth()` using formula = 'y ~ x'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
>
> proc.time()
user system elapsed
92.733 2.085 95.008
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0.000 | 0.001 | 0.000 | |
| calcRP_TFHit | 4.042 | 0.079 | 4.302 | |
| calcRP_coverage | 10.714 | 0.703 | 11.442 | |
| calcRP_region | 7.167 | 0.152 | 7.334 | |
| enhancerPromoterCor | 3.965 | 0.076 | 4.050 | |
| findIT_MARA | 0.607 | 0.016 | 0.625 | |
| findIT_TFHit | 1.485 | 0.016 | 1.503 | |
| findIT_TTPair | 0.098 | 0.004 | 0.101 | |
| findIT_enrichFisher | 0.220 | 0.000 | 0.221 | |
| findIT_enrichWilcox | 0.246 | 0.000 | 0.246 | |
| findIT_regionRP | 9.656 | 0.147 | 9.822 | |
| getAssocPairNumber | 1.617 | 0.040 | 1.660 | |
| integrate_ChIP_RNA | 2.964 | 0.056 | 3.026 | |
| integrate_replicates | 0.003 | 0.000 | 0.002 | |
| jaccard_findIT_TTpair | 0.131 | 0.008 | 0.139 | |
| jaccard_findIT_enrichFisher | 0.282 | 0.000 | 0.283 | |
| loadPeakFile | 0.083 | 0.004 | 0.088 | |
| mm_geneBound | 1.743 | 0.004 | 1.751 | |
| mm_geneScan | 1.785 | 0.020 | 1.809 | |
| mm_nearestGene | 1.543 | 0.012 | 1.559 | |
| peakGeneCor | 3.399 | 0.044 | 3.450 | |
| plot_annoDistance | 2.146 | 0.024 | 2.175 | |
| plot_peakGeneAlias_summary | 1.930 | 0.004 | 1.937 | |
| plot_peakGeneCor | 4.306 | 0.028 | 4.343 | |
| test_geneSet | 0.001 | 0.000 | 0.001 | |