Guandong Shang
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1bcb4fc |
| git_last_commit_date: 2024-10-29 11:01:40 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 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 716/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.12.0 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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. |
| Package: FindIT2 |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FindIT2_1.12.0.tar.gz |
| StartedAt: 2025-03-31 22:11:04 -0400 (Mon, 31 Mar 2025) |
| EndedAt: 2025-03-31 22:17:45 -0400 (Mon, 31 Mar 2025) |
| EllapsedTime: 400.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FindIT2_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FindIT2.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.12.0’
* 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 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
findIT_regionRP 5.968 0.204 6.173
calcRP_region 5.381 0.082 5.463
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
FindIT2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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, saveRDS, 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... 2025-03-31 22:15:51
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:15:52
>> preparing weight info... 2025-03-31 22:15:52
>> loading E50h_sampleChr5.bw info... 2025-03-31 22:15:52
------------
>> extracting and calcluating Chr5 signal... 2025-03-31 22:15:52
>> dealing with Chr5 left gene signal... 2025-03-31 22:15:55
>> norming Chr5RP accoring to the whole Chr RP... 2025-03-31 22:15:55
>> merging all Chr RP together... 2025-03-31 22:15:55
>> done 2025-03-31 22:15:55
>> checking seqlevels match... 2025-03-31 22:15:55
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2025-03-31 22:15:55
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:15:56
>> finding overlap peak in gene scan region... 2025-03-31 22:15:56
>> dealing with left peak not your gene scan region... 2025-03-31 22:15:56
>> merging two set peaks... 2025-03-31 22:15:56
>> calculating distance and dealing with gene strand... 2025-03-31 22:15:56
>> merging all info together ... 2025-03-31 22:15:56
>> done 2025-03-31 22:15:56
>> calculating peakCenter to TSS using peak-gene pair... 2025-03-31 22:15:56
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-03-31 22:15:57
>> calculating RP using centerToTSS and peak score2025-03-31 22:15:57
>> merging all info together 2025-03-31 22:15:59
>> done 2025-03-31 22:16:00
>> calculating peakCenter to TSS using peak-gene pair... 2025-03-31 22:16:00
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-03-31 22:16:01
>> calculating RP using centerToTSS and peak score2025-03-31 22:16:01
>> merging all info together 2025-03-31 22:16:03
>> done 2025-03-31 22:16:03
>> checking seqlevels match... 2025-03-31 22:16:03
>> 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... 2025-03-31 22:16:03
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:16:04
>> finding overlap peak in gene scan region... 2025-03-31 22:16:04
>> dealing with left peak not your gene scan region... 2025-03-31 22:16:04
>> merging two set peaks... 2025-03-31 22:16:04
>> calculating distance and dealing with gene strand... 2025-03-31 22:16:05
>> merging all info together ... 2025-03-31 22:16:05
>> done 2025-03-31 22:16:05
>> calculating peakCenter to TSS using peak-gene pair... 2025-03-31 22:16:05
>> calculating RP using centerToTSS and TF hit 2025-03-31 22:16:05
>> merging all info together 2025-03-31 22:16:05
>> done 2025-03-31 22:16:05
>> calculating peakCenter to TSS using peak-gene pair... 2025-03-31 22:16:05
>> calculating RP using centerToTSS and TF hit 2025-03-31 22:16:07
>> merging all info together 2025-03-31 22:16:07
>> done 2025-03-31 22:16:07
>> checking seqlevels match... 2025-03-31 22:16:08
>> 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... 2025-03-31 22:16:08
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:16:08
>> finding overlap peak in gene scan region... 2025-03-31 22:16:08
>> dealing with left peak not your gene scan region... 2025-03-31 22:16:08
>> merging two set peaks... 2025-03-31 22:16:09
>> calculating distance and dealing with gene strand... 2025-03-31 22:16:09
>> merging all info together ... 2025-03-31 22:16:09
>> done 2025-03-31 22:16:09
>> calculating peakCenter to TSS using peak-gene pair... 2025-03-31 22:16:09
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-03-31 22:16:09
>> calculating RP using centerToTSS and peak score2025-03-31 22:16:09
>> merging all info together 2025-03-31 22:16:11
>> done 2025-03-31 22:16:11
>> extracting RP info from regionRP... 2025-03-31 22:16:12
>> dealing with TF_GR_databse... 2025-03-31 22:16:12
>> calculating percent and p-value... 2025-03-31 22:16:12
>> dealing withE5_0h_R1... 2025-03-31 22:16:12
>> dealing withE5_0h_R2... 2025-03-31 22:16:12
>> dealing withE5_4h_R1... 2025-03-31 22:16:12
>> dealing withE5_4h_R2... 2025-03-31 22:16:12
>> dealing withE5_8h_R1... 2025-03-31 22:16:12
>> dealing withE5_8h_R2... 2025-03-31 22:16:12
>> dealing withE5_16h_R1... 2025-03-31 22:16:12
>> dealing withE5_16h_R2... 2025-03-31 22:16:12
>> dealing withE5_24h_R1... 2025-03-31 22:16:12
>> dealing withE5_24h_R2... 2025-03-31 22:16:12
>> dealing withE5_48h_R1... 2025-03-31 22:16:12
>> dealing withE5_48h_R2... 2025-03-31 22:16:12
>> dealing withE5_48h_R3... 2025-03-31 22:16:12
>> dealing withE5_72h_R1... 2025-03-31 22:16:12
>> dealing withE5_72h_R2... 2025-03-31 22:16:13
>> dealing withE5_72h_R3... 2025-03-31 22:16:13
>> merging all info together... 2025-03-31 22:16:13
>> done 2025-03-31 22:16:13
>> preparing gene features information... 2025-03-31 22:16:13
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:16:13
>> calculating p-value for each TF, which may be time consuming... 2025-03-31 22:16:13
>> merging all info together... 2025-03-31 22:16:14
>> done 2025-03-31 22:16:14
>> dealing with TF_GR_database... 2025-03-31 22:16:14
>> calculating coef and converting into z-score using INT... 2025-03-31 22:16:14
>> dealing with E5_0h_R1... 2025-03-31 22:16:14
>> dealing with E5_0h_R2... 2025-03-31 22:16:14
>> dealing with E5_4h_R1... 2025-03-31 22:16:14
>> dealing with E5_4h_R2... 2025-03-31 22:16:14
>> dealing with E5_8h_R1... 2025-03-31 22:16:14
>> dealing with E5_8h_R2... 2025-03-31 22:16:14
>> dealing with E5_16h_R1... 2025-03-31 22:16:14
>> dealing with E5_16h_R2... 2025-03-31 22:16:14
>> dealing with E5_24h_R1... 2025-03-31 22:16:14
>> dealing with E5_24h_R2... 2025-03-31 22:16:14
>> dealing with E5_48h_R1... 2025-03-31 22:16:15
>> dealing with E5_48h_R2... 2025-03-31 22:16:15
>> dealing with E5_48h_R3... 2025-03-31 22:16:15
>> dealing with E5_72h_R1... 2025-03-31 22:16:15
>> dealing with E5_72h_R2... 2025-03-31 22:16:15
>> dealing with E5_72h_R3... 2025-03-31 22:16:15
>> merging all info together... 2025-03-31 22:16:15
>> done 2025-03-31 22:16:15
>> checking seqlevels match... 2025-03-31 22:16:15
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2025-03-31 22:16:15
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:16:16
>> finding overlap peak in gene scan region... 2025-03-31 22:16:16
>> dealing with left peak not your gene scan region... 2025-03-31 22:16:16
>> merging two set peaks... 2025-03-31 22:16:16
>> calculating distance and dealing with gene strand... 2025-03-31 22:16:16
>> merging all info together ... 2025-03-31 22:16:16
>> done 2025-03-31 22:16:16
>> calculating peakCenter to TSS using peak-gene pair... 2025-03-31 22:16:16
>> calculating RP using centerToTSS and TF hit 2025-03-31 22:16:17
>> merging all info together 2025-03-31 22:16:17
>> done 2025-03-31 22:16:17
>> checking seqlevels match... 2025-03-31 22:16:17
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2025-03-31 22:16:17
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2025-03-31 22:16:21
>> 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... 2025-03-31 22:16:21
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2025-03-31 22:16:21
>> finding nearest gene and calculating distance... 2025-03-31 22:16:22
>> dealing with gene strand ... 2025-03-31 22:16:22
>> merging all info together ... 2025-03-31 22:16:22
>> done 2025-03-31 22:16:22
>> checking seqlevels match... 2025-03-31 22:16:22
>> 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... 2025-03-31 22:16:22
>> 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... 2025-03-31 22:16:22
>> finding nearest gene and calculating distance... 2025-03-31 22:16:23
>> dealing with gene strand ... 2025-03-31 22:16:23
>> merging all info together ... 2025-03-31 22:16:23
>> done 2025-03-31 22:16:23
>> checking seqlevels match... 2025-03-31 22:16:24
>> 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... 2025-03-31 22:16:24
>> 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... 2025-03-31 22:16:24
>> finding nearest gene and calculating distance... 2025-03-31 22:16:24
>> dealing with gene strand ... 2025-03-31 22:16:24
>> merging all info together ... 2025-03-31 22:16:24
>> done 2025-03-31 22:16:24
>> checking seqlevels match... 2025-03-31 22:16:25
>> 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... 2025-03-31 22:16:25
>> 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... 2025-03-31 22:16:25
>> finding nearest gene and calculating distance... 2025-03-31 22:16:26
>> dealing with gene strand ... 2025-03-31 22:16:26
>> merging all info together ... 2025-03-31 22:16:26
>> done 2025-03-31 22:16:26
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2025-03-31 22:16:27
>> 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... 2025-03-31 22:16:27
>> 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... 2025-03-31 22:16:27
>> finding nearest gene and calculating distance... 2025-03-31 22:16:28
>> dealing with gene strand ... 2025-03-31 22:16:29
>> merging all info together ... 2025-03-31 22:16:29
>> done 2025-03-31 22:16:29
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2025-03-31 22:16:29
>> 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... 2025-03-31 22:16:30
>> 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
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:16:31
>> checking seqlevels match... 2025-03-31 22:16:32
>> 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... 2025-03-31 22:16:32
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2025-03-31 22:16:33
>> merging all info together... 2025-03-31 22:16:33
>> done 2025-03-31 22:16:33
>> checking seqlevels match... 2025-03-31 22:16:33
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2025-03-31 22:16:33
>> checking seqlevels match... 2025-03-31 22:16:33
>> 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
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:16:34
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2025-03-31 22:16:34
>> checking seqlevels match... 2025-03-31 22:16:34
>> 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... 2025-03-31 22:16:35
>> calculating cor and pvalue, which may be time consuming... 2025-03-31 22:16:35
>> merging all info together... 2025-03-31 22:16:35
>> done 2025-03-31 22:16:35
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2025-03-31 22:16:35
>> merging all info together... 2025-03-31 22:16:35
>> done 2025-03-31 22:16:35
>> checking seqlevels match... 2025-03-31 22:16:36
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2025-03-31 22:16:36
>> some scan range may cross Chr bound, trimming... 2025-03-31 22:16:36
>> finding overlap peak in gene scan region... 2025-03-31 22:16:36
>> dealing with left peak not your gene scan region... 2025-03-31 22:16:36
>> merging two set peaks... 2025-03-31 22:16:36
>> calculating distance and dealing with gene strand... 2025-03-31 22:16:36
>> merging all info together ... 2025-03-31 22:16:37
>> done 2025-03-31 22:16:37
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2025-03-31 22:16:37
>> merging all info together... 2025-03-31 22:16:37
>> done 2025-03-31 22:16:37
>> checking seqlevels match... 2025-03-31 22:16:37
>> 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... 2025-03-31 22:16:37
>> checking seqlevels match... 2025-03-31 22:16:38
>> 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... 2025-03-31 22:16:38
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2025-03-31 22:16:38
>> checking seqlevels match... 2025-03-31 22:16:38
>> 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... 2025-03-31 22:16:39
>> calculating cor and pvalue, which may be time consuming... 2025-03-31 22:16:39
>> merging all info together... 2025-03-31 22:16:39
>> done 2025-03-31 22:16:39
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
59.887 1.767 61.645
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0 | 0 | 0 | |
| calcRP_TFHit | 3.362 | 0.175 | 3.596 | |
| calcRP_coverage | 2.631 | 0.095 | 2.727 | |
| calcRP_region | 5.381 | 0.082 | 5.463 | |
| enhancerPromoterCor | 2.450 | 0.054 | 2.503 | |
| findIT_MARA | 0.407 | 0.006 | 0.412 | |
| findIT_TFHit | 0.828 | 0.013 | 0.841 | |
| findIT_TTPair | 0.066 | 0.000 | 0.065 | |
| findIT_enrichFisher | 0.137 | 0.001 | 0.139 | |
| findIT_enrichWilcox | 0.167 | 0.000 | 0.168 | |
| findIT_regionRP | 5.968 | 0.204 | 6.173 | |
| getAssocPairNumber | 1.049 | 0.044 | 1.094 | |
| integrate_ChIP_RNA | 1.777 | 0.013 | 1.791 | |
| integrate_replicates | 0.002 | 0.000 | 0.002 | |
| jaccard_findIT_TTpair | 0.110 | 0.001 | 0.111 | |
| jaccard_findIT_enrichFisher | 0.179 | 0.001 | 0.180 | |
| loadPeakFile | 0.054 | 0.000 | 0.055 | |
| mm_geneBound | 1.070 | 0.026 | 1.096 | |
| mm_geneScan | 1.160 | 0.028 | 1.187 | |
| mm_nearestGene | 0.956 | 0.006 | 0.962 | |
| peakGeneCor | 2.033 | 0.020 | 2.054 | |
| plot_annoDistance | 1.302 | 0.008 | 1.310 | |
| plot_peakGeneAlias_summary | 1.249 | 0.007 | 1.256 | |
| plot_peakGeneCor | 2.677 | 0.009 | 2.685 | |
| test_geneSet | 0.001 | 0.000 | 0.000 | |