Guandong Shang
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: devel |
| git_last_commit: 30235ec |
| git_last_commit_date: 2024-10-29 11:01:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:38 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 711/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.13.0 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | 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: 1.13.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FindIT2_1.13.0.tar.gz |
| StartedAt: 2025-01-25 06:57:35 -0000 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 07:05:29 -0000 (Sat, 25 Jan 2025) |
| EllapsedTime: 473.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FindIT2_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ...Warning: program compiled against libxml 212 using older 211
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 8.558 0.172 8.745
findIT_regionRP 8.258 0.220 8.492
calcRP_region 6.793 0.192 7.001
calcRP_TFHit 4.779 0.203 5.142
* 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/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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) (2024-11-24 r87369) -- "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
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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... 2025-01-25 07:04:09
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:04:10
>> preparing weight info... 2025-01-25 07:04:10
>> loading E50h_sampleChr5.bw info... 2025-01-25 07:04:10
------------
>> extracting and calcluating Chr5 signal... 2025-01-25 07:04:10
>> dealing with Chr5 left gene signal... 2025-01-25 07:04:18
>> norming Chr5RP accoring to the whole Chr RP... 2025-01-25 07:04:18
>> merging all Chr RP together... 2025-01-25 07:04:18
>> done 2025-01-25 07:04:18
>> checking seqlevels match... 2025-01-25 07:04:18
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2025-01-25 07:04:18
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:04:19
>> finding overlap peak in gene scan region... 2025-01-25 07:04:19
>> dealing with left peak not your gene scan region... 2025-01-25 07:04:20
>> merging two set peaks... 2025-01-25 07:04:20
>> calculating distance and dealing with gene strand... 2025-01-25 07:04:20
>> merging all info together ... 2025-01-25 07:04:20
>> done 2025-01-25 07:04:20
>> calculating peakCenter to TSS using peak-gene pair... 2025-01-25 07:04:20
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-01-25 07:04:21
>> calculating RP using centerToTSS and peak score2025-01-25 07:04:21
>> merging all info together 2025-01-25 07:04:24
>> done 2025-01-25 07:04:25
>> calculating peakCenter to TSS using peak-gene pair... 2025-01-25 07:04:25
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-01-25 07:04:26
>> calculating RP using centerToTSS and peak score2025-01-25 07:04:26
>> merging all info together 2025-01-25 07:04:30
>> done 2025-01-25 07:04:31
>> checking seqlevels match... 2025-01-25 07:04:31
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2025-01-25 07:04:31
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:04:32
>> finding overlap peak in gene scan region... 2025-01-25 07:04:32
>> dealing with left peak not your gene scan region... 2025-01-25 07:04:32
>> merging two set peaks... 2025-01-25 07:04:32
>> calculating distance and dealing with gene strand... 2025-01-25 07:04:32
>> merging all info together ... 2025-01-25 07:04:33
>> done 2025-01-25 07:04:33
>> calculating peakCenter to TSS using peak-gene pair... 2025-01-25 07:04:33
>> calculating RP using centerToTSS and TF hit 2025-01-25 07:04:34
>> merging all info together 2025-01-25 07:04:34
>> done 2025-01-25 07:04:34
>> calculating peakCenter to TSS using peak-gene pair... 2025-01-25 07:04:34
>> calculating RP using centerToTSS and TF hit 2025-01-25 07:04:35
>> merging all info together 2025-01-25 07:04:35
>> done 2025-01-25 07:04:35
>> checking seqlevels match... 2025-01-25 07:04:36
>> 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... 2025-01-25 07:04:36
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:04:38
>> finding overlap peak in gene scan region... 2025-01-25 07:04:38
>> dealing with left peak not your gene scan region... 2025-01-25 07:04:38
>> merging two set peaks... 2025-01-25 07:04:38
>> calculating distance and dealing with gene strand... 2025-01-25 07:04:38
>> merging all info together ... 2025-01-25 07:04:38
>> done 2025-01-25 07:04:38
>> calculating peakCenter to TSS using peak-gene pair... 2025-01-25 07:04:38
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-01-25 07:04:39
>> calculating RP using centerToTSS and peak score2025-01-25 07:04:39
>> merging all info together 2025-01-25 07:04:42
>> done 2025-01-25 07:04:43
>> extracting RP info from regionRP... 2025-01-25 07:04:43
>> dealing with TF_GR_databse... 2025-01-25 07:04:44
>> calculating percent and p-value... 2025-01-25 07:04:44
>> dealing withE5_0h_R1... 2025-01-25 07:04:44
>> dealing withE5_0h_R2... 2025-01-25 07:04:44
>> dealing withE5_4h_R1... 2025-01-25 07:04:44
>> dealing withE5_4h_R2... 2025-01-25 07:04:44
>> dealing withE5_8h_R1... 2025-01-25 07:04:44
>> dealing withE5_8h_R2... 2025-01-25 07:04:44
>> dealing withE5_16h_R1... 2025-01-25 07:04:44
>> dealing withE5_16h_R2... 2025-01-25 07:04:44
>> dealing withE5_24h_R1... 2025-01-25 07:04:44
>> dealing withE5_24h_R2... 2025-01-25 07:04:44
>> dealing withE5_48h_R1... 2025-01-25 07:04:44
>> dealing withE5_48h_R2... 2025-01-25 07:04:44
>> dealing withE5_48h_R3... 2025-01-25 07:04:44
>> dealing withE5_72h_R1... 2025-01-25 07:04:44
>> dealing withE5_72h_R2... 2025-01-25 07:04:45
>> dealing withE5_72h_R3... 2025-01-25 07:04:45
>> merging all info together... 2025-01-25 07:04:45
>> done 2025-01-25 07:04:45
>> preparing gene features information... 2025-01-25 07:04:45
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:04:46
>> calculating p-value for each TF, which may be time consuming... 2025-01-25 07:04:46
>> merging all info together... 2025-01-25 07:04:46
>> done 2025-01-25 07:04:46
>> dealing with TF_GR_database... 2025-01-25 07:04:46
>> calculating coef and converting into z-score using INT... 2025-01-25 07:04:47
>> dealing with E5_0h_R1... 2025-01-25 07:04:47
>> dealing with E5_0h_R2... 2025-01-25 07:04:47
>> dealing with E5_4h_R1... 2025-01-25 07:04:47
>> dealing with E5_4h_R2... 2025-01-25 07:04:47
>> dealing with E5_8h_R1... 2025-01-25 07:04:47
>> dealing with E5_8h_R2... 2025-01-25 07:04:47
>> dealing with E5_16h_R1... 2025-01-25 07:04:47
>> dealing with E5_16h_R2... 2025-01-25 07:04:47
>> dealing with E5_24h_R1... 2025-01-25 07:04:47
>> dealing with E5_24h_R2... 2025-01-25 07:04:47
>> dealing with E5_48h_R1... 2025-01-25 07:04:48
>> dealing with E5_48h_R2... 2025-01-25 07:04:48
>> dealing with E5_48h_R3... 2025-01-25 07:04:48
>> dealing with E5_72h_R1... 2025-01-25 07:04:48
>> dealing with E5_72h_R2... 2025-01-25 07:04:48
>> dealing with E5_72h_R3... 2025-01-25 07:04:48
>> merging all info together... 2025-01-25 07:04:48
>> done 2025-01-25 07:04:48
>> checking seqlevels match... 2025-01-25 07:04:49
>> 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... 2025-01-25 07:04:49
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:04:50
>> finding overlap peak in gene scan region... 2025-01-25 07:04:50
>> dealing with left peak not your gene scan region... 2025-01-25 07:04:50
>> merging two set peaks... 2025-01-25 07:04:50
>> calculating distance and dealing with gene strand... 2025-01-25 07:04:50
>> merging all info together ... 2025-01-25 07:04:50
>> done 2025-01-25 07:04:50
>> calculating peakCenter to TSS using peak-gene pair... 2025-01-25 07:04:50
>> calculating RP using centerToTSS and TF hit 2025-01-25 07:04:51
>> merging all info together 2025-01-25 07:04:51
>> done 2025-01-25 07:04:51
>> checking seqlevels match... 2025-01-25 07:04:51
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2025-01-25 07:04:52
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2025-01-25 07:04:56
>> 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... 2025-01-25 07:04:56
>> 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... 2025-01-25 07:04:56
>> finding nearest gene and calculating distance... 2025-01-25 07:04:57
>> dealing with gene strand ... 2025-01-25 07:04:57
>> merging all info together ... 2025-01-25 07:04:57
>> done 2025-01-25 07:04:57
>> checking seqlevels match... 2025-01-25 07:04:57
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2025-01-25 07:04:57
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2025-01-25 07:04:57
>> finding nearest gene and calculating distance... 2025-01-25 07:04:58
>> dealing with gene strand ... 2025-01-25 07:04:59
>> merging all info together ... 2025-01-25 07:04:59
>> done 2025-01-25 07:04:59
>> checking seqlevels match... 2025-01-25 07:05:00
>> 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... 2025-01-25 07:05:00
>> 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... 2025-01-25 07:05:00
>> finding nearest gene and calculating distance... 2025-01-25 07:05:01
>> dealing with gene strand ... 2025-01-25 07:05:01
>> merging all info together ... 2025-01-25 07:05:01
>> done 2025-01-25 07:05:01
>> checking seqlevels match... 2025-01-25 07:05:02
>> 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
>> checking seqlevels match... 2025-01-25 07:05:02
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2025-01-25 07:05:02
>> finding nearest gene and calculating distance... 2025-01-25 07:05:03
>> dealing with gene strand ... 2025-01-25 07:05:03
>> merging all info together ... 2025-01-25 07:05:03
>> done 2025-01-25 07:05:03
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2025-01-25 07:05:05
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2025-01-25 07:05:05
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2025-01-25 07:05:05
>> finding nearest gene and calculating distance... 2025-01-25 07:05:06
>> dealing with gene strand ... 2025-01-25 07:05:06
>> merging all info together ... 2025-01-25 07:05:06
>> done 2025-01-25 07:05:06
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2025-01-25 07:05:07
>> 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... 2025-01-25 07:05:08
>> 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... 2025-01-25 07:05:09
>> checking seqlevels match... 2025-01-25 07:05:10
>> 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
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:05:11
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2025-01-25 07:05:13
>> merging all info together... 2025-01-25 07:05:13
>> done 2025-01-25 07:05:13
>> checking seqlevels match... 2025-01-25 07:05:13
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2025-01-25 07:05:14
>> checking seqlevels match... 2025-01-25 07:05:14
>> 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... 2025-01-25 07:05:15
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2025-01-25 07:05:15
>> checking seqlevels match... 2025-01-25 07:05:15
>> 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... 2025-01-25 07:05:16
>> calculating cor and pvalue, which may be time consuming... 2025-01-25 07:05:16
>> merging all info together... 2025-01-25 07:05:17
>> done 2025-01-25 07:05:17
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2025-01-25 07:05:17
>> merging all info together... 2025-01-25 07:05:17
>> done 2025-01-25 07:05:17
>> checking seqlevels match... 2025-01-25 07:05:17
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2025-01-25 07:05:17
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:05:18
>> finding overlap peak in gene scan region... 2025-01-25 07:05:18
>> dealing with left peak not your gene scan region... 2025-01-25 07:05:18
>> merging two set peaks... 2025-01-25 07:05:19
>> calculating distance and dealing with gene strand... 2025-01-25 07:05:19
>> merging all info together ... 2025-01-25 07:05:19
>> done 2025-01-25 07:05:19
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2025-01-25 07:05:20
>> merging all info together... 2025-01-25 07:05:20
>> done 2025-01-25 07:05:20
>> checking seqlevels match... 2025-01-25 07:05:20
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2025-01-25 07:05:20
>> checking seqlevels match... 2025-01-25 07:05:20
>> 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
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:05:21
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2025-01-25 07:05:22
>> checking seqlevels match... 2025-01-25 07:05:22
>> 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
>> some scan range may cross Chr bound, trimming... 2025-01-25 07:05:23
>> calculating cor and pvalue, which may be time consuming... 2025-01-25 07:05:23
>> merging all info together... 2025-01-25 07:05:23
>> done 2025-01-25 07:05:23
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
90.536 2.458 93.181
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0 | 0 | 0 | |
| calcRP_TFHit | 4.779 | 0.203 | 5.142 | |
| calcRP_coverage | 8.558 | 0.172 | 8.745 | |
| calcRP_region | 6.793 | 0.192 | 7.001 | |
| enhancerPromoterCor | 3.558 | 0.147 | 3.712 | |
| findIT_MARA | 0.618 | 0.040 | 0.660 | |
| findIT_TFHit | 1.391 | 0.059 | 1.454 | |
| findIT_TTPair | 0.094 | 0.000 | 0.094 | |
| findIT_enrichFisher | 0.215 | 0.000 | 0.215 | |
| findIT_enrichWilcox | 0.242 | 0.004 | 0.247 | |
| findIT_regionRP | 8.258 | 0.220 | 8.492 | |
| getAssocPairNumber | 1.550 | 0.024 | 1.577 | |
| integrate_ChIP_RNA | 2.851 | 0.068 | 2.925 | |
| integrate_replicates | 0.003 | 0.000 | 0.003 | |
| jaccard_findIT_TTpair | 0.130 | 0.004 | 0.135 | |
| jaccard_findIT_enrichFisher | 0.260 | 0.000 | 0.261 | |
| loadPeakFile | 0.072 | 0.008 | 0.079 | |
| mm_geneBound | 1.623 | 0.044 | 1.670 | |
| mm_geneScan | 2.673 | 0.147 | 2.826 | |
| mm_nearestGene | 1.462 | 0.004 | 1.470 | |
| peakGeneCor | 3.120 | 0.059 | 3.186 | |
| plot_annoDistance | 1.938 | 0.132 | 2.073 | |
| plot_peakGeneAlias_summary | 1.810 | 0.072 | 1.885 | |
| plot_peakGeneCor | 4.009 | 0.084 | 4.101 | |
| test_geneSet | 0 | 0 | 0 | |