Guandong Shang
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_18 |
| git_last_commit: f4ef6c4 |
| git_last_commit_date: 2023-10-24 11:34:37 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:41 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 711/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.8.0 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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: 1.8.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings FindIT2_1.8.0.tar.gz |
| StartedAt: 2023-11-02 10:30:56 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 10:39:00 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 484.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings FindIT2_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FindIT2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘1.8.0’
* 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 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 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 9.412 0.216 9.648
calcRP_coverage 8.834 0.240 9.094
calcRP_region 6.844 0.124 6.984
calcRP_TFHit 5.687 0.223 6.072
* 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: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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, 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, sort, 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... 2023-11-02 10:37:37
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:37:39
>> preparing weight info... 2023-11-02 10:37:39
>> loading E50h_sampleChr5.bw info... 2023-11-02 10:37:39
------------
>> extracting and calcluating Chr5 signal... 2023-11-02 10:37:39
>> dealing with Chr5 left gene signal... 2023-11-02 10:37:48
>> norming Chr5RP accoring to the whole Chr RP... 2023-11-02 10:37:48
>> merging all Chr RP together... 2023-11-02 10:37:48
>> done 2023-11-02 10:37:48
>> checking seqlevels match... 2023-11-02 10:37:49
>> 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... 2023-11-02 10:37:49
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:37:50
>> finding overlap peak in gene scan region... 2023-11-02 10:37:50
>> dealing with left peak not your gene scan region... 2023-11-02 10:37:50
>> merging two set peaks... 2023-11-02 10:37:50
>> calculating distance and dealing with gene strand... 2023-11-02 10:37:50
>> merging all info together ... 2023-11-02 10:37:50
>> done 2023-11-02 10:37:50
>> calculating peakCenter to TSS using peak-gene pair... 2023-11-02 10:37:50
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-11-02 10:37:51
>> calculating RP using centerToTSS and peak score2023-11-02 10:37:51
>> merging all info together 2023-11-02 10:37:55
>> done 2023-11-02 10:37:56
>> calculating peakCenter to TSS using peak-gene pair... 2023-11-02 10:37:56
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-11-02 10:37:57
>> calculating RP using centerToTSS and peak score2023-11-02 10:37:57
>> merging all info together 2023-11-02 10:38:01
>> done 2023-11-02 10:38:02
>> checking seqlevels match... 2023-11-02 10:38:02
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-11-02 10:38:02
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:04
>> finding overlap peak in gene scan region... 2023-11-02 10:38:04
>> dealing with left peak not your gene scan region... 2023-11-02 10:38:04
>> merging two set peaks... 2023-11-02 10:38:05
>> calculating distance and dealing with gene strand... 2023-11-02 10:38:05
>> merging all info together ... 2023-11-02 10:38:05
>> done 2023-11-02 10:38:05
>> calculating peakCenter to TSS using peak-gene pair... 2023-11-02 10:38:05
>> calculating RP using centerToTSS and TF hit 2023-11-02 10:38:06
>> merging all info together 2023-11-02 10:38:06
>> done 2023-11-02 10:38:06
>> calculating peakCenter to TSS using peak-gene pair... 2023-11-02 10:38:06
>> calculating RP using centerToTSS and TF hit 2023-11-02 10:38:07
>> merging all info together 2023-11-02 10:38:07
>> done 2023-11-02 10:38:07
>> checking seqlevels match... 2023-11-02 10:38:08
>> 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... 2023-11-02 10:38:08
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:09
>> finding overlap peak in gene scan region... 2023-11-02 10:38:09
>> dealing with left peak not your gene scan region... 2023-11-02 10:38:09
>> merging two set peaks... 2023-11-02 10:38:09
>> calculating distance and dealing with gene strand... 2023-11-02 10:38:09
>> merging all info together ... 2023-11-02 10:38:09
>> done 2023-11-02 10:38:09
>> calculating peakCenter to TSS using peak-gene pair... 2023-11-02 10:38:09
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-11-02 10:38:10
>> calculating RP using centerToTSS and peak score2023-11-02 10:38:10
>> merging all info together 2023-11-02 10:38:13
>> done 2023-11-02 10:38:14
>> extracting RP info from regionRP... 2023-11-02 10:38:15
>> dealing with TF_GR_databse... 2023-11-02 10:38:15
>> calculating percent and p-value... 2023-11-02 10:38:15
>> dealing withE5_0h_R1... 2023-11-02 10:38:15
>> dealing withE5_0h_R2... 2023-11-02 10:38:15
>> dealing withE5_4h_R1... 2023-11-02 10:38:15
>> dealing withE5_4h_R2... 2023-11-02 10:38:15
>> dealing withE5_8h_R1... 2023-11-02 10:38:15
>> dealing withE5_8h_R2... 2023-11-02 10:38:15
>> dealing withE5_16h_R1... 2023-11-02 10:38:15
>> dealing withE5_16h_R2... 2023-11-02 10:38:15
>> dealing withE5_24h_R1... 2023-11-02 10:38:15
>> dealing withE5_24h_R2... 2023-11-02 10:38:16
>> dealing withE5_48h_R1... 2023-11-02 10:38:16
>> dealing withE5_48h_R2... 2023-11-02 10:38:16
>> dealing withE5_48h_R3... 2023-11-02 10:38:16
>> dealing withE5_72h_R1... 2023-11-02 10:38:16
>> dealing withE5_72h_R2... 2023-11-02 10:38:16
>> dealing withE5_72h_R3... 2023-11-02 10:38:16
>> merging all info together... 2023-11-02 10:38:16
>> done 2023-11-02 10:38:16
>> preparing gene features information... 2023-11-02 10:38:16
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:17
>> calculating p-value for each TF, which may be time consuming... 2023-11-02 10:38:17
>> merging all info together... 2023-11-02 10:38:17
>> done 2023-11-02 10:38:17
>> dealing with TF_GR_database... 2023-11-02 10:38:18
>> calculating coef and converting into z-score using INT... 2023-11-02 10:38:18
>> dealing with E5_0h_R1... 2023-11-02 10:38:18
>> dealing with E5_0h_R2... 2023-11-02 10:38:18
>> dealing with E5_4h_R1... 2023-11-02 10:38:18
>> dealing with E5_4h_R2... 2023-11-02 10:38:18
>> dealing with E5_8h_R1... 2023-11-02 10:38:18
>> dealing with E5_8h_R2... 2023-11-02 10:38:19
>> dealing with E5_16h_R1... 2023-11-02 10:38:19
>> dealing with E5_16h_R2... 2023-11-02 10:38:19
>> dealing with E5_24h_R1... 2023-11-02 10:38:19
>> dealing with E5_24h_R2... 2023-11-02 10:38:19
>> dealing with E5_48h_R1... 2023-11-02 10:38:19
>> dealing with E5_48h_R2... 2023-11-02 10:38:19
>> dealing with E5_48h_R3... 2023-11-02 10:38:19
>> dealing with E5_72h_R1... 2023-11-02 10:38:19
>> dealing with E5_72h_R2... 2023-11-02 10:38:20
>> dealing with E5_72h_R3... 2023-11-02 10:38:20
>> merging all info together... 2023-11-02 10:38:20
>> done 2023-11-02 10:38:20
>> checking seqlevels match... 2023-11-02 10:38:20
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-11-02 10:38:20
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:21
>> finding overlap peak in gene scan region... 2023-11-02 10:38:21
>> dealing with left peak not your gene scan region... 2023-11-02 10:38:21
>> merging two set peaks... 2023-11-02 10:38:21
>> calculating distance and dealing with gene strand... 2023-11-02 10:38:22
>> merging all info together ... 2023-11-02 10:38:22
>> done 2023-11-02 10:38:22
>> calculating peakCenter to TSS using peak-gene pair... 2023-11-02 10:38:22
>> calculating RP using centerToTSS and TF hit 2023-11-02 10:38:23
>> merging all info together 2023-11-02 10:38:23
>> done 2023-11-02 10:38:23
>> checking seqlevels match... 2023-11-02 10:38:23
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-11-02 10:38:23
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-11-02 10:38:27
>> 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... 2023-11-02 10:38:28
>> 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... 2023-11-02 10:38:28
>> finding nearest gene and calculating distance... 2023-11-02 10:38:30
>> dealing with gene strand ... 2023-11-02 10:38:30
>> merging all info together ... 2023-11-02 10:38:30
>> done 2023-11-02 10:38:30
>> checking seqlevels match... 2023-11-02 10:38:30
>> 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
>> checking seqlevels match... 2023-11-02 10:38:30
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-11-02 10:38:30
>> finding nearest gene and calculating distance... 2023-11-02 10:38:31
>> dealing with gene strand ... 2023-11-02 10:38:31
>> merging all info together ... 2023-11-02 10:38:31
>> done 2023-11-02 10:38:31
>> checking seqlevels match... 2023-11-02 10:38:32
>> 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
>> checking seqlevels match... 2023-11-02 10:38:32
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-11-02 10:38:33
>> finding nearest gene and calculating distance... 2023-11-02 10:38:33
>> dealing with gene strand ... 2023-11-02 10:38:34
>> merging all info together ... 2023-11-02 10:38:34
>> done 2023-11-02 10:38:34
>> checking seqlevels match... 2023-11-02 10:38:35
>> 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... 2023-11-02 10:38:35
>> 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... 2023-11-02 10:38:35
>> finding nearest gene and calculating distance... 2023-11-02 10:38:36
>> dealing with gene strand ... 2023-11-02 10:38:36
>> merging all info together ... 2023-11-02 10:38:36
>> done 2023-11-02 10:38:36
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-11-02 10:38:37
>> 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
>> checking seqlevels match... 2023-11-02 10:38:37
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-11-02 10:38:37
>> finding nearest gene and calculating distance... 2023-11-02 10:38:38
>> dealing with gene strand ... 2023-11-02 10:38:38
>> merging all info together ... 2023-11-02 10:38:38
>> done 2023-11-02 10:38:38
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-11-02 10:38:40
>> 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
>> checking seqlevels match... 2023-11-02 10:38:41
>> 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
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:42
>> checking seqlevels match... 2023-11-02 10:38:43
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:44
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-11-02 10:38:46
>> merging all info together... 2023-11-02 10:38:46
>> done 2023-11-02 10:38:46
>> checking seqlevels match... 2023-11-02 10:38:46
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2023-11-02 10:38:46
>> checking seqlevels match... 2023-11-02 10:38:46
>> 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... 2023-11-02 10:38:47
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-11-02 10:38:47
>> checking seqlevels match... 2023-11-02 10:38:47
>> 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... 2023-11-02 10:38:48
>> calculating cor and pvalue, which may be time consuming... 2023-11-02 10:38:49
>> merging all info together... 2023-11-02 10:38:49
>> done 2023-11-02 10:38:49
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-11-02 10:38:49
>> merging all info together... 2023-11-02 10:38:49
>> done 2023-11-02 10:38:49
>> checking seqlevels match... 2023-11-02 10:38:50
>> 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... 2023-11-02 10:38:50
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:51
>> finding overlap peak in gene scan region... 2023-11-02 10:38:51
>> dealing with left peak not your gene scan region... 2023-11-02 10:38:51
>> merging two set peaks... 2023-11-02 10:38:51
>> calculating distance and dealing with gene strand... 2023-11-02 10:38:51
>> merging all info together ... 2023-11-02 10:38:51
>> done 2023-11-02 10:38:51
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-11-02 10:38:52
>> merging all info together... 2023-11-02 10:38:52
>> done 2023-11-02 10:38:53
>> checking seqlevels match... 2023-11-02 10:38:53
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2023-11-02 10:38:53
>> checking seqlevels match... 2023-11-02 10:38:53
>> 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
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:54
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-11-02 10:38:54
>> checking seqlevels match... 2023-11-02 10:38:54
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2023-11-02 10:38:55
>> calculating cor and pvalue, which may be time consuming... 2023-11-02 10:38:55
>> merging all info together... 2023-11-02 10:38:56
>> done 2023-11-02 10:38:56
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
93.829 2.115 96.130
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0 | 0 | 0 | |
| calcRP_TFHit | 5.687 | 0.223 | 6.072 | |
| calcRP_coverage | 8.834 | 0.240 | 9.094 | |
| calcRP_region | 6.844 | 0.124 | 6.984 | |
| enhancerPromoterCor | 3.693 | 0.060 | 3.762 | |
| findIT_MARA | 0.632 | 0.003 | 0.636 | |
| findIT_TFHit | 1.321 | 0.048 | 1.371 | |
| findIT_TTPair | 0.11 | 0.00 | 0.11 | |
| findIT_enrichFisher | 0.235 | 0.000 | 0.234 | |
| findIT_enrichWilcox | 0.263 | 0.000 | 0.264 | |
| findIT_regionRP | 9.412 | 0.216 | 9.648 | |
| getAssocPairNumber | 1.599 | 0.008 | 1.611 | |
| integrate_ChIP_RNA | 2.856 | 0.012 | 2.873 | |
| integrate_replicates | 0.003 | 0.000 | 0.003 | |
| jaccard_findIT_TTpair | 0.153 | 0.000 | 0.153 | |
| jaccard_findIT_enrichFisher | 0.327 | 0.008 | 0.335 | |
| loadPeakFile | 0.082 | 0.000 | 0.082 | |
| mm_geneBound | 1.644 | 0.008 | 1.656 | |
| mm_geneScan | 1.708 | 0.048 | 1.761 | |
| mm_nearestGene | 1.501 | 0.004 | 1.508 | |
| peakGeneCor | 3.287 | 0.024 | 3.318 | |
| plot_annoDistance | 2.062 | 0.020 | 2.088 | |
| plot_peakGeneAlias_summary | 1.813 | 0.004 | 1.822 | |
| plot_peakGeneCor | 4.136 | 0.020 | 4.165 | |
| test_geneSet | 0 | 0 | 0 | |