Guandong Shang
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_17 |
| git_last_commit: ed293ae |
| git_last_commit_date: 2023-04-25 11:31:01 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:02 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 700/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.6.0 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.6.0.tar.gz |
| StartedAt: 2023-10-16 01:41:41 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 01:56:16 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 875.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.6.0’
* 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 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 13.392 0.171 17.516
calcRP_region 10.204 0.311 14.244
calcRP_coverage 7.201 0.561 10.639
plot_peakGeneCor 6.687 0.082 8.939
calcRP_TFHit 6.512 0.217 8.960
enhancerPromoterCor 5.484 0.090 7.112
peakGeneCor 5.292 0.104 7.339
integrate_ChIP_RNA 3.984 0.054 5.122
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
FindIT2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘FindIT2’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FindIT2)
FindIT2.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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... 2023-10-16 01:53:32
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:53:36
>> preparing weight info... 2023-10-16 01:53:36
>> loading E50h_sampleChr5.bw info... 2023-10-16 01:53:36
------------
>> extracting and calcluating Chr5 signal... 2023-10-16 01:53:36
>> dealing with Chr5 left gene signal... 2023-10-16 01:53:44
>> norming Chr5RP accoring to the whole Chr RP... 2023-10-16 01:53:44
>> merging all Chr RP together... 2023-10-16 01:53:44
>> done 2023-10-16 01:53:44
>> checking seqlevels match... 2023-10-16 01:53:44
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-10-16 01:53:45
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:53:47
>> finding overlap peak in gene scan region... 2023-10-16 01:53:47
>> dealing with left peak not your gene scan region... 2023-10-16 01:53:47
>> merging two set peaks... 2023-10-16 01:53:48
>> calculating distance and dealing with gene strand... 2023-10-16 01:53:48
>> merging all info together ... 2023-10-16 01:53:48
>> done 2023-10-16 01:53:48
>> calculating peakCenter to TSS using peak-gene pair... 2023-10-16 01:53:48
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-10-16 01:53:50
>> calculating RP using centerToTSS and peak score2023-10-16 01:53:50
>> merging all info together 2023-10-16 01:53:56
>> done 2023-10-16 01:53:58
>> calculating peakCenter to TSS using peak-gene pair... 2023-10-16 01:53:58
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-10-16 01:54:00
>> calculating RP using centerToTSS and peak score2023-10-16 01:54:00
>> merging all info together 2023-10-16 01:54:08
>> done 2023-10-16 01:54:09
>> checking seqlevels match... 2023-10-16 01:54:09
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-10-16 01:54:09
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:54:11
>> finding overlap peak in gene scan region... 2023-10-16 01:54:11
>> dealing with left peak not your gene scan region... 2023-10-16 01:54:11
>> merging two set peaks... 2023-10-16 01:54:12
>> calculating distance and dealing with gene strand... 2023-10-16 01:54:12
>> merging all info together ... 2023-10-16 01:54:12
>> done 2023-10-16 01:54:12
>> calculating peakCenter to TSS using peak-gene pair... 2023-10-16 01:54:12
>> calculating RP using centerToTSS and TF hit 2023-10-16 01:54:14
>> merging all info together 2023-10-16 01:54:14
>> done 2023-10-16 01:54:14
>> calculating peakCenter to TSS using peak-gene pair... 2023-10-16 01:54:14
>> calculating RP using centerToTSS and TF hit 2023-10-16 01:54:16
>> merging all info together 2023-10-16 01:54:16
>> done 2023-10-16 01:54:16
>> checking seqlevels match... 2023-10-16 01:54:19
>> 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... 2023-10-16 01:54:19
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:54:21
>> finding overlap peak in gene scan region... 2023-10-16 01:54:21
>> dealing with left peak not your gene scan region... 2023-10-16 01:54:21
>> merging two set peaks... 2023-10-16 01:54:22
>> calculating distance and dealing with gene strand... 2023-10-16 01:54:22
>> merging all info together ... 2023-10-16 01:54:22
>> done 2023-10-16 01:54:22
>> calculating peakCenter to TSS using peak-gene pair... 2023-10-16 01:54:22
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-10-16 01:54:25
>> calculating RP using centerToTSS and peak score2023-10-16 01:54:25
>> merging all info together 2023-10-16 01:54:31
>> done 2023-10-16 01:54:32
>> extracting RP info from regionRP... 2023-10-16 01:54:33
>> dealing with TF_GR_databse... 2023-10-16 01:54:34
>> calculating percent and p-value... 2023-10-16 01:54:34
>> dealing withE5_0h_R1... 2023-10-16 01:54:34
>> dealing withE5_0h_R2... 2023-10-16 01:54:34
>> dealing withE5_4h_R1... 2023-10-16 01:54:34
>> dealing withE5_4h_R2... 2023-10-16 01:54:34
>> dealing withE5_8h_R1... 2023-10-16 01:54:34
>> dealing withE5_8h_R2... 2023-10-16 01:54:34
>> dealing withE5_16h_R1... 2023-10-16 01:54:34
>> dealing withE5_16h_R2... 2023-10-16 01:54:34
>> dealing withE5_24h_R1... 2023-10-16 01:54:35
>> dealing withE5_24h_R2... 2023-10-16 01:54:35
>> dealing withE5_48h_R1... 2023-10-16 01:54:35
>> dealing withE5_48h_R2... 2023-10-16 01:54:35
>> dealing withE5_48h_R3... 2023-10-16 01:54:35
>> dealing withE5_72h_R1... 2023-10-16 01:54:35
>> dealing withE5_72h_R2... 2023-10-16 01:54:35
>> dealing withE5_72h_R3... 2023-10-16 01:54:35
>> merging all info together... 2023-10-16 01:54:36
>> done 2023-10-16 01:54:36
>> preparing gene features information... 2023-10-16 01:54:36
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:54:38
>> calculating p-value for each TF, which may be time consuming... 2023-10-16 01:54:38
>> merging all info together... 2023-10-16 01:54:38
>> done 2023-10-16 01:54:38
>> dealing with TF_GR_database... 2023-10-16 01:54:39
>> calculating coef and converting into z-score using INT... 2023-10-16 01:54:39
>> dealing with E5_0h_R1... 2023-10-16 01:54:39
>> dealing with E5_0h_R2... 2023-10-16 01:54:40
>> dealing with E5_4h_R1... 2023-10-16 01:54:40
>> dealing with E5_4h_R2... 2023-10-16 01:54:40
>> dealing with E5_8h_R1... 2023-10-16 01:54:40
>> dealing with E5_8h_R2... 2023-10-16 01:54:40
>> dealing with E5_16h_R1... 2023-10-16 01:54:41
>> dealing with E5_16h_R2... 2023-10-16 01:54:41
>> dealing with E5_24h_R1... 2023-10-16 01:54:41
>> dealing with E5_24h_R2... 2023-10-16 01:54:41
>> dealing with E5_48h_R1... 2023-10-16 01:54:42
>> dealing with E5_48h_R2... 2023-10-16 01:54:42
>> dealing with E5_48h_R3... 2023-10-16 01:54:42
>> dealing with E5_72h_R1... 2023-10-16 01:54:43
>> dealing with E5_72h_R2... 2023-10-16 01:54:43
>> dealing with E5_72h_R3... 2023-10-16 01:54:43
>> merging all info together... 2023-10-16 01:54:43
>> done 2023-10-16 01:54:44
>> checking seqlevels match... 2023-10-16 01:54:44
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-10-16 01:54:44
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:54:46
>> finding overlap peak in gene scan region... 2023-10-16 01:54:46
>> dealing with left peak not your gene scan region... 2023-10-16 01:54:46
>> merging two set peaks... 2023-10-16 01:54:47
>> calculating distance and dealing with gene strand... 2023-10-16 01:54:47
>> merging all info together ... 2023-10-16 01:54:47
>> done 2023-10-16 01:54:47
>> calculating peakCenter to TSS using peak-gene pair... 2023-10-16 01:54:47
>> calculating RP using centerToTSS and TF hit 2023-10-16 01:54:49
>> merging all info together 2023-10-16 01:54:49
>> done 2023-10-16 01:54:49
>> checking seqlevels match... 2023-10-16 01:54:50
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-10-16 01:54:50
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-10-16 01:54:59
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2023-10-16 01:54:59
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-10-16 01:54:59
>> finding nearest gene and calculating distance... 2023-10-16 01:55:01
>> dealing with gene strand ... 2023-10-16 01:55:01
>> merging all info together ... 2023-10-16 01:55:01
>> done 2023-10-16 01:55:01
>> checking seqlevels match... 2023-10-16 01:55:02
>> 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... 2023-10-16 01:55:02
>> 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... 2023-10-16 01:55:02
>> finding nearest gene and calculating distance... 2023-10-16 01:55:05
>> dealing with gene strand ... 2023-10-16 01:55:06
>> merging all info together ... 2023-10-16 01:55:06
>> done 2023-10-16 01:55:06
>> checking seqlevels match... 2023-10-16 01:55:08
>> 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
>> checking seqlevels match... 2023-10-16 01:55:08
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-10-16 01:55:08
>> finding nearest gene and calculating distance... 2023-10-16 01:55:10
>> dealing with gene strand ... 2023-10-16 01:55:11
>> merging all info together ... 2023-10-16 01:55:11
>> done 2023-10-16 01:55:11
>> checking seqlevels match... 2023-10-16 01:55:13
>> 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
>> checking seqlevels match... 2023-10-16 01:55:13
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-10-16 01:55:13
>> finding nearest gene and calculating distance... 2023-10-16 01:55:15
>> dealing with gene strand ... 2023-10-16 01:55:15
>> merging all info together ... 2023-10-16 01:55:15
>> done 2023-10-16 01:55:15
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-10-16 01:55:17
>> 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
>> checking seqlevels match... 2023-10-16 01:55:18
>> 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... 2023-10-16 01:55:18
>> finding nearest gene and calculating distance... 2023-10-16 01:55:20
>> dealing with gene strand ... 2023-10-16 01:55:20
>> merging all info together ... 2023-10-16 01:55:20
>> done 2023-10-16 01:55:20
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-10-16 01:55:23
>> 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... 2023-10-16 01:55:25
>> 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
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:55:27
>> checking seqlevels match... 2023-10-16 01:55:29
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:55:31
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-10-16 01:55:35
>> merging all info together... 2023-10-16 01:55:35
>> done 2023-10-16 01:55:36
>> checking seqlevels match... 2023-10-16 01:55:36
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2023-10-16 01:55:36
>> checking seqlevels match... 2023-10-16 01:55:36
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:55:38
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-10-16 01:55:39
>> checking seqlevels match... 2023-10-16 01:55:39
>> 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... 2023-10-16 01:55:41
>> calculating cor and pvalue, which may be time consuming... 2023-10-16 01:55:41
>> merging all info together... 2023-10-16 01:55:42
>> done 2023-10-16 01:55:42
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-10-16 01:55:42
>> merging all info together... 2023-10-16 01:55:42
>> done 2023-10-16 01:55:43
>> checking seqlevels match... 2023-10-16 01:55:43
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-10-16 01:55:43
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:55:45
>> finding overlap peak in gene scan region... 2023-10-16 01:55:45
>> dealing with left peak not your gene scan region... 2023-10-16 01:55:45
>> merging two set peaks... 2023-10-16 01:55:45
>> calculating distance and dealing with gene strand... 2023-10-16 01:55:46
>> merging all info together ... 2023-10-16 01:55:46
>> done 2023-10-16 01:55:46
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-10-16 01:55:49
>> merging all info together... 2023-10-16 01:55:49
>> done 2023-10-16 01:55:49
>> checking seqlevels match... 2023-10-16 01:55:49
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2023-10-16 01:55:49
>> checking seqlevels match... 2023-10-16 01:55:49
>> 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
>> some scan range may cross Chr bound, trimming... 2023-10-16 01:55:51
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-10-16 01:55:52
>> checking seqlevels match... 2023-10-16 01:55:52
>> 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... 2023-10-16 01:55:54
>> calculating cor and pvalue, which may be time consuming... 2023-10-16 01:55:54
>> merging all info together... 2023-10-16 01:55:55
>> done 2023-10-16 01:55:55
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
131.127 3.408 176.227
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0.001 | 0.001 | 0.007 | |
| calcRP_TFHit | 6.512 | 0.217 | 8.960 | |
| calcRP_coverage | 7.201 | 0.561 | 10.639 | |
| calcRP_region | 10.204 | 0.311 | 14.244 | |
| enhancerPromoterCor | 5.484 | 0.090 | 7.112 | |
| findIT_MARA | 0.962 | 0.034 | 1.231 | |
| findIT_TFHit | 2.001 | 0.097 | 3.184 | |
| findIT_TTPair | 0.205 | 0.016 | 0.278 | |
| findIT_enrichFisher | 0.347 | 0.008 | 0.476 | |
| findIT_enrichWilcox | 0.382 | 0.009 | 0.548 | |
| findIT_regionRP | 13.392 | 0.171 | 17.516 | |
| getAssocPairNumber | 2.301 | 0.038 | 3.211 | |
| integrate_ChIP_RNA | 3.984 | 0.054 | 5.122 | |
| integrate_replicates | 0.004 | 0.002 | 0.010 | |
| jaccard_findIT_TTpair | 0.226 | 0.010 | 0.290 | |
| jaccard_findIT_enrichFisher | 0.462 | 0.011 | 0.653 | |
| loadPeakFile | 0.128 | 0.003 | 0.174 | |
| mm_geneBound | 2.399 | 0.039 | 3.289 | |
| mm_geneScan | 2.421 | 0.031 | 3.228 | |
| mm_nearestGene | 2.181 | 0.042 | 2.902 | |
| peakGeneCor | 5.292 | 0.104 | 7.339 | |
| plot_annoDistance | 2.969 | 0.056 | 4.185 | |
| plot_peakGeneAlias_summary | 2.733 | 0.051 | 3.807 | |
| plot_peakGeneCor | 6.687 | 0.082 | 8.939 | |
| test_geneSet | 0.000 | 0.001 | 0.002 | |