Guandong Shang
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_19 |
| git_last_commit: ca624b0 |
| git_last_commit_date: 2024-04-30 11:35:36 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:34 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 723/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.10.0 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / 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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2024-05-29 20:50:39 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 20:57:34 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 414.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FindIT2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.10.0’
* 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 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 6.862 0.176 7.108
calcRP_region 5.529 0.174 5.771
calcRP_coverage 4.453 0.637 5.161
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(FindIT2)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
> if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) {
+ stop("unable to load TxDb.Athaliana.BioMart.plantsmart28")
+ }
Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28
>
> test_check("FindIT2")
>> preparing gene features information... 2024-05-29 20:56:18
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:56:20
>> preparing weight info... 2024-05-29 20:56:20
>> loading E50h_sampleChr5.bw info... 2024-05-29 20:56:20
------------
>> extracting and calcluating Chr5 signal... 2024-05-29 20:56:20
>> dealing with Chr5 left gene signal... 2024-05-29 20:56:23
>> norming Chr5RP accoring to the whole Chr RP... 2024-05-29 20:56:24
>> merging all Chr RP together... 2024-05-29 20:56:24
>> done 2024-05-29 20:56:24
>> checking seqlevels match... 2024-05-29 20:56:24
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-05-29 20:56:25
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:56:26
>> finding overlap peak in gene scan region... 2024-05-29 20:56:26
>> dealing with left peak not your gene scan region... 2024-05-29 20:56:26
>> merging two set peaks... 2024-05-29 20:56:26
>> calculating distance and dealing with gene strand... 2024-05-29 20:56:26
>> merging all info together ... 2024-05-29 20:56:26
>> done 2024-05-29 20:56:26
>> calculating peakCenter to TSS using peak-gene pair... 2024-05-29 20:56:26
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-05-29 20:56:27
>> calculating RP using centerToTSS and peak score2024-05-29 20:56:27
>> merging all info together 2024-05-29 20:56:29
>> done 2024-05-29 20:56:30
>> calculating peakCenter to TSS using peak-gene pair... 2024-05-29 20:56:30
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-05-29 20:56:31
>> calculating RP using centerToTSS and peak score2024-05-29 20:56:31
>> merging all info together 2024-05-29 20:56:34
>> done 2024-05-29 20:56:35
>> checking seqlevels match... 2024-05-29 20:56:35
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-05-29 20:56:35
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:56:36
>> finding overlap peak in gene scan region... 2024-05-29 20:56:36
>> dealing with left peak not your gene scan region... 2024-05-29 20:56:36
>> merging two set peaks... 2024-05-29 20:56:36
>> calculating distance and dealing with gene strand... 2024-05-29 20:56:36
>> merging all info together ... 2024-05-29 20:56:36
>> done 2024-05-29 20:56:36
>> calculating peakCenter to TSS using peak-gene pair... 2024-05-29 20:56:36
>> calculating RP using centerToTSS and TF hit 2024-05-29 20:56:37
>> merging all info together 2024-05-29 20:56:37
>> done 2024-05-29 20:56:37
>> calculating peakCenter to TSS using peak-gene pair... 2024-05-29 20:56:37
>> calculating RP using centerToTSS and TF hit 2024-05-29 20:56:38
>> merging all info together 2024-05-29 20:56:38
>> done 2024-05-29 20:56:38
>> checking seqlevels match... 2024-05-29 20:56:39
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-05-29 20:56:39
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:56:40
>> finding overlap peak in gene scan region... 2024-05-29 20:56:40
>> dealing with left peak not your gene scan region... 2024-05-29 20:56:40
>> merging two set peaks... 2024-05-29 20:56:41
>> calculating distance and dealing with gene strand... 2024-05-29 20:56:41
>> merging all info together ... 2024-05-29 20:56:41
>> done 2024-05-29 20:56:41
>> calculating peakCenter to TSS using peak-gene pair... 2024-05-29 20:56:41
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-05-29 20:56:42
>> calculating RP using centerToTSS and peak score2024-05-29 20:56:42
>> merging all info together 2024-05-29 20:56:45
>> done 2024-05-29 20:56:45
>> extracting RP info from regionRP... 2024-05-29 20:56:46
>> dealing with TF_GR_databse... 2024-05-29 20:56:46
>> calculating percent and p-value... 2024-05-29 20:56:46
>> dealing withE5_0h_R1... 2024-05-29 20:56:46
>> dealing withE5_0h_R2... 2024-05-29 20:56:46
>> dealing withE5_4h_R1... 2024-05-29 20:56:46
>> dealing withE5_4h_R2... 2024-05-29 20:56:46
>> dealing withE5_8h_R1... 2024-05-29 20:56:46
>> dealing withE5_8h_R2... 2024-05-29 20:56:46
>> dealing withE5_16h_R1... 2024-05-29 20:56:47
>> dealing withE5_16h_R2... 2024-05-29 20:56:47
>> dealing withE5_24h_R1... 2024-05-29 20:56:47
>> dealing withE5_24h_R2... 2024-05-29 20:56:47
>> dealing withE5_48h_R1... 2024-05-29 20:56:47
>> dealing withE5_48h_R2... 2024-05-29 20:56:47
>> dealing withE5_48h_R3... 2024-05-29 20:56:47
>> dealing withE5_72h_R1... 2024-05-29 20:56:47
>> dealing withE5_72h_R2... 2024-05-29 20:56:47
>> dealing withE5_72h_R3... 2024-05-29 20:56:47
>> merging all info together... 2024-05-29 20:56:47
>> done 2024-05-29 20:56:47
>> preparing gene features information... 2024-05-29 20:56:47
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:56:48
>> calculating p-value for each TF, which may be time consuming... 2024-05-29 20:56:48
>> merging all info together... 2024-05-29 20:56:48
>> done 2024-05-29 20:56:48
>> dealing with TF_GR_database... 2024-05-29 20:56:48
>> calculating coef and converting into z-score using INT... 2024-05-29 20:56:49
>> dealing with E5_0h_R1... 2024-05-29 20:56:49
>> dealing with E5_0h_R2... 2024-05-29 20:56:49
>> dealing with E5_4h_R1... 2024-05-29 20:56:49
>> dealing with E5_4h_R2... 2024-05-29 20:56:49
>> dealing with E5_8h_R1... 2024-05-29 20:56:49
>> dealing with E5_8h_R2... 2024-05-29 20:56:49
>> dealing with E5_16h_R1... 2024-05-29 20:56:49
>> dealing with E5_16h_R2... 2024-05-29 20:56:49
>> dealing with E5_24h_R1... 2024-05-29 20:56:49
>> dealing with E5_24h_R2... 2024-05-29 20:56:49
>> dealing with E5_48h_R1... 2024-05-29 20:56:49
>> dealing with E5_48h_R2... 2024-05-29 20:56:50
>> dealing with E5_48h_R3... 2024-05-29 20:56:50
>> dealing with E5_72h_R1... 2024-05-29 20:56:50
>> dealing with E5_72h_R2... 2024-05-29 20:56:50
>> dealing with E5_72h_R3... 2024-05-29 20:56:50
>> merging all info together... 2024-05-29 20:56:50
>> done 2024-05-29 20:56:50
>> checking seqlevels match... 2024-05-29 20:56:50
>> 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... 2024-05-29 20:56:50
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:56:51
>> finding overlap peak in gene scan region... 2024-05-29 20:56:51
>> dealing with left peak not your gene scan region... 2024-05-29 20:56:51
>> merging two set peaks... 2024-05-29 20:56:51
>> calculating distance and dealing with gene strand... 2024-05-29 20:56:51
>> merging all info together ... 2024-05-29 20:56:51
>> done 2024-05-29 20:56:51
>> calculating peakCenter to TSS using peak-gene pair... 2024-05-29 20:56:51
>> calculating RP using centerToTSS and TF hit 2024-05-29 20:56:52
>> merging all info together 2024-05-29 20:56:52
>> done 2024-05-29 20:56:52
>> checking seqlevels match... 2024-05-29 20:56:53
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2024-05-29 20:56:53
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2024-05-29 20:56:57
>> 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... 2024-05-29 20:56:57
>> 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... 2024-05-29 20:56:57
>> finding nearest gene and calculating distance... 2024-05-29 20:56:59
>> dealing with gene strand ... 2024-05-29 20:56:59
>> merging all info together ... 2024-05-29 20:56:59
>> done 2024-05-29 20:56:59
>> checking seqlevels match... 2024-05-29 20:56:59
>> 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... 2024-05-29 20:56:59
>> 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... 2024-05-29 20:56:59
>> finding nearest gene and calculating distance... 2024-05-29 20:57:00
>> dealing with gene strand ... 2024-05-29 20:57:00
>> merging all info together ... 2024-05-29 20:57:00
>> done 2024-05-29 20:57:00
>> checking seqlevels match... 2024-05-29 20:57:01
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2024-05-29 20:57:01
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-05-29 20:57:01
>> finding nearest gene and calculating distance... 2024-05-29 20:57:02
>> dealing with gene strand ... 2024-05-29 20:57:02
>> merging all info together ... 2024-05-29 20:57:02
>> done 2024-05-29 20:57:02
>> checking seqlevels match... 2024-05-29 20:57:03
>> 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
>> checking seqlevels match... 2024-05-29 20:57:03
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2024-05-29 20:57:03
>> finding nearest gene and calculating distance... 2024-05-29 20:57:04
>> dealing with gene strand ... 2024-05-29 20:57:04
>> merging all info together ... 2024-05-29 20:57:04
>> done 2024-05-29 20:57:04
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2024-05-29 20:57:05
>> 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... 2024-05-29 20:57:05
>> 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... 2024-05-29 20:57:05
>> finding nearest gene and calculating distance... 2024-05-29 20:57:06
>> dealing with gene strand ... 2024-05-29 20:57:06
>> merging all info together ... 2024-05-29 20:57:06
>> done 2024-05-29 20:57:06
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2024-05-29 20:57:08
>> 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... 2024-05-29 20:57:09
>> 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
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:57:10
>> checking seqlevels match... 2024-05-29 20:57:10
>> 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... 2024-05-29 20:57:11
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-05-29 20:57:13
>> merging all info together... 2024-05-29 20:57:13
>> done 2024-05-29 20:57:13
>> checking seqlevels match... 2024-05-29 20:57:13
>> 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... 2024-05-29 20:57:13
>> checking seqlevels match... 2024-05-29 20:57:13
>> 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
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:57:14
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2024-05-29 20:57:15
>> checking seqlevels match... 2024-05-29 20:57:15
>> 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... 2024-05-29 20:57:16
>> calculating cor and pvalue, which may be time consuming... 2024-05-29 20:57:16
>> merging all info together... 2024-05-29 20:57:16
>> done 2024-05-29 20:57:16
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-05-29 20:57:16
>> merging all info together... 2024-05-29 20:57:16
>> done 2024-05-29 20:57:16
>> checking seqlevels match... 2024-05-29 20:57:16
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2024-05-29 20:57:17
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:57:18
>> finding overlap peak in gene scan region... 2024-05-29 20:57:18
>> dealing with left peak not your gene scan region... 2024-05-29 20:57:18
>> merging two set peaks... 2024-05-29 20:57:18
>> calculating distance and dealing with gene strand... 2024-05-29 20:57:18
>> merging all info together ... 2024-05-29 20:57:18
>> done 2024-05-29 20:57:18
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2024-05-29 20:57:19
>> merging all info together... 2024-05-29 20:57:19
>> done 2024-05-29 20:57:19
>> checking seqlevels match... 2024-05-29 20:57:19
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2024-05-29 20:57:19
>> checking seqlevels match... 2024-05-29 20:57:19
>> 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
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:57:20
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2024-05-29 20:57:21
>> checking seqlevels match... 2024-05-29 20:57:21
>> 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
>> some scan range may cross Chr bound, trimming... 2024-05-29 20:57:22
>> calculating cor and pvalue, which may be time consuming... 2024-05-29 20:57:22
>> merging all info together... 2024-05-29 20:57:22
>> done 2024-05-29 20:57:22
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
75.841 3.315 79.900
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0.000 | 0.001 | 0.001 | |
| calcRP_TFHit | 4.195 | 0.209 | 4.527 | |
| calcRP_coverage | 4.453 | 0.637 | 5.161 | |
| calcRP_region | 5.529 | 0.174 | 5.771 | |
| enhancerPromoterCor | 3.449 | 0.117 | 3.604 | |
| findIT_MARA | 0.498 | 0.014 | 0.516 | |
| findIT_TFHit | 1.232 | 0.042 | 1.285 | |
| findIT_TTPair | 0.096 | 0.007 | 0.106 | |
| findIT_enrichFisher | 0.191 | 0.006 | 0.200 | |
| findIT_enrichWilcox | 0.219 | 0.005 | 0.226 | |
| findIT_regionRP | 6.862 | 0.176 | 7.108 | |
| getAssocPairNumber | 2.374 | 0.078 | 2.479 | |
| integrate_ChIP_RNA | 2.358 | 0.082 | 2.464 | |
| integrate_replicates | 0.003 | 0.001 | 0.004 | |
| jaccard_findIT_TTpair | 0.121 | 0.008 | 0.131 | |
| jaccard_findIT_enrichFisher | 0.246 | 0.008 | 0.258 | |
| loadPeakFile | 0.074 | 0.002 | 0.077 | |
| mm_geneBound | 1.442 | 0.047 | 1.504 | |
| mm_geneScan | 1.484 | 0.061 | 1.562 | |
| mm_nearestGene | 1.297 | 0.039 | 1.351 | |
| peakGeneCor | 2.681 | 0.079 | 2.784 | |
| plot_annoDistance | 1.745 | 0.056 | 1.818 | |
| plot_peakGeneAlias_summary | 1.507 | 0.035 | 1.552 | |
| plot_peakGeneCor | 3.347 | 0.086 | 3.463 | |
| test_geneSet | 0.000 | 0.001 | 0.001 | |