Guandong Shang
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_16 |
| git_last_commit: 081e7ae |
| git_last_commit_date: 2022-11-01 11:25:15 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:33 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the FindIT2 package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 677/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.4.0 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FindIT2 |
| Version: 1.4.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings FindIT2_1.4.0.tar.gz |
| StartedAt: 2023-04-11 01:29:07 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:34:50 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 343.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings FindIT2_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/FindIT2.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FindIT2/DESCRIPTION' ... OK
* this is package 'FindIT2' version '1.4.0'
* 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 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
calcRP_region 6.26 0.23 6.78
findIT_regionRP 6.33 0.12 6.45
* 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: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")
>> checking seqlevels match... 2023-04-11 1:33:43 AM
>> 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... 2023-04-11 1:33:43 AM
>> some scan range may cross Chr bound, trimming... 2023-04-11 1:33:45 AM
>> finding overlap peak in gene scan region... 2023-04-11 1:33:45 AM
>> dealing with left peak not your gene scan region... 2023-04-11 1:33:45 AM
>> merging two set peaks... 2023-04-11 1:33:46 AM
>> calculating distance and dealing with gene strand... 2023-04-11 1:33:46 AM
>> merging all info together ... 2023-04-11 1:33:46 AM
>> done 2023-04-11 1:33:46 AM
>> calculating peakCenter to TSS using peak-gene pair... 2023-04-11 1:33:46 AM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-04-11 1:33:47 AM
>> calculating RP using centerToTSS and peak score2023-04-11 1:33:47 AM
>> merging all info together 2023-04-11 1:33:49 AM
>> done 2023-04-11 1:33:50 AM
>> calculating peakCenter to TSS using peak-gene pair... 2023-04-11 1:33:50 AM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-04-11 1:33:52 AM
>> calculating RP using centerToTSS and peak score2023-04-11 1:33:52 AM
>> merging all info together 2023-04-11 1:33:55 AM
>> done 2023-04-11 1:33:55 AM
>> checking seqlevels match... 2023-04-11 1:33:56 AM
>> 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... 2023-04-11 1:33:56 AM
>> some scan range may cross Chr bound, trimming... 2023-04-11 1:33:57 AM
>> finding overlap peak in gene scan region... 2023-04-11 1:33:57 AM
>> dealing with left peak not your gene scan region... 2023-04-11 1:33:57 AM
>> merging two set peaks... 2023-04-11 1:33:57 AM
>> calculating distance and dealing with gene strand... 2023-04-11 1:33:57 AM
>> merging all info together ... 2023-04-11 1:33:57 AM
>> done 2023-04-11 1:33:57 AM
>> calculating peakCenter to TSS using peak-gene pair... 2023-04-11 1:33:57 AM
>> calculating RP using centerToTSS and TF hit 2023-04-11 1:33:58 AM
>> merging all info together 2023-04-11 1:33:58 AM
>> done 2023-04-11 1:33:58 AM
>> calculating peakCenter to TSS using peak-gene pair... 2023-04-11 1:33:58 AM
>> calculating RP using centerToTSS and TF hit 2023-04-11 1:33:59 AM
>> merging all info together 2023-04-11 1:33:59 AM
>> done 2023-04-11 1:33:59 AM
>> checking seqlevels match... 2023-04-11 1:34:00 AM
>> 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... 2023-04-11 1:34:00 AM
>> some scan range may cross Chr bound, trimming... 2023-04-11 1:34:01 AM
>> finding overlap peak in gene scan region... 2023-04-11 1:34:01 AM
>> dealing with left peak not your gene scan region... 2023-04-11 1:34:01 AM
>> merging two set peaks... 2023-04-11 1:34:01 AM
>> calculating distance and dealing with gene strand... 2023-04-11 1:34:01 AM
>> merging all info together ... 2023-04-11 1:34:01 AM
>> done 2023-04-11 1:34:01 AM
>> calculating peakCenter to TSS using peak-gene pair... 2023-04-11 1:34:01 AM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-04-11 1:34:02 AM
>> calculating RP using centerToTSS and peak score2023-04-11 1:34:02 AM
>> merging all info together 2023-04-11 1:34:04 AM
>> done 2023-04-11 1:34:04 AM
>> extracting RP info from regionRP... 2023-04-11 1:34:05 AM
>> dealing with TF_GR_databse... 2023-04-11 1:34:05 AM
>> calculating percent and p-value... 2023-04-11 1:34:05 AM
>> dealing withE5_0h_R1... 2023-04-11 1:34:05 AM
>> dealing withE5_0h_R2... 2023-04-11 1:34:05 AM
>> dealing withE5_4h_R1... 2023-04-11 1:34:05 AM
>> dealing withE5_4h_R2... 2023-04-11 1:34:05 AM
>> dealing withE5_8h_R1... 2023-04-11 1:34:05 AM
>> dealing withE5_8h_R2... 2023-04-11 1:34:05 AM
>> dealing withE5_16h_R1... 2023-04-11 1:34:05 AM
>> dealing withE5_16h_R2... 2023-04-11 1:34:05 AM
>> dealing withE5_24h_R1... 2023-04-11 1:34:05 AM
>> dealing withE5_24h_R2... 2023-04-11 1:34:05 AM
>> dealing withE5_48h_R1... 2023-04-11 1:34:05 AM
>> dealing withE5_48h_R2... 2023-04-11 1:34:05 AM
>> dealing withE5_48h_R3... 2023-04-11 1:34:05 AM
>> dealing withE5_72h_R1... 2023-04-11 1:34:06 AM
>> dealing withE5_72h_R2... 2023-04-11 1:34:06 AM
>> dealing withE5_72h_R3... 2023-04-11 1:34:06 AM
>> merging all info together... 2023-04-11 1:34:06 AM
>> done 2023-04-11 1:34:06 AM
>> preparing gene features information... 2023-04-11 1:34:06 AM
>> some scan range may cross Chr bound, trimming... 2023-04-11 1:34:07 AM
>> calculating p-value for each TF, which may be time consuming... 2023-04-11 1:34:07 AM
>> merging all info together... 2023-04-11 1:34:07 AM
>> done 2023-04-11 1:34:07 AM
>> dealing with TF_GR_database... 2023-04-11 1:34:07 AM
>> calculating coef and converting into z-score using INT... 2023-04-11 1:34:07 AM
>> dealing with E5_0h_R1... 2023-04-11 1:34:07 AM
>> dealing with E5_0h_R2... 2023-04-11 1:34:07 AM
>> dealing with E5_4h_R1... 2023-04-11 1:34:07 AM
>> dealing with E5_4h_R2... 2023-04-11 1:34:07 AM
>> dealing with E5_8h_R1... 2023-04-11 1:34:08 AM
>> dealing with E5_8h_R2... 2023-04-11 1:34:08 AM
>> dealing with E5_16h_R1... 2023-04-11 1:34:08 AM
>> dealing with E5_16h_R2... 2023-04-11 1:34:08 AM
>> dealing with E5_24h_R1... 2023-04-11 1:34:08 AM
>> dealing with E5_24h_R2... 2023-04-11 1:34:08 AM
>> dealing with E5_48h_R1... 2023-04-11 1:34:08 AM
>> dealing with E5_48h_R2... 2023-04-11 1:34:08 AM
>> dealing with E5_48h_R3... 2023-04-11 1:34:08 AM
>> dealing with E5_72h_R1... 2023-04-11 1:34:08 AM
>> dealing with E5_72h_R2... 2023-04-11 1:34:08 AM
>> dealing with E5_72h_R3... 2023-04-11 1:34:08 AM
>> merging all info together... 2023-04-11 1:34:08 AM
>> done 2023-04-11 1:34:09 AM
>> checking seqlevels match... 2023-04-11 1:34:09 AM
>> 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... 2023-04-11 1:34:09 AM
>> some scan range may cross Chr bound, trimming... 2023-04-11 1:34:10 AM
>> finding overlap peak in gene scan region... 2023-04-11 1:34:10 AM
>> dealing with left peak not your gene scan region... 2023-04-11 1:34:10 AM
>> merging two set peaks... 2023-04-11 1:34:10 AM
>> calculating distance and dealing with gene strand... 2023-04-11 1:34:10 AM
>> merging all info together ... 2023-04-11 1:34:10 AM
>> done 2023-04-11 1:34:10 AM
>> calculating peakCenter to TSS using peak-gene pair... 2023-04-11 1:34:10 AM
>> calculating RP using centerToTSS and TF hit 2023-04-11 1:34:11 AM
>> merging all info together 2023-04-11 1:34:11 AM
>> done 2023-04-11 1:34:11 AM
>> checking seqlevels match... 2023-04-11 1:34:11 AM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-04-11 1:34:11 AM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-04-11 1:34:15 AM
>> 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... 2023-04-11 1:34:16 AM
>> 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... 2023-04-11 1:34:16 AM
>> finding nearest gene and calculating distance... 2023-04-11 1:34:16 AM
>> dealing with gene strand ... 2023-04-11 1:34:16 AM
>> merging all info together ... 2023-04-11 1:34:16 AM
>> done 2023-04-11 1:34:16 AM
>> checking seqlevels match... 2023-04-11 1:34:17 AM
>> 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... 2023-04-11 1:34:17 AM
>> 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... 2023-04-11 1:34:17 AM
>> finding nearest gene and calculating distance... 2023-04-11 1:34:17 AM
>> dealing with gene strand ... 2023-04-11 1:34:17 AM
>> merging all info together ... 2023-04-11 1:34:17 AM
>> done 2023-04-11 1:34:17 AM
>> checking seqlevels match... 2023-04-11 1:34:18 AM
>> 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... 2023-04-11 1:34:18 AM
>> 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... 2023-04-11 1:34:18 AM
>> finding nearest gene and calculating distance... 2023-04-11 1:34:19 AM
>> dealing with gene strand ... 2023-04-11 1:34:19 AM
>> merging all info together ... 2023-04-11 1:34:19 AM
>> done 2023-04-11 1:34:19 AM
>> checking seqlevels match... 2023-04-11 1:34:20 AM
>> 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... 2023-04-11 1:34:20 AM
>> 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... 2023-04-11 1:34:20 AM
>> finding nearest gene and calculating distance... 2023-04-11 1:34:21 AM
>> dealing with gene strand ... 2023-04-11 1:34:21 AM
>> merging all info together ... 2023-04-11 1:34:21 AM
>> done 2023-04-11 1:34:21 AM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-04-11 1:34:22 AM
>> 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... 2023-04-11 1:34:22 AM
>> 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... 2023-04-11 1:34:22 AM
>> finding nearest gene and calculating distance... 2023-04-11 1:34:23 AM
>> dealing with gene strand ... 2023-04-11 1:34:23 AM
>> merging all info together ... 2023-04-11 1:34:23 AM
>> done 2023-04-11 1:34:23 AM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-04-11 1:34:24 AM
>> 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... 2023-04-11 1:34:25 AM
>> 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... 2023-04-11 1:34:26 AM
>> checking seqlevels match... 2023-04-11 1:34:27 AM
>> 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... 2023-04-11 1:34:27 AM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-04-11 1:34:29 AM
>> merging all info together... 2023-04-11 1:34:29 AM
>> done 2023-04-11 1:34:29 AM
>> checking seqlevels match... 2023-04-11 1:34:29 AM
>> 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... 2023-04-11 1:34:29 AM
>> checking seqlevels match... 2023-04-11 1:34:29 AM
>> 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... 2023-04-11 1:34:30 AM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-04-11 1:34:30 AM
>> checking seqlevels match... 2023-04-11 1:34:30 AM
>> 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... 2023-04-11 1:34:31 AM
>> calculating cor and pvalue, which may be time consuming... 2023-04-11 1:34:31 AM
>> merging all info together... 2023-04-11 1:34:31 AM
>> done 2023-04-11 1:34:31 AM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-04-11 1:34:31 AM
>> merging all info together... 2023-04-11 1:34:31 AM
>> done 2023-04-11 1:34:31 AM
>> checking seqlevels match... 2023-04-11 1:34:31 AM
>> 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... 2023-04-11 1:34:32 AM
>> some scan range may cross Chr bound, trimming... 2023-04-11 1:34:32 AM
>> finding overlap peak in gene scan region... 2023-04-11 1:34:32 AM
>> dealing with left peak not your gene scan region... 2023-04-11 1:34:32 AM
>> merging two set peaks... 2023-04-11 1:34:33 AM
>> calculating distance and dealing with gene strand... 2023-04-11 1:34:33 AM
>> merging all info together ... 2023-04-11 1:34:33 AM
>> done 2023-04-11 1:34:33 AM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-04-11 1:34:34 AM
>> merging all info together... 2023-04-11 1:34:34 AM
>> done 2023-04-11 1:34:34 AM
>> checking seqlevels match... 2023-04-11 1:34:34 AM
>> 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... 2023-04-11 1:34:34 AM
>> checking seqlevels match... 2023-04-11 1:34:34 AM
>> 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... 2023-04-11 1:34:35 AM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-04-11 1:34:35 AM
>> checking seqlevels match... 2023-04-11 1:34:35 AM
>> 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... 2023-04-11 1:34:37 AM
>> calculating cor and pvalue, which may be time consuming... 2023-04-11 1:34:37 AM
>> merging all info together... 2023-04-11 1:34:37 AM
>> done 2023-04-11 1:34:37 AM
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 63 ]
>
> proc.time()
user system elapsed
65.34 2.15 67.51
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0 | 0 | 0 | |
| calcRP_TFHit | 3.87 | 0.19 | 4.16 | |
| calcRP_coverage | 0.08 | 0.00 | 0.08 | |
| calcRP_region | 6.26 | 0.23 | 6.78 | |
| enhancerPromoterCor | 2.94 | 0.03 | 2.97 | |
| findIT_MARA | 0.42 | 0.04 | 0.45 | |
| findIT_TFHit | 0.99 | 0.04 | 1.03 | |
| findIT_TTPair | 0.10 | 0.08 | 0.19 | |
| findIT_enrichFisher | 0.22 | 0.00 | 0.22 | |
| findIT_enrichWilcox | 0.24 | 0.02 | 0.25 | |
| findIT_regionRP | 6.33 | 0.12 | 6.45 | |
| getAssocPairNumber | 1.29 | 0.02 | 1.32 | |
| integrate_ChIP_RNA | 2.11 | 0.01 | 2.12 | |
| integrate_replicates | 0 | 0 | 0 | |
| jaccard_findIT_TTpair | 0.11 | 0.08 | 0.18 | |
| jaccard_findIT_enrichFisher | 0.19 | 0.01 | 0.21 | |
| loadPeakFile | 0.06 | 0.00 | 0.06 | |
| mm_geneBound | 1.31 | 0.00 | 1.31 | |
| mm_geneScan | 1.27 | 0.02 | 1.28 | |
| mm_nearestGene | 1.09 | 0.04 | 1.14 | |
| peakGeneCor | 3.53 | 0.10 | 3.62 | |
| plot_annoDistance | 1.61 | 0.05 | 1.66 | |
| plot_peakGeneAlias_summary | 1.41 | 0.00 | 1.41 | |
| plot_peakGeneCor | 2.93 | 0.06 | 3.00 | |
| test_geneSet | 0 | 0 | 0 | |