| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-03 02:35:56 -0000 (Fri, 03 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4039 |
| 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 | ||||
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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 669/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.5.0 (landing page) Guandong Shang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: FindIT2 |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings FindIT2_1.5.0.tar.gz |
| StartedAt: 2023-02-02 07:22:13 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 07:32:10 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 597.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings FindIT2_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.5.0’
* 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
calcRP_coverage 9.454 0.912 12.883
findIT_regionRP 9.915 0.065 9.985
calcRP_region 7.060 0.132 8.308
calcRP_TFHit 4.870 0.108 6.276
* 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 ...
‘FindIT2.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
FindIT2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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 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... 2023-02-02 07:28:56
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:28:59
>> preparing weight info... 2023-02-02 07:28:59
>> loading E50h_sampleChr5.bw info... 2023-02-02 07:28:59
------------
>> extracting and calcluating Chr5 signal... 2023-02-02 07:28:59
>> dealing with Chr5 left gene signal... 2023-02-02 07:29:09
>> norming Chr5RP accoring to the whole Chr RP... 2023-02-02 07:29:09
>> merging all Chr RP together... 2023-02-02 07:29:09
>> done 2023-02-02 07:29:09
>> checking seqlevels match... 2023-02-02 07:29:09
>> 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... 2023-02-02 07:29:09
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:29:10
>> finding overlap peak in gene scan region... 2023-02-02 07:29:10
>> dealing with left peak not your gene scan region... 2023-02-02 07:29:11
>> merging two set peaks... 2023-02-02 07:29:11
>> calculating distance and dealing with gene strand... 2023-02-02 07:29:11
>> merging all info together ... 2023-02-02 07:29:11
>> done 2023-02-02 07:29:11
>> calculating peakCenter to TSS using peak-gene pair... 2023-02-02 07:29:11
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-02-02 07:29:12
>> calculating RP using centerToTSS and peak score2023-02-02 07:29:12
>> merging all info together 2023-02-02 07:29:16
>> done 2023-02-02 07:29:17
>> calculating peakCenter to TSS using peak-gene pair... 2023-02-02 07:29:17
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-02-02 07:29:19
>> calculating RP using centerToTSS and peak score2023-02-02 07:29:19
>> merging all info together 2023-02-02 07:29:23
>> done 2023-02-02 07:29:24
>> checking seqlevels match... 2023-02-02 07:29:24
>> 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... 2023-02-02 07:29:24
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:29:26
>> finding overlap peak in gene scan region... 2023-02-02 07:29:26
>> dealing with left peak not your gene scan region... 2023-02-02 07:29:26
>> merging two set peaks... 2023-02-02 07:29:26
>> calculating distance and dealing with gene strand... 2023-02-02 07:29:26
>> merging all info together ... 2023-02-02 07:29:26
>> done 2023-02-02 07:29:26
>> calculating peakCenter to TSS using peak-gene pair... 2023-02-02 07:29:26
>> calculating RP using centerToTSS and TF hit 2023-02-02 07:29:27
>> merging all info together 2023-02-02 07:29:27
>> done 2023-02-02 07:29:27
>> calculating peakCenter to TSS using peak-gene pair... 2023-02-02 07:29:27
>> calculating RP using centerToTSS and TF hit 2023-02-02 07:29:28
>> merging all info together 2023-02-02 07:29:28
>> done 2023-02-02 07:29:29
>> checking seqlevels match... 2023-02-02 07:29:30
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-02-02 07:29:30
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:29:31
>> finding overlap peak in gene scan region... 2023-02-02 07:29:31
>> dealing with left peak not your gene scan region... 2023-02-02 07:29:31
>> merging two set peaks... 2023-02-02 07:29:31
>> calculating distance and dealing with gene strand... 2023-02-02 07:29:31
>> merging all info together ... 2023-02-02 07:29:31
>> done 2023-02-02 07:29:31
>> calculating peakCenter to TSS using peak-gene pair... 2023-02-02 07:29:31
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-02-02 07:29:32
>> calculating RP using centerToTSS and peak score2023-02-02 07:29:32
>> merging all info together 2023-02-02 07:29:36
>> done 2023-02-02 07:29:36
>> extracting RP info from regionRP... 2023-02-02 07:29:38
>> dealing with TF_GR_databse... 2023-02-02 07:29:38
>> calculating percent and p-value... 2023-02-02 07:29:38
>> dealing withE5_0h_R1... 2023-02-02 07:29:38
>> dealing withE5_0h_R2... 2023-02-02 07:29:38
>> dealing withE5_4h_R1... 2023-02-02 07:29:38
>> dealing withE5_4h_R2... 2023-02-02 07:29:39
>> dealing withE5_8h_R1... 2023-02-02 07:29:39
>> dealing withE5_8h_R2... 2023-02-02 07:29:39
>> dealing withE5_16h_R1... 2023-02-02 07:29:39
>> dealing withE5_16h_R2... 2023-02-02 07:29:39
>> dealing withE5_24h_R1... 2023-02-02 07:29:39
>> dealing withE5_24h_R2... 2023-02-02 07:29:39
>> dealing withE5_48h_R1... 2023-02-02 07:29:39
>> dealing withE5_48h_R2... 2023-02-02 07:29:39
>> dealing withE5_48h_R3... 2023-02-02 07:29:39
>> dealing withE5_72h_R1... 2023-02-02 07:29:39
>> dealing withE5_72h_R2... 2023-02-02 07:29:39
>> dealing withE5_72h_R3... 2023-02-02 07:29:39
>> merging all info together... 2023-02-02 07:29:40
>> done 2023-02-02 07:29:40
>> preparing gene features information... 2023-02-02 07:29:40
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:29:41
>> calculating p-value for each TF, which may be time consuming... 2023-02-02 07:29:41
>> merging all info together... 2023-02-02 07:29:41
>> done 2023-02-02 07:29:41
>> dealing with TF_GR_database... 2023-02-02 07:29:41
>> calculating coef and converting into z-score using INT... 2023-02-02 07:29:42
>> dealing with E5_0h_R1... 2023-02-02 07:29:42
>> dealing with E5_0h_R2... 2023-02-02 07:29:42
>> dealing with E5_4h_R1... 2023-02-02 07:29:42
>> dealing with E5_4h_R2... 2023-02-02 07:29:42
>> dealing with E5_8h_R1... 2023-02-02 07:29:42
>> dealing with E5_8h_R2... 2023-02-02 07:29:42
>> dealing with E5_16h_R1... 2023-02-02 07:29:43
>> dealing with E5_16h_R2... 2023-02-02 07:29:43
>> dealing with E5_24h_R1... 2023-02-02 07:29:43
>> dealing with E5_24h_R2... 2023-02-02 07:29:43
>> dealing with E5_48h_R1... 2023-02-02 07:29:43
>> dealing with E5_48h_R2... 2023-02-02 07:29:43
>> dealing with E5_48h_R3... 2023-02-02 07:29:43
>> dealing with E5_72h_R1... 2023-02-02 07:29:43
>> dealing with E5_72h_R2... 2023-02-02 07:29:43
>> dealing with E5_72h_R3... 2023-02-02 07:29:43
>> merging all info together... 2023-02-02 07:29:43
>> done 2023-02-02 07:29:44
>> checking seqlevels match... 2023-02-02 07:29:44
>> 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... 2023-02-02 07:29:44
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:29:45
>> finding overlap peak in gene scan region... 2023-02-02 07:29:45
>> dealing with left peak not your gene scan region... 2023-02-02 07:29:45
>> merging two set peaks... 2023-02-02 07:29:46
>> calculating distance and dealing with gene strand... 2023-02-02 07:29:46
>> merging all info together ... 2023-02-02 07:29:46
>> done 2023-02-02 07:29:46
>> calculating peakCenter to TSS using peak-gene pair... 2023-02-02 07:29:46
>> calculating RP using centerToTSS and TF hit 2023-02-02 07:29:47
>> merging all info together 2023-02-02 07:29:47
>> done 2023-02-02 07:29:47
>> checking seqlevels match... 2023-02-02 07:29:48
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-02-02 07:29:48
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-02-02 07:29:53
>> 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
>> checking seqlevels match... 2023-02-02 07:29:53
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-02-02 07:29:53
>> finding nearest gene and calculating distance... 2023-02-02 07:29:55
>> dealing with gene strand ... 2023-02-02 07:29:55
>> merging all info together ... 2023-02-02 07:29:55
>> done 2023-02-02 07:29:55
>> checking seqlevels match... 2023-02-02 07:29:55
>> 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... 2023-02-02 07:29:55
>> 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... 2023-02-02 07:29:55
>> finding nearest gene and calculating distance... 2023-02-02 07:29:56
>> dealing with gene strand ... 2023-02-02 07:29:56
>> merging all info together ... 2023-02-02 07:29:57
>> done 2023-02-02 07:29:57
>> checking seqlevels match... 2023-02-02 07:29:58
>> 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... 2023-02-02 07:29:58
>> 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... 2023-02-02 07:29:58
>> finding nearest gene and calculating distance... 2023-02-02 07:29:59
>> dealing with gene strand ... 2023-02-02 07:29:59
>> merging all info together ... 2023-02-02 07:29:59
>> done 2023-02-02 07:29:59
>> checking seqlevels match... 2023-02-02 07:30:01
>> 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... 2023-02-02 07:30:01
>> 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... 2023-02-02 07:30:01
>> finding nearest gene and calculating distance... 2023-02-02 07:30:03
>> dealing with gene strand ... 2023-02-02 07:30:03
>> merging all info together ... 2023-02-02 07:30:03
>> done 2023-02-02 07:30:03
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-02-02 07:30:04
>> 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... 2023-02-02 07:30:04
>> 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... 2023-02-02 07:30:04
>> finding nearest gene and calculating distance... 2023-02-02 07:30:05
>> dealing with gene strand ... 2023-02-02 07:30:06
>> merging all info together ... 2023-02-02 07:30:06
>> done 2023-02-02 07:30:06
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-02-02 07:30:07
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2023-02-02 07:30:08
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:30:09
>> checking seqlevels match... 2023-02-02 07:30:11
>> 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... 2023-02-02 07:30:12
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-02-02 07:30:15
>> merging all info together... 2023-02-02 07:30:15
>> done 2023-02-02 07:30:15
>> checking seqlevels match... 2023-02-02 07:30:15
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2023-02-02 07:30:15
>> checking seqlevels match... 2023-02-02 07:30:15
>> 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... 2023-02-02 07:30:16
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-02-02 07:30:17
>> checking seqlevels match... 2023-02-02 07:30:17
>> 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
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:30:18
>> calculating cor and pvalue, which may be time consuming... 2023-02-02 07:30:18
>> merging all info together... 2023-02-02 07:30:19
>> done 2023-02-02 07:30:19
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-02-02 07:30:19
>> merging all info together... 2023-02-02 07:30:19
>> done 2023-02-02 07:30:19
>> checking seqlevels match... 2023-02-02 07:30:19
>> 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... 2023-02-02 07:30:20
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:30:21
>> finding overlap peak in gene scan region... 2023-02-02 07:30:21
>> dealing with left peak not your gene scan region... 2023-02-02 07:30:21
>> merging two set peaks... 2023-02-02 07:30:21
>> calculating distance and dealing with gene strand... 2023-02-02 07:30:21
>> merging all info together ... 2023-02-02 07:30:21
>> done 2023-02-02 07:30:21
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-02-02 07:30:23
>> merging all info together... 2023-02-02 07:30:23
>> done 2023-02-02 07:30:23
>> checking seqlevels match... 2023-02-02 07:30:23
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2023-02-02 07:30:23
>> checking seqlevels match... 2023-02-02 07:30:23
>> 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
>> some scan range may cross Chr bound, trimming... 2023-02-02 07:30:25
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-02-02 07:30:25
>> checking seqlevels match... 2023-02-02 07:30:25
>> 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... 2023-02-02 07:30:26
>> calculating cor and pvalue, which may be time consuming... 2023-02-02 07:30:27
>> merging all info together... 2023-02-02 07:30:27
>> done 2023-02-02 07:30:27
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
97.505 1.217 109.005
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0 | 0 | 0 | |
| calcRP_TFHit | 4.870 | 0.108 | 6.276 | |
| calcRP_coverage | 9.454 | 0.912 | 12.883 | |
| calcRP_region | 7.060 | 0.132 | 8.308 | |
| enhancerPromoterCor | 3.901 | 0.020 | 4.028 | |
| findIT_MARA | 0.616 | 0.004 | 0.621 | |
| findIT_TFHit | 1.431 | 0.008 | 1.441 | |
| findIT_TTPair | 0.161 | 0.000 | 0.162 | |
| findIT_enrichFisher | 0.259 | 0.004 | 0.263 | |
| findIT_enrichWilcox | 0.271 | 0.004 | 0.275 | |
| findIT_regionRP | 9.915 | 0.065 | 9.985 | |
| getAssocPairNumber | 1.609 | 0.032 | 1.643 | |
| integrate_ChIP_RNA | 3.013 | 0.007 | 3.226 | |
| integrate_replicates | 0.002 | 0.000 | 0.003 | |
| jaccard_findIT_TTpair | 0.217 | 0.004 | 0.222 | |
| jaccard_findIT_enrichFisher | 0.343 | 0.000 | 0.349 | |
| loadPeakFile | 0.082 | 0.000 | 0.084 | |
| mm_geneBound | 1.715 | 0.008 | 1.920 | |
| mm_geneScan | 1.710 | 0.020 | 1.792 | |
| mm_nearestGene | 1.478 | 0.000 | 1.479 | |
| peakGeneCor | 3.370 | 0.012 | 3.387 | |
| plot_annoDistance | 2.101 | 0.016 | 2.197 | |
| plot_peakGeneAlias_summary | 1.948 | 0.002 | 2.034 | |
| plot_peakGeneCor | 4.355 | 0.016 | 4.701 | |
| test_geneSet | 0.000 | 0.000 | 0.001 | |