| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 691/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.7.0 (landing page) Guandong Shang
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: FindIT2 |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FindIT2_1.7.0.tar.gz |
| StartedAt: 2023-06-05 22:25:46 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 22:35:11 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 564.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FindIT2_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FindIT2.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘FindIT2/DESCRIPTION’ ... OK
* this is package ‘FindIT2’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FindIT2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcRP_coverage 9.884 0.327 10.232
findIT_regionRP 8.415 0.056 8.488
calcRP_region 6.672 0.086 6.770
calcRP_TFHit 4.805 0.089 5.065
* 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/R/R-4.3.0/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘FindIT2’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FindIT2)
FindIT2.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(FindIT2)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
> if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) {
+ stop("unable to load TxDb.Athaliana.BioMart.plantsmart28")
+ }
Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28
>
> test_check("FindIT2")
>> preparing gene features information... 2023-06-05 10:32:16 PM
>> some scan range may cross Chr bound, trimming... 2023-06-05 10:32:17 PM
>> preparing weight info... 2023-06-05 10:32:17 PM
>> loading E50h_sampleChr5.bw info... 2023-06-05 10:32:17 PM
------------
>> extracting and calcluating Chr5 signal... 2023-06-05 10:32:17 PM
>> dealing with Chr5 left gene signal... 2023-06-05 10:32:26 PM
>> norming Chr5RP accoring to the whole Chr RP... 2023-06-05 10:32:26 PM
>> merging all Chr RP together... 2023-06-05 10:32:26 PM
>> done 2023-06-05 10:32:26 PM
>> checking seqlevels match... 2023-06-05 10:32:26 PM
>> 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... 2023-06-05 10:32:26 PM
>> some scan range may cross Chr bound, trimming... 2023-06-05 10:32:27 PM
>> finding overlap peak in gene scan region... 2023-06-05 10:32:28 PM
>> dealing with left peak not your gene scan region... 2023-06-05 10:32:28 PM
>> merging two set peaks... 2023-06-05 10:32:28 PM
>> calculating distance and dealing with gene strand... 2023-06-05 10:32:28 PM
>> merging all info together ... 2023-06-05 10:32:28 PM
>> done 2023-06-05 10:32:28 PM
>> calculating peakCenter to TSS using peak-gene pair... 2023-06-05 10:32:28 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-06-05 10:32:29 PM
>> calculating RP using centerToTSS and peak score2023-06-05 10:32:29 PM
>> merging all info together 2023-06-05 10:32:32 PM
>> done 2023-06-05 10:32:33 PM
>> calculating peakCenter to TSS using peak-gene pair... 2023-06-05 10:32:33 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-06-05 10:32:34 PM
>> calculating RP using centerToTSS and peak score2023-06-05 10:32:34 PM
>> merging all info together 2023-06-05 10:32:38 PM
>> done 2023-06-05 10:32:39 PM
>> checking seqlevels match... 2023-06-05 10:32:39 PM
>> 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... 2023-06-05 10:32:39 PM
>> some scan range may cross Chr bound, trimming... 2023-06-05 10:32:40 PM
>> finding overlap peak in gene scan region... 2023-06-05 10:32:41 PM
>> dealing with left peak not your gene scan region... 2023-06-05 10:32:41 PM
>> merging two set peaks... 2023-06-05 10:32:42 PM
>> calculating distance and dealing with gene strand... 2023-06-05 10:32:42 PM
>> merging all info together ... 2023-06-05 10:32:42 PM
>> done 2023-06-05 10:32:42 PM
>> calculating peakCenter to TSS using peak-gene pair... 2023-06-05 10:32:42 PM
>> calculating RP using centerToTSS and TF hit 2023-06-05 10:32:43 PM
>> merging all info together 2023-06-05 10:32:43 PM
>> done 2023-06-05 10:32:43 PM
>> calculating peakCenter to TSS using peak-gene pair... 2023-06-05 10:32:43 PM
>> calculating RP using centerToTSS and TF hit 2023-06-05 10:32:44 PM
>> merging all info together 2023-06-05 10:32:44 PM
>> done 2023-06-05 10:32:44 PM
>> checking seqlevels match... 2023-06-05 10:32:45 PM
>> 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... 2023-06-05 10:32:45 PM
>> some scan range may cross Chr bound, trimming... 2023-06-05 10:32:46 PM
>> finding overlap peak in gene scan region... 2023-06-05 10:32:46 PM
>> dealing with left peak not your gene scan region... 2023-06-05 10:32:46 PM
>> merging two set peaks... 2023-06-05 10:32:46 PM
>> calculating distance and dealing with gene strand... 2023-06-05 10:32:46 PM
>> merging all info together ... 2023-06-05 10:32:46 PM
>> done 2023-06-05 10:32:46 PM
>> calculating peakCenter to TSS using peak-gene pair... 2023-06-05 10:32:46 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-06-05 10:32:47 PM
>> calculating RP using centerToTSS and peak score2023-06-05 10:32:47 PM
>> merging all info together 2023-06-05 10:32:50 PM
>> done 2023-06-05 10:32:51 PM
>> extracting RP info from regionRP... 2023-06-05 10:32:51 PM
>> dealing with TF_GR_databse... 2023-06-05 10:32:52 PM
>> calculating percent and p-value... 2023-06-05 10:32:52 PM
>> dealing withE5_0h_R1... 2023-06-05 10:32:52 PM
>> dealing withE5_0h_R2... 2023-06-05 10:32:52 PM
>> dealing withE5_4h_R1... 2023-06-05 10:32:52 PM
>> dealing withE5_4h_R2... 2023-06-05 10:32:52 PM
>> dealing withE5_8h_R1... 2023-06-05 10:32:52 PM
>> dealing withE5_8h_R2... 2023-06-05 10:32:52 PM
>> dealing withE5_16h_R1... 2023-06-05 10:32:52 PM
>> dealing withE5_16h_R2... 2023-06-05 10:32:52 PM
>> dealing withE5_24h_R1... 2023-06-05 10:32:52 PM
>> dealing withE5_24h_R2... 2023-06-05 10:32:52 PM
>> dealing withE5_48h_R1... 2023-06-05 10:32:52 PM
>> dealing withE5_48h_R2... 2023-06-05 10:32:52 PM
>> dealing withE5_48h_R3... 2023-06-05 10:32:52 PM
>> dealing withE5_72h_R1... 2023-06-05 10:32:52 PM
>> dealing withE5_72h_R2... 2023-06-05 10:32:53 PM
>> dealing withE5_72h_R3... 2023-06-05 10:32:53 PM
>> merging all info together... 2023-06-05 10:32:53 PM
>> done 2023-06-05 10:32:53 PM
>> preparing gene features information... 2023-06-05 10:32:53 PM
>> some scan range may cross Chr bound, trimming... 2023-06-05 10:32:55 PM
>> calculating p-value for each TF, which may be time consuming... 2023-06-05 10:32:55 PM
>> merging all info together... 2023-06-05 10:32:55 PM
>> done 2023-06-05 10:32:55 PM
>> dealing with TF_GR_database... 2023-06-05 10:32:55 PM
>> calculating coef and converting into z-score using INT... 2023-06-05 10:32:56 PM
>> dealing with E5_0h_R1... 2023-06-05 10:32:56 PM
>> dealing with E5_0h_R2... 2023-06-05 10:32:56 PM
>> dealing with E5_4h_R1... 2023-06-05 10:32:56 PM
>> dealing with E5_4h_R2... 2023-06-05 10:32:56 PM
>> dealing with E5_8h_R1... 2023-06-05 10:32:56 PM
>> dealing with E5_8h_R2... 2023-06-05 10:32:56 PM
>> dealing with E5_16h_R1... 2023-06-05 10:32:56 PM
>> dealing with E5_16h_R2... 2023-06-05 10:32:56 PM
>> dealing with E5_24h_R1... 2023-06-05 10:32:56 PM
>> dealing with E5_24h_R2... 2023-06-05 10:32:57 PM
>> dealing with E5_48h_R1... 2023-06-05 10:32:57 PM
>> dealing with E5_48h_R2... 2023-06-05 10:32:57 PM
>> dealing with E5_48h_R3... 2023-06-05 10:32:57 PM
>> dealing with E5_72h_R1... 2023-06-05 10:32:57 PM
>> dealing with E5_72h_R2... 2023-06-05 10:32:57 PM
>> dealing with E5_72h_R3... 2023-06-05 10:32:57 PM
>> merging all info together... 2023-06-05 10:32:57 PM
>> done 2023-06-05 10:32:58 PM
>> checking seqlevels match... 2023-06-05 10:32:58 PM
>> 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... 2023-06-05 10:32:58 PM
>> some scan range may cross Chr bound, trimming... 2023-06-05 10:33:00 PM
>> finding overlap peak in gene scan region... 2023-06-05 10:33:00 PM
>> dealing with left peak not your gene scan region... 2023-06-05 10:33:00 PM
>> merging two set peaks... 2023-06-05 10:33:00 PM
>> calculating distance and dealing with gene strand... 2023-06-05 10:33:00 PM
>> merging all info together ... 2023-06-05 10:33:00 PM
>> done 2023-06-05 10:33:00 PM
>> calculating peakCenter to TSS using peak-gene pair... 2023-06-05 10:33:00 PM
>> calculating RP using centerToTSS and TF hit 2023-06-05 10:33:01 PM
>> merging all info together 2023-06-05 10:33:01 PM
>> done 2023-06-05 10:33:01 PM
>> checking seqlevels match... 2023-06-05 10:33:02 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-06-05 10:33:02 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-06-05 10:33:07 PM
>> 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... 2023-06-05 10:33:07 PM
>> 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... 2023-06-05 10:33:08 PM
>> finding nearest gene and calculating distance... 2023-06-05 10:33:09 PM
>> dealing with gene strand ... 2023-06-05 10:33:10 PM
>> merging all info together ... 2023-06-05 10:33:10 PM
>> done 2023-06-05 10:33:10 PM
>> checking seqlevels match... 2023-06-05 10:33:10 PM
>> 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... 2023-06-05 10:33:10 PM
>> 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... 2023-06-05 10:33:10 PM
>> finding nearest gene and calculating distance... 2023-06-05 10:33:11 PM
>> dealing with gene strand ... 2023-06-05 10:33:11 PM
>> merging all info together ... 2023-06-05 10:33:11 PM
>> done 2023-06-05 10:33:11 PM
>> checking seqlevels match... 2023-06-05 10:33:13 PM
>> 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... 2023-06-05 10:33:13 PM
>> 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... 2023-06-05 10:33:13 PM
>> finding nearest gene and calculating distance... 2023-06-05 10:33:14 PM
>> dealing with gene strand ... 2023-06-05 10:33:14 PM
>> merging all info together ... 2023-06-05 10:33:14 PM
>> done 2023-06-05 10:33:14 PM
>> checking seqlevels match... 2023-06-05 10:33:15 PM
>> 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... 2023-06-05 10:33:15 PM
>> 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... 2023-06-05 10:33:15 PM
>> finding nearest gene and calculating distance... 2023-06-05 10:33:17 PM
>> dealing with gene strand ... 2023-06-05 10:33:17 PM
>> merging all info together ... 2023-06-05 10:33:17 PM
>> done 2023-06-05 10:33:17 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-06-05 10:33:19 PM
>> 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... 2023-06-05 10:33:19 PM
>> 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... 2023-06-05 10:33:19 PM
>> finding nearest gene and calculating distance... 2023-06-05 10:33:20 PM
>> dealing with gene strand ... 2023-06-05 10:33:21 PM
>> merging all info together ... 2023-06-05 10:33:21 PM
>> done 2023-06-05 10:33:21 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-06-05 10:33:23 PM
>> 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... 2023-06-05 10:33:24 PM
>> 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... 2023-06-05 10:33:25 PM
>> checking seqlevels match... 2023-06-05 10:33:26 PM
>> 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... 2023-06-05 10:33:28 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-06-05 10:33:30 PM
>> merging all info together... 2023-06-05 10:33:30 PM
>> done 2023-06-05 10:33:30 PM
>> checking seqlevels match... 2023-06-05 10:33:30 PM
>> 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... 2023-06-05 10:33:31 PM
>> checking seqlevels match... 2023-06-05 10:33:31 PM
>> 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... 2023-06-05 10:33:32 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-06-05 10:33:32 PM
>> checking seqlevels match... 2023-06-05 10:33:32 PM
>> 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... 2023-06-05 10:33:33 PM
>> calculating cor and pvalue, which may be time consuming... 2023-06-05 10:33:34 PM
>> merging all info together... 2023-06-05 10:33:34 PM
>> done 2023-06-05 10:33:34 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-06-05 10:33:34 PM
>> merging all info together... 2023-06-05 10:33:34 PM
>> done 2023-06-05 10:33:34 PM
>> checking seqlevels match... 2023-06-05 10:33:35 PM
>> 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... 2023-06-05 10:33:35 PM
>> some scan range may cross Chr bound, trimming... 2023-06-05 10:33:36 PM
>> finding overlap peak in gene scan region... 2023-06-05 10:33:36 PM
>> dealing with left peak not your gene scan region... 2023-06-05 10:33:36 PM
>> merging two set peaks... 2023-06-05 10:33:36 PM
>> calculating distance and dealing with gene strand... 2023-06-05 10:33:36 PM
>> merging all info together ... 2023-06-05 10:33:36 PM
>> done 2023-06-05 10:33:36 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-06-05 10:33:37 PM
>> merging all info together... 2023-06-05 10:33:37 PM
>> done 2023-06-05 10:33:38 PM
>> checking seqlevels match... 2023-06-05 10:33:38 PM
>> 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... 2023-06-05 10:33:38 PM
>> checking seqlevels match... 2023-06-05 10:33:38 PM
>> 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... 2023-06-05 10:33:39 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-06-05 10:33:39 PM
>> checking seqlevels match... 2023-06-05 10:33:39 PM
>> 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... 2023-06-05 10:33:41 PM
>> calculating cor and pvalue, which may be time consuming... 2023-06-05 10:33:42 PM
>> merging all info together... 2023-06-05 10:33:42 PM
>> done 2023-06-05 10:33:42 PM
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
95.866 2.219 103.971
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0 | 0 | 0 | |
| calcRP_TFHit | 4.805 | 0.089 | 5.065 | |
| calcRP_coverage | 9.884 | 0.327 | 10.232 | |
| calcRP_region | 6.672 | 0.086 | 6.770 | |
| enhancerPromoterCor | 3.629 | 0.020 | 3.655 | |
| findIT_MARA | 0.604 | 0.000 | 0.605 | |
| findIT_TFHit | 1.260 | 0.000 | 1.262 | |
| findIT_TTPair | 0.099 | 0.000 | 0.099 | |
| findIT_enrichFisher | 0.209 | 0.000 | 0.209 | |
| findIT_enrichWilcox | 0.230 | 0.000 | 0.231 | |
| findIT_regionRP | 8.415 | 0.056 | 8.488 | |
| getAssocPairNumber | 1.657 | 0.024 | 1.684 | |
| integrate_ChIP_RNA | 2.827 | 0.020 | 2.852 | |
| integrate_replicates | 0.002 | 0.000 | 0.003 | |
| jaccard_findIT_TTpair | 0.142 | 0.000 | 0.141 | |
| jaccard_findIT_enrichFisher | 0.280 | 0.000 | 0.281 | |
| loadPeakFile | 0.080 | 0.000 | 0.081 | |
| mm_geneBound | 1.655 | 0.008 | 1.666 | |
| mm_geneScan | 1.704 | 0.004 | 1.711 | |
| mm_nearestGene | 1.536 | 0.008 | 1.547 | |
| peakGeneCor | 4.358 | 0.099 | 4.464 | |
| plot_annoDistance | 1.915 | 0.067 | 1.986 | |
| plot_peakGeneAlias_summary | 1.747 | 0.012 | 1.762 | |
| plot_peakGeneCor | 4.008 | 0.012 | 4.028 | |
| test_geneSet | 0 | 0 | 0 | |