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HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
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Package 709/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindIT2 1.9.0  (landing page)
Guandong Shang
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/FindIT2
git_branch: devel
git_last_commit: ca8588a
git_last_commit_date: 2023-10-24 11:34:37 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for FindIT2 on merida1


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.

raw results


Summary

Package: FindIT2
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2024-02-17 03:56:48 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 04:10:18 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 809.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: FindIT2.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FindIT2.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 ‘1.9.0’
* 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_region       10.837  0.268  14.004
findIT_regionRP      9.878  0.238  10.438
plot_peakGeneCor     8.007  0.359   9.771
calcRP_TFHit         6.486  0.326  29.408
calcRP_coverage      5.684  0.494   7.666
enhancerPromoterCor  5.369  0.109   6.348
peakGeneCor          4.998  0.103   5.950
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `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 1 | WARN 0 | SKIP 0 | PASS 64 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_mmPeakAnno_parse.R:37:5'): plot_annoDistance test ────────────
  pb_2$data[[1]]$density[250] (`actual`) not equal to 0.0001044554 (`expected`).
  
  actual != expected but don't know how to show the difference
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/FindIT2.Rcheck/00check.log’
for details.


Installation output

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)

Tests output

FindIT2.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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...		2024-02-17 04:07:57
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:08:00
>> preparing weight info...		2024-02-17 04:08:00
>> loading E50h_sampleChr5.bw info...		2024-02-17 04:08:00
------------
>> extracting and calcluating Chr5 signal...		2024-02-17 04:08:01
>> dealing with Chr5 left gene signal...		2024-02-17 04:08:06
>> norming Chr5RP accoring to the whole Chr RP...		2024-02-17 04:08:06
>> merging all Chr RP together...		2024-02-17 04:08:06
>> done		2024-02-17 04:08:06
>> checking seqlevels match...		2024-02-17 04:08:06
>> 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...		2024-02-17 04:08:07
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:08:08
>> finding overlap peak in gene scan region...		2024-02-17 04:08:08
>> dealing with left peak not your gene scan region...		2024-02-17 04:08:09
>> merging two set peaks...		2024-02-17 04:08:09
>> calculating distance and dealing with gene strand...		2024-02-17 04:08:09
>> merging all info together ...		2024-02-17 04:08:09
>> done		2024-02-17 04:08:09
>> calculating peakCenter to TSS using peak-gene pair...		2024-02-17 04:08:09
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-02-17 04:08:11
>> calculating RP using centerToTSS and peak score2024-02-17 04:08:11
>> merging all info together		2024-02-17 04:08:17
>> done		2024-02-17 04:08:19
>> calculating peakCenter to TSS using peak-gene pair...		2024-02-17 04:08:19
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-02-17 04:08:21
>> calculating RP using centerToTSS and peak score2024-02-17 04:08:21
>> merging all info together		2024-02-17 04:08:27
>> done		2024-02-17 04:08:28
>> checking seqlevels match...		2024-02-17 04:08:29
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-02-17 04:08:29
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:08:31
>> finding overlap peak in gene scan region...		2024-02-17 04:08:31
>> dealing with left peak not your gene scan region...		2024-02-17 04:08:31
>> merging two set peaks...		2024-02-17 04:08:31
>> calculating distance and dealing with gene strand...		2024-02-17 04:08:32
>> merging all info together ...		2024-02-17 04:08:32
>> done		2024-02-17 04:08:32
>> calculating peakCenter to TSS using peak-gene pair...		2024-02-17 04:08:32
>> calculating RP using centerToTSS and TF hit		2024-02-17 04:08:33
>> merging all info together		2024-02-17 04:08:34
>> done		2024-02-17 04:08:34
>> calculating peakCenter to TSS using peak-gene pair...		2024-02-17 04:08:34
>> calculating RP using centerToTSS and TF hit		2024-02-17 04:08:35
>> merging all info together		2024-02-17 04:08:35
>> done		2024-02-17 04:08:36
>> checking seqlevels match...		2024-02-17 04:08:38
>> 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...		2024-02-17 04:08:38
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:08:39
>> finding overlap peak in gene scan region...		2024-02-17 04:08:39
>> dealing with left peak not your gene scan region...		2024-02-17 04:08:39
>> merging two set peaks...		2024-02-17 04:08:40
>> calculating distance and dealing with gene strand...		2024-02-17 04:08:40
>> merging all info together ...		2024-02-17 04:08:40
>> done		2024-02-17 04:08:40
>> calculating peakCenter to TSS using peak-gene pair...		2024-02-17 04:08:40
>> pre-filling 1356 noAssoc peak gene's RP with 0...		2024-02-17 04:08:42
>> calculating RP using centerToTSS and peak score2024-02-17 04:08:42
>> merging all info together		2024-02-17 04:08:46
>> done		2024-02-17 04:08:47
>> extracting RP info from regionRP...		2024-02-17 04:08:48
>> dealing with TF_GR_databse...		2024-02-17 04:08:49
>> calculating percent and p-value...		2024-02-17 04:08:49
>> dealing withE5_0h_R1...		2024-02-17 04:08:49
>> dealing withE5_0h_R2...		2024-02-17 04:08:49
>> dealing withE5_4h_R1...		2024-02-17 04:08:49
>> dealing withE5_4h_R2...		2024-02-17 04:08:49
>> dealing withE5_8h_R1...		2024-02-17 04:08:49
>> dealing withE5_8h_R2...		2024-02-17 04:08:49
>> dealing withE5_16h_R1...		2024-02-17 04:08:49
>> dealing withE5_16h_R2...		2024-02-17 04:08:49
>> dealing withE5_24h_R1...		2024-02-17 04:08:49
>> dealing withE5_24h_R2...		2024-02-17 04:08:50
>> dealing withE5_48h_R1...		2024-02-17 04:08:50
>> dealing withE5_48h_R2...		2024-02-17 04:08:50
>> dealing withE5_48h_R3...		2024-02-17 04:08:50
>> dealing withE5_72h_R1...		2024-02-17 04:08:50
>> dealing withE5_72h_R2...		2024-02-17 04:08:50
>> dealing withE5_72h_R3...		2024-02-17 04:08:50
>> merging all info together...		2024-02-17 04:08:50
>> done		2024-02-17 04:08:51
>> preparing gene features information...		2024-02-17 04:08:51
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:08:52
>> calculating p-value for each TF, which may be time consuming...		2024-02-17 04:08:53
>> merging all info together...		2024-02-17 04:08:53
>> done		2024-02-17 04:08:53
>> dealing with TF_GR_database...		2024-02-17 04:08:53
>> calculating coef and converting into z-score using INT...		2024-02-17 04:08:54
>> dealing with E5_0h_R1...		2024-02-17 04:08:54
>> dealing with E5_0h_R2...		2024-02-17 04:08:54
>> dealing with E5_4h_R1...		2024-02-17 04:08:54
>> dealing with E5_4h_R2...		2024-02-17 04:08:54
>> dealing with E5_8h_R1...		2024-02-17 04:08:54
>> dealing with E5_8h_R2...		2024-02-17 04:08:55
>> dealing with E5_16h_R1...		2024-02-17 04:08:55
>> dealing with E5_16h_R2...		2024-02-17 04:08:55
>> dealing with E5_24h_R1...		2024-02-17 04:08:55
>> dealing with E5_24h_R2...		2024-02-17 04:08:55
>> dealing with E5_48h_R1...		2024-02-17 04:08:56
>> dealing with E5_48h_R2...		2024-02-17 04:08:56
>> dealing with E5_48h_R3...		2024-02-17 04:08:56
>> dealing with E5_72h_R1...		2024-02-17 04:08:56
>> dealing with E5_72h_R2...		2024-02-17 04:08:56
>> dealing with E5_72h_R3...		2024-02-17 04:08:57
>> merging all info together...		2024-02-17 04:08:57
>> done		2024-02-17 04:08:57
>> checking seqlevels match...		2024-02-17 04:08:58
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region...		2024-02-17 04:08:58
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:08:59
>> finding overlap peak in gene scan region...		2024-02-17 04:08:59
>> dealing with left peak not your gene scan region...		2024-02-17 04:08:59
>> merging two set peaks...		2024-02-17 04:09:00
>> calculating distance and dealing with gene strand...		2024-02-17 04:09:00
>> merging all info together ...		2024-02-17 04:09:00
>> done		2024-02-17 04:09:00
>> calculating peakCenter to TSS using peak-gene pair...		2024-02-17 04:09:00
>> calculating RP using centerToTSS and TF hit		2024-02-17 04:09:02
>> merging all info together		2024-02-17 04:09:02
>> done		2024-02-17 04:09:02
>> checking seqlevels match...		2024-02-17 04:09:03
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-02-17 04:09:03
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match...		2024-02-17 04:09:10
>> 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
>> checking seqlevels match...		2024-02-17 04:09:10
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-02-17 04:09:10
>> finding nearest gene and calculating distance...		2024-02-17 04:09:12
>> dealing with gene strand ...		2024-02-17 04:09:12
>> merging all info together ...		2024-02-17 04:09:12
>> done		2024-02-17 04:09:12
>> checking seqlevels match...		2024-02-17 04:09:12
>> 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...		2024-02-17 04:09:13
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-02-17 04:09:13
>> finding nearest gene and calculating distance...		2024-02-17 04:09:14
>> dealing with gene strand ...		2024-02-17 04:09:15
>> merging all info together ...		2024-02-17 04:09:15
>> done		2024-02-17 04:09:15
>> checking seqlevels match...		2024-02-17 04:09:17
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match...		2024-02-17 04:09:18
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-02-17 04:09:18
>> finding nearest gene and calculating distance...		2024-02-17 04:09:19
>> dealing with gene strand ...		2024-02-17 04:09:19
>> merging all info together ...		2024-02-17 04:09:20
>> done		2024-02-17 04:09:20
>> checking seqlevels match...		2024-02-17 04:09:21
>> 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
>> checking seqlevels match...		2024-02-17 04:09:22
>> 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...		2024-02-17 04:09:22
>> finding nearest gene and calculating distance...		2024-02-17 04:09:23
>> dealing with gene strand ...		2024-02-17 04:09:23
>> merging all info together ...		2024-02-17 04:09:23
>> done		2024-02-17 04:09:23
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-02-17 04:09:25
>> 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
>> checking seqlevels match...		2024-02-17 04:09:25
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information...		2024-02-17 04:09:26
>> finding nearest gene and calculating distance...		2024-02-17 04:09:27
>> dealing with gene strand ...		2024-02-17 04:09:28
>> merging all info together ...		2024-02-17 04:09:28
>> done		2024-02-17 04:09:28
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match...		2024-02-17 04:09:30
>> 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
>> checking seqlevels match...		2024-02-17 04:09:32
>> 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...		2024-02-17 04:09:34
>> checking seqlevels match...		2024-02-17 04:09:36
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:09:38
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-02-17 04:09:41
>> merging all info together...		2024-02-17 04:09:41
>> done		2024-02-17 04:09:42
>> checking seqlevels match...		2024-02-17 04:09:42
>> 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...		2024-02-17 04:09:42
>> checking seqlevels match...		2024-02-17 04:09:42
>> 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...		2024-02-17 04:09:44
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-02-17 04:09:45
>> checking seqlevels match...		2024-02-17 04:09:45
>> 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...		2024-02-17 04:09:46
>> calculating cor and pvalue, which may be time consuming...		2024-02-17 04:09:47
>> merging all info together...		2024-02-17 04:09:47
>> done		2024-02-17 04:09:47
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-02-17 04:09:48
>> merging all info together...		2024-02-17 04:09:48
>> done		2024-02-17 04:09:48
>> checking seqlevels match...		2024-02-17 04:09:48
>> 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...		2024-02-17 04:09:48
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:09:50
>> finding overlap peak in gene scan region...		2024-02-17 04:09:50
>> dealing with left peak not your gene scan region...		2024-02-17 04:09:50
>> merging two set peaks...		2024-02-17 04:09:51
>> calculating distance and dealing with gene strand...		2024-02-17 04:09:51
>> merging all info together ...		2024-02-17 04:09:51
>> done		2024-02-17 04:09:51
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming...		2024-02-17 04:09:54
>> merging all info together...		2024-02-17 04:09:54
>> done		2024-02-17 04:09:54
>> checking seqlevels match...		2024-02-17 04:09:54
>> 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...		2024-02-17 04:09:54
>> checking seqlevels match...		2024-02-17 04:09:54
>> 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...		2024-02-17 04:09:56
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene...		2024-02-17 04:09:57
>> checking seqlevels match...		2024-02-17 04:09:57
>> 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
>> some scan range may cross Chr bound, trimming...		2024-02-17 04:09:59
>> calculating cor and pvalue, which may be time consuming...		2024-02-17 04:09:59
>> merging all info together...		2024-02-17 04:10:00
>> done		2024-02-17 04:10:00
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 1 | WARN 0 | SKIP 0 | PASS 64 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_mmPeakAnno_parse.R:37:5'): plot_annoDistance test ────────────
pb_2$data[[1]]$density[250] (`actual`) not equal to 0.0001044554 (`expected`).

actual != expected but don't know how to show the difference

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
Error: Test failures
Execution halted

Example timings

FindIT2.Rcheck/FindIT2-Ex.timings

nameusersystemelapsed
TF_target_database0.0010.0020.002
calcRP_TFHit 6.486 0.32629.408
calcRP_coverage5.6840.4947.666
calcRP_region10.837 0.26814.004
enhancerPromoterCor5.3690.1096.348
findIT_MARA0.9380.0261.336
findIT_TFHit1.6360.0441.739
findIT_TTPair0.1190.0090.146
findIT_enrichFisher0.2790.0090.297
findIT_enrichWilcox0.3070.0100.322
findIT_regionRP 9.878 0.23810.438
getAssocPairNumber1.8510.0531.948
integrate_ChIP_RNA3.4230.0973.629
integrate_replicates0.0050.0030.010
jaccard_findIT_TTpair0.1970.0090.208
jaccard_findIT_enrichFisher0.4310.0160.463
loadPeakFile0.1110.0060.118
mm_geneBound2.0660.0442.143
mm_geneScan2.1410.0522.265
mm_nearestGene1.9070.0622.001
peakGeneCor4.9980.1035.950
plot_annoDistance3.1180.0783.750
plot_peakGeneAlias_summary2.8120.0493.291
plot_peakGeneCor8.0070.3599.771
test_geneSet0.0000.0010.003