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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ChIPseeker.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ChIPseeker_1.47.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ChIPseeker.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ChIPseeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseeker’ version ‘1.47.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘ChIPseeker’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-txdb.R:25:5'): txdb ──────────────────────────────────────────
  ChIPseeker:::TXID2EG("70455") not equal to "uc002qsd.4/1".
  1/1 mismatches
  x[1]: "ENST00000487630.1_3/ENST00000487630.1_3"
  y[1]: "uc002qsd.4/1"
  ── Failure ('test-txdb.R:26:5'): txdb ──────────────────────────────────────────
  ChIPseeker:::TXID2EG("70455", geneIdOnly = TRUE) not equal to "1".
  1/1 mismatches
  x[1]: "ENST00000487630.1_3"
  y[1]: "1"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 28 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ChIPseeker.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ChIPseeker
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ChIPseeker’ ...
** this is package ‘ChIPseeker’ version ‘1.47.0’
** 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 (ChIPseeker)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(ChIPseeker)

ChIPseeker v1.47.0 Learn more at https://yulab-smu.top/contribution-knowledge-mining/

Please cite:

Guangchuang Yu, Li-Gen Wang, and Qing-Yu He. ChIPseeker: an
R/Bioconductor package for ChIP peak annotation, comparison and
visualization. Bioinformatics. 2015, 31(14):2382-2383
> 
> test_check("ChIPseeker")
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> preparing start_site regions by gene... 2025-11-02 21:53:25
>> preparing tag matrix...  2025-11-02 21:53:25 
>> binning method is used...2025-11-02 21:53:39
>> preparing body regions by enhancer... 2025-11-02 21:53:39
>> preparing tag matrix by binning...  2025-11-02 21:53:39 
>> preparing matrix for body region with no flank extension... 2025-11-02 21:53:39
>> 1 peaks(1.162791%), having lengths smaller than 800bp, are filtered... 2025-11-02 21:53:39
>> binning method is used...2025-11-02 21:53:40
>> preparing body regions by enhancer... 2025-11-02 21:53:40
>> preparing tag matrix by binning...  2025-11-02 21:53:40 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2025-11-02 21:53:40
>> 1 peaks(0.7352941%), having lengths smaller than 800bp, are filtered... 2025-11-02 21:53:40
>> binning method is used...2025-11-02 21:53:43
>> preparing body regions by enhancer... 2025-11-02 21:53:43
>> preparing tag matrix by binning...  2025-11-02 21:53:43 
>> preparing matrix with flank extension from (enhancer_SS-1000bp)~(enhancer_TS+1000bp)... 2025-11-02 21:53:43
>> 1 peaks(1.136364%), having lengths smaller than 800bp, are filtered... 2025-11-02 21:53:43
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> preparing start_site regions by gene... 2025-11-02 21:53:44
>> preparing tag matrix...  2025-11-02 21:53:44 
>> preparing start_site regions by gene... 2025-11-02 21:53:59
>> preparing tag matrix...  2025-11-02 21:53:59 
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> binning method is used...2025-11-02 21:54:00
>> preparing body regions by gene... 2025-11-02 21:54:00
>> preparing tag matrix by binning...  2025-11-02 21:54:00 
>> preparing matrix for body region with no flank extension... 2025-11-02 21:54:00
>> 7 peaks(0.7021063%), having lengths smaller than 800bp, are filtered... 2025-11-02 21:54:03
>> binning method is used...2025-11-02 21:54:40
>> preparing body regions by enhancer... 2025-11-02 21:54:40
>> preparing tag matrix by binning...  2025-11-02 21:54:40 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2025-11-02 21:54:40
>> 1 peaks(0.7352941%), having lengths smaller than 800bp, are filtered... 2025-11-02 21:54:40
>> Using Genome: hg19 ...
>> Using Genome: hg19 ...
>> binning method is used...2025-11-02 21:54:43
>> preparing body regions by gene... 2025-11-02 21:54:43
>> preparing tag matrix by binning...  2025-11-02 21:54:43 
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2025-11-02 21:54:43
>> 15 peaks(1.39795%), having lengths smaller than 800bp, are filtered... 2025-11-02 21:54:46
>> Using Genome: hg19 ...
>> Update txdb in cache...
>> Using Genome: hg38 ...
>> Update txdb in cache...
>> Using Genome: hg19 ...
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 28 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-txdb.R:25:5'): txdb ──────────────────────────────────────────
ChIPseeker:::TXID2EG("70455") not equal to "uc002qsd.4/1".
1/1 mismatches
x[1]: "ENST00000487630.1_3/ENST00000487630.1_3"
y[1]: "uc002qsd.4/1"
── Failure ('test-txdb.R:26:5'): txdb ──────────────────────────────────────────
ChIPseeker:::TXID2EG("70455", geneIdOnly = TRUE) not equal to "1".
1/1 mismatches
x[1]: "ENST00000487630.1_3"
y[1]: "1"

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 28 ]
Error: Test failures
Execution halted