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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPseeker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPseeker_1.41.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPseeker.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPseeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseeker’ version ‘1.41.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘ChIPseeker’ can be installed ... OK
* checking installed package size ... NOTE
  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 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’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPseeker.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPseeker
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘ChIPseeker’ ...
** 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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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(ChIPseeker)

ChIPseeker v1.41.3 Learn more at https://yulab-smu.top/contribution-knowledge-mining/

Please cite:

Qianwen Wang, Ming Li, Tianzhi Wu, Li Zhan, Lin Li, Meijun Chen, Wenqin
Xie, Zijing Xie, Erqiang Hu, Shuangbin Xu, Guangchuang Yu. Exploring
epigenomic datasets by ChIPseeker. Current Protocols. 2022, 2(10): e585
> 
> test_check("ChIPseeker")
>> preparing start_site regions by gene... 2024-10-27 11:39:48
>> preparing tag matrix...  2024-10-27 11:39:48 
>> binning method is used...2024-10-27 11:39:52
>> preparing body regions by enhancer... 2024-10-27 11:39:52
>> preparing tag matrix by binning...  2024-10-27 11:39:52 
>> preparing matrix for body region with no flank extension... 2024-10-27 11:39:52
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-10-27 11:39:52
>> binning method is used...2024-10-27 11:39:53
>> preparing body regions by enhancer... 2024-10-27 11:39:53
>> preparing tag matrix by binning...  2024-10-27 11:39:53 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2024-10-27 11:39:53
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-10-27 11:39:54
>> binning method is used...2024-10-27 11:39:56
>> preparing body regions by enhancer... 2024-10-27 11:39:56
>> preparing tag matrix by binning...  2024-10-27 11:39:56 
>> preparing matrix with flank extension from (enhancer_SS-1000bp)~(enhancer_TS+1000bp)... 2024-10-27 11:39:56
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-10-27 11:39:56
>> preparing start_site regions by gene... 2024-10-27 11:39:57
>> preparing tag matrix...  2024-10-27 11:39:57 
>> preparing start_site regions by gene... 2024-10-27 11:40:01
>> preparing tag matrix...  2024-10-27 11:40:01 
>> binning method is used...2024-10-27 11:40:01
>> preparing body regions by gene... 2024-10-27 11:40:01
>> preparing tag matrix by binning...  2024-10-27 11:40:01 
>> preparing matrix for body region with no flank extension... 2024-10-27 11:40:01
>> 9 peaks(1.2%), having lengths smaller than 800bp, are filtered... 2024-10-27 11:40:01
>> binning method is used...2024-10-27 11:40:13
>> preparing body regions by enhancer... 2024-10-27 11:40:13
>> preparing tag matrix by binning...  2024-10-27 11:40:13 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2024-10-27 11:40:13
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-10-27 11:40:13
>> binning method is used...2024-10-27 11:40:15
>> preparing body regions by gene... 2024-10-27 11:40:15
>> preparing tag matrix by binning...  2024-10-27 11:40:15 
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2024-10-27 11:40:15
>> 15 peaks(1.80072%), having lengths smaller than 800bp, are filtered... 2024-10-27 11:40:16
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
> 
> proc.time()
   user  system elapsed 
 44.589   1.786  46.376