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This page was generated on 2024-03-04 11:36:30 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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

Package 335/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseeker 1.39.0  (landing page)
Guangchuang Yu
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/ChIPseeker
git_branch: devel
git_last_commit: cb681a6
git_last_commit_date: 2023-10-25 05:07:35 -0500 (Wed, 25 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ChIPseeker on nebbiolo1


To the developers/maintainers of the ChIPseeker package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPseeker.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: ChIPseeker
Version: 1.39.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChIPseeker.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChIPseeker_1.39.0.tar.gz
StartedAt: 2024-03-01 20:49:45 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 21:14:02 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 1456.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPseeker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChIPseeker.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChIPseeker_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ChIPseeker.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ChIPseeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseeker’ version ‘1.39.0’
* 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 ‘ChIPseeker’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  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 ... NOTE
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    ChIPseeker\n\n+ Bioconductor RELEASE_3_17 (2023-05-03, Wed)\n
* 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ChIPseeker.Rcheck/00check.log’
for details.



Installation output

ChIPseeker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ChIPseeker
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output

ChIPseeker.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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 v1.39.0

If you use ChIPseeker in published research, 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... 2024-03-01 20:55:21
>> preparing tag matrix...  2024-03-01 20:55:21 
>> binning method is used...2024-03-01 20:55:32
>> preparing body regions by enhancer... 2024-03-01 20:55:32
>> preparing tag matrix by binning...  2024-03-01 20:55:32 
>> preparing matrix for body region with no flank extension... 2024-03-01 20:55:32
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:55:32
>> binning method is used...2024-03-01 20:55:35
>> preparing body regions by enhancer... 2024-03-01 20:55:35
>> preparing tag matrix by binning...  2024-03-01 20:55:35 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2024-03-01 20:55:35
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:55:35
>> binning method is used...2024-03-01 20:55:40
>> preparing body regions by enhancer... 2024-03-01 20:55:40
>> preparing tag matrix by binning...  2024-03-01 20:55:40 
>> preparing matrix with flank extension from (enhancer_SS-1000bp)~(enhancer_TS+1000bp)... 2024-03-01 20:55:40
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:55:41
>> preparing start_site regions by gene... 2024-03-01 20:55:43
>> preparing tag matrix...  2024-03-01 20:55:43 
>> preparing start_site regions by gene... 2024-03-01 20:55:56
>> preparing tag matrix...  2024-03-01 20:55:56 
>> binning method is used...2024-03-01 20:55:57
>> preparing body regions by gene... 2024-03-01 20:55:57
>> preparing tag matrix by binning...  2024-03-01 20:55:57 
>> preparing matrix for body region with no flank extension... 2024-03-01 20:55:57
>> 9 peaks(1.2%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:55:59
>> binning method is used...2024-03-01 20:56:28
>> preparing body regions by enhancer... 2024-03-01 20:56:28
>> preparing tag matrix by binning...  2024-03-01 20:56:28 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2024-03-01 20:56:28
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:56:29
>> binning method is used...2024-03-01 20:56:34
>> preparing body regions by gene... 2024-03-01 20:56:34
>> preparing tag matrix by binning...  2024-03-01 20:56:34 
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2024-03-01 20:56:34
>> 15 peaks(1.80072%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:56:36
>> preparing start_site regions by enhancer non-enhancer... 2024-03-01 20:57:09
>> preparing tag matrix...  2024-03-01 20:57:09 
>> plotting figure...			 2024-03-01 20:57:10 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:57:15 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:57:20 
>> preparing start_site regions by enhancer non-enhancer... 2024-03-01 20:57:20
>> preparing tag matrix...  2024-03-01 20:57:20 
>> preparing start_site regions by enhancer non-enhancer... 2024-03-01 20:57:21
>> preparing tag matrix...  2024-03-01 20:57:21 
>> plotting figure...			 2024-03-01 20:57:22 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:57:27 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:57:33 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:57:38 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:57:43 
>> preparing start_site regions by enhancer gene... 2024-03-01 20:57:44
>> preparing tag matrix...  2024-03-01 20:57:44 
>> plotting figure...			 2024-03-01 20:57:48 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:57:54 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:58:01 
>> binning method is used...2024-03-01 20:58:02
>> preparing body regions by enhancer gene... 2024-03-01 20:58:02
>> preparing tag matrix by binning...  2024-03-01 20:58:02 
>> preparing matrix with flank extension from (enhancer_SS-1000bp)~(enhancer_TS+1000bp)... 2024-03-01 20:58:02
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:58:04
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2024-03-01 20:58:07
>> 15 peaks(1.80072%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:58:09
>> Running bootstrapping for tag matrix...		 2024-03-01 20:58:44 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:58:50 
>> binning method is used...2024-03-01 20:58:50
>> preparing body regions by enhancer gene... 2024-03-01 20:58:50
>> preparing tag matrix by binning...  2024-03-01 20:58:50 
>> preparing matrix for body region with no flank extension... 2024-03-01 20:58:50
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:58:51
>> preparing matrix for body region with no flank extension... 2024-03-01 20:58:53
>> 9 peaks(1.2%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:58:56
>> Running bootstrapping for tag matrix...		 2024-03-01 20:59:29 
>> Running bootstrapping for tag matrix...		 2024-03-01 20:59:35 
>> binning method is used...2024-03-01 20:59:35
>> preparing body regions by enhancer gene... 2024-03-01 20:59:35
>> preparing tag matrix by binning...  2024-03-01 20:59:35 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2024-03-01 20:59:35
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:59:35
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-03-01 20:59:43
>> 9 peaks(0.872093%), having lengths smaller than 800bp, are filtered... 2024-03-01 20:59:47
>> Running bootstrapping for tag matrix...		 2024-03-01 21:00:49 
>> Running bootstrapping for tag matrix...		 2024-03-01 21:00:54 
>> binning method is used...2024-03-01 21:00:54
>> preparing body regions by enhancer gene... 2024-03-01 21:00:54
>> preparing tag matrix by binning...  2024-03-01 21:00:54 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2024-03-01 21:00:55
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:00:55
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-03-01 21:01:01
>> 9 peaks(0.872093%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:01:06
>> binning method is used...2024-03-01 21:02:02
>> preparing body regions by enhancer gene... 2024-03-01 21:02:02
>> preparing tag matrix by binning...  2024-03-01 21:02:02 
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2024-03-01 21:02:02
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:02:02
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-03-01 21:02:09
>> 9 peaks(0.7874016%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:02:13
>> Running bootstrapping for tag matrix...		 2024-03-01 21:03:21 
>> Running bootstrapping for tag matrix...		 2024-03-01 21:03:27 
>> Running bootstrapping for tag matrix...		 2024-03-01 21:03:34 
>> Running bootstrapping for tag matrix...		 2024-03-01 21:03:40 
>> binning method is used...2024-03-01 21:03:41
>> preparing start_site regions by gene... 2024-03-01 21:03:41
>> preparing tag matrix by binning...  2024-03-01 21:03:41 
>> binning method is used...2024-03-01 21:03:43
>> preparing start_site regions by gene... 2024-03-01 21:03:43
>> preparing tag matrix by binning...  2024-03-01 21:03:43 
>> binning method is used...2024-03-01 21:03:45
>> preparing start_site regions by gene... 2024-03-01 21:03:45
>> preparing tag matrix by binning...  2024-03-01 21:03:45 
>> binning method is used...2024-03-01 21:03:47
>> preparing body regions by gene... 2024-03-01 21:03:47
>> preparing tag matrix by binning...  2024-03-01 21:03:47 
>> preparing matrix for body region with no flank extension... 2024-03-01 21:03:47
>> 9 peaks(1.2%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:03:49
>> binning method is used...2024-03-01 21:04:20
>> preparing body regions by gene... 2024-03-01 21:04:20
>> preparing tag matrix by binning...  2024-03-01 21:04:20 
>> preparing matrix for body region with no flank extension... 2024-03-01 21:04:20
>> 8 peaks(0.9791922%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:04:22
>> binning method is used...2024-03-01 21:04:52
>> preparing body regions by gene... 2024-03-01 21:04:52
>> preparing tag matrix by binning...  2024-03-01 21:04:52 
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-03-01 21:04:52
>> 9 peaks(0.872093%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:04:56
>> binning method is used...2024-03-01 21:05:52
>> preparing body regions by gene... 2024-03-01 21:05:52
>> preparing tag matrix by binning...  2024-03-01 21:05:52 
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-03-01 21:05:52
>> 9 peaks(0.7874016%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:05:56
>> binning method is used...2024-03-01 21:07:00
>> preparing body regions by gene... 2024-03-01 21:07:00
>> preparing tag matrix by binning...  2024-03-01 21:07:00 
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2024-03-01 21:07:00
>> 15 peaks(1.80072%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:07:03
>> binning method is used...2024-03-01 21:07:34
>> preparing body regions by gene... 2024-03-01 21:07:34
>> preparing tag matrix by binning...  2024-03-01 21:07:34 
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2024-03-01 21:07:34
>> 16 peaks(1.758242%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:07:36
>> binning method is used...2024-03-01 21:08:10
>> preparing start_site regions by gene... 2024-03-01 21:08:10
>> preparing tag matrix by binning...  2024-03-01 21:08:10 
>> binning method is used...2024-03-01 21:08:10
>> preparing start_site regions by gene... 2024-03-01 21:08:10
>> preparing tag matrix by binning...  2024-03-01 21:08:10 
>> binning method is used...2024-03-01 21:08:10
>> preparing start_site regions by gene... 2024-03-01 21:08:10
>> preparing tag matrix by binning...  2024-03-01 21:08:10 
>> binning method is used...2024-03-01 21:08:10
>> preparing body regions by gene... 2024-03-01 21:08:10
>> preparing tag matrix by binning...  2024-03-01 21:08:10 
>> preparing matrix for body region with no flank extension... 2024-03-01 21:08:11
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:08:11
>> binning method is used...2024-03-01 21:08:13
>> preparing body regions by gene... 2024-03-01 21:08:13
>> preparing tag matrix by binning...  2024-03-01 21:08:13 
>> preparing matrix for body region with no flank extension... 2024-03-01 21:08:13
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:08:13
>> binning method is used...2024-03-01 21:08:15
>> preparing body regions by gene... 2024-03-01 21:08:15
>> preparing tag matrix by binning...  2024-03-01 21:08:15 
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-03-01 21:08:15
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:08:16
>> binning method is used...2024-03-01 21:08:21
>> preparing body regions by gene... 2024-03-01 21:08:21
>> preparing tag matrix by binning...  2024-03-01 21:08:21 
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2024-03-01 21:08:21
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:08:21
>> binning method is used...2024-03-01 21:08:28
>> preparing body regions by gene... 2024-03-01 21:08:28
>> preparing tag matrix by binning...  2024-03-01 21:08:28 
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2024-03-01 21:08:28
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:08:28
>> binning method is used...2024-03-01 21:08:30
>> preparing body regions by gene... 2024-03-01 21:08:30
>> preparing tag matrix by binning...  2024-03-01 21:08:30 
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2024-03-01 21:08:30
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2024-03-01 21:08:30
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 45 ]
> 
> proc.time()
   user  system elapsed 
734.880 478.643 812.139 

Example timings

ChIPseeker.Rcheck/ChIPseeker-Ex.timings

nameusersystemelapsed
annotatePeak000
dotFun0.0000.0000.001
plotAnnoPie0.0010.0010.000
plotDistToTSS.data.frame000
readPeakFile0.1020.0220.125
seq2gene000
vennplot0.0010.0010.001