Guangchuang Yu
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ChIPseeker |
| git_branch: RELEASE_3_17 |
| git_last_commit: 3179a1f |
| git_last_commit_date: 2023-04-25 10:32:01 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 330/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPseeker 1.36.0 (landing page) Guangchuang Yu
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the ChIPseeker package: - 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. |
| Package: ChIPseeker |
| Version: 1.36.0 |
| 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_1.36.0.tar.gz |
| StartedAt: 2023-10-17 09:00:42 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 09:33:42 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 1980.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPseeker.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.36.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ChIPseeker.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPseeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseeker’ version ‘1.36.0’
* 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 6.1Mb
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 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 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 in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/meat/ChIPseeker.Rcheck/00check.log’
for details.
ChIPseeker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPseeker ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)
ChIPseeker.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(ChIPseeker)
ChIPseeker v1.36.0
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... 2023-10-17 09:09:25
>> preparing tag matrix... 2023-10-17 09:09:25
>> binning method is used...2023-10-17 09:09:39
>> preparing body regions by enhancer... 2023-10-17 09:09:39
>> preparing tag matrix by binning... 2023-10-17 09:09:39
>> preparing matrix for body region with no flank extension... 2023-10-17 09:09:39
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:09:40
>> binning method is used...2023-10-17 09:09:45
>> preparing body regions by enhancer... 2023-10-17 09:09:45
>> preparing tag matrix by binning... 2023-10-17 09:09:45
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2023-10-17 09:09:45
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:09:45
>> binning method is used...2023-10-17 09:09:56
>> preparing body regions by enhancer... 2023-10-17 09:09:56
>> preparing tag matrix by binning... 2023-10-17 09:09:56
>> preparing matrix with flank extension from (enhancer_SS-1000bp)~(enhancer_TS+1000bp)... 2023-10-17 09:09:56
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:09:56
>> preparing start_site regions by gene... 2023-10-17 09:10:03
>> preparing tag matrix... 2023-10-17 09:10:03
>> preparing start_site regions by gene... 2023-10-17 09:10:20
>> preparing tag matrix... 2023-10-17 09:10:20
>> binning method is used...2023-10-17 09:10:21
>> preparing body regions by gene... 2023-10-17 09:10:21
>> preparing tag matrix by binning... 2023-10-17 09:10:21
>> preparing matrix for body region with no flank extension... 2023-10-17 09:10:21
>> 9 peaks(1.2%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:10:25
>> binning method is used...2023-10-17 09:11:25
>> preparing body regions by enhancer... 2023-10-17 09:11:25
>> preparing tag matrix by binning... 2023-10-17 09:11:25
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2023-10-17 09:11:26
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:11:26
>> binning method is used...2023-10-17 09:11:37
>> preparing body regions by gene... 2023-10-17 09:11:37
>> preparing tag matrix by binning... 2023-10-17 09:11:37
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2023-10-17 09:11:37
>> 15 peaks(1.80072%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:11:42
>> preparing start_site regions by enhancer non-enhancer... 2023-10-17 09:12:49
>> preparing tag matrix... 2023-10-17 09:12:49
>> plotting figure... 2023-10-17 09:12:51
>> Running bootstrapping for tag matrix... 2023-10-17 09:12:51
>> Running bootstrapping for tag matrix... 2023-10-17 09:12:53
>> preparing start_site regions by enhancer non-enhancer... 2023-10-17 09:12:55
>> preparing tag matrix... 2023-10-17 09:12:55
>> preparing start_site regions by enhancer non-enhancer... 2023-10-17 09:12:56
>> preparing tag matrix... 2023-10-17 09:12:56
>> plotting figure... 2023-10-17 09:12:58
>> Running bootstrapping for tag matrix... 2023-10-17 09:12:58
>> Running bootstrapping for tag matrix... 2023-10-17 09:13:00
>> Running bootstrapping for tag matrix... 2023-10-17 09:13:01
>> Running bootstrapping for tag matrix... 2023-10-17 09:13:03
>> preparing start_site regions by enhancer gene... 2023-10-17 09:13:04
>> preparing tag matrix... 2023-10-17 09:13:04
>> plotting figure... 2023-10-17 09:13:10
>> Running bootstrapping for tag matrix... 2023-10-17 09:13:11
>> Running bootstrapping for tag matrix... 2023-10-17 09:13:17
>> binning method is used...2023-10-17 09:13:19
>> preparing body regions by enhancer gene... 2023-10-17 09:13:19
>> preparing tag matrix by binning... 2023-10-17 09:13:19
>> preparing matrix with flank extension from (enhancer_SS-1000bp)~(enhancer_TS+1000bp)... 2023-10-17 09:13:19
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:13:20
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2023-10-17 09:13:25
>> 15 peaks(1.80072%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:13:32
>> Running bootstrapping for tag matrix... 2023-10-17 09:14:32
>> Running bootstrapping for tag matrix... 2023-10-17 09:14:35
>> binning method is used...2023-10-17 09:14:36
>> preparing body regions by enhancer gene... 2023-10-17 09:14:36
>> preparing tag matrix by binning... 2023-10-17 09:14:36
>> preparing matrix for body region with no flank extension... 2023-10-17 09:14:36
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:14:36
>> preparing matrix for body region with no flank extension... 2023-10-17 09:14:41
>> 9 peaks(1.2%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:14:46
>> Running bootstrapping for tag matrix... 2023-10-17 09:15:43
>> Running bootstrapping for tag matrix... 2023-10-17 09:15:45
>> binning method is used...2023-10-17 09:15:45
>> preparing body regions by enhancer gene... 2023-10-17 09:15:45
>> preparing tag matrix by binning... 2023-10-17 09:15:45
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2023-10-17 09:15:45
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:15:46
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-10-17 09:15:58
>> 9 peaks(0.872093%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:16:03
>> Running bootstrapping for tag matrix... 2023-10-17 09:17:57
>> Running bootstrapping for tag matrix... 2023-10-17 09:18:01
>> binning method is used...2023-10-17 09:18:02
>> preparing body regions by enhancer gene... 2023-10-17 09:18:02
>> preparing tag matrix by binning... 2023-10-17 09:18:02
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2023-10-17 09:18:02
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:18:03
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-10-17 09:18:14
>> 9 peaks(0.872093%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:18:21
>> binning method is used...2023-10-17 09:20:16
>> preparing body regions by enhancer gene... 2023-10-17 09:20:16
>> preparing tag matrix by binning... 2023-10-17 09:20:16
>> preparing matrix with extension from (enhancer_SS-20%)~(enhancer_TS+20%)... 2023-10-17 09:20:16
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:20:17
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-10-17 09:20:31
>> 9 peaks(0.7874016%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:20:38
>> Running bootstrapping for tag matrix... 2023-10-17 09:22:50
>> Running bootstrapping for tag matrix... 2023-10-17 09:22:54
>> Running bootstrapping for tag matrix... 2023-10-17 09:22:55
>> Running bootstrapping for tag matrix... 2023-10-17 09:23:00
>> binning method is used...2023-10-17 09:23:01
>> preparing start_site regions by gene... 2023-10-17 09:23:01
>> preparing tag matrix by binning... 2023-10-17 09:23:01
>> binning method is used...2023-10-17 09:23:05
>> preparing start_site regions by gene... 2023-10-17 09:23:05
>> preparing tag matrix by binning... 2023-10-17 09:23:05
>> binning method is used...2023-10-17 09:23:09
>> preparing start_site regions by gene... 2023-10-17 09:23:09
>> preparing tag matrix by binning... 2023-10-17 09:23:09
>> binning method is used...2023-10-17 09:23:12
>> preparing body regions by gene... 2023-10-17 09:23:12
>> preparing tag matrix by binning... 2023-10-17 09:23:12
>> preparing matrix for body region with no flank extension... 2023-10-17 09:23:13
>> 9 peaks(1.2%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:23:17
>> binning method is used...2023-10-17 09:24:17
>> preparing body regions by gene... 2023-10-17 09:24:17
>> preparing tag matrix by binning... 2023-10-17 09:24:17
>> preparing matrix for body region with no flank extension... 2023-10-17 09:24:17
>> 8 peaks(0.9791922%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:24:22
>> binning method is used...2023-10-17 09:25:23
>> preparing body regions by gene... 2023-10-17 09:25:23
>> preparing tag matrix by binning... 2023-10-17 09:25:23
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-10-17 09:25:23
>> 9 peaks(0.872093%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:25:28
>> binning method is used...2023-10-17 09:27:50
>> preparing body regions by gene... 2023-10-17 09:27:50
>> preparing tag matrix by binning... 2023-10-17 09:27:50
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-10-17 09:27:50
>> 9 peaks(0.7874016%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:27:55
>> binning method is used...2023-10-17 09:30:07
>> preparing body regions by gene... 2023-10-17 09:30:07
>> preparing tag matrix by binning... 2023-10-17 09:30:07
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2023-10-17 09:30:07
>> 15 peaks(1.80072%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:30:13
>> binning method is used...2023-10-17 09:31:14
>> preparing body regions by gene... 2023-10-17 09:31:14
>> preparing tag matrix by binning... 2023-10-17 09:31:14
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2023-10-17 09:31:14
>> 16 peaks(1.758242%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:31:20
>> binning method is used...2023-10-17 09:32:27
>> preparing start_site regions by gene... 2023-10-17 09:32:27
>> preparing tag matrix by binning... 2023-10-17 09:32:27
>> binning method is used...2023-10-17 09:32:27
>> preparing start_site regions by gene... 2023-10-17 09:32:27
>> preparing tag matrix by binning... 2023-10-17 09:32:27
>> binning method is used...2023-10-17 09:32:28
>> preparing start_site regions by gene... 2023-10-17 09:32:28
>> preparing tag matrix by binning... 2023-10-17 09:32:28
>> binning method is used...2023-10-17 09:32:28
>> preparing body regions by gene... 2023-10-17 09:32:28
>> preparing tag matrix by binning... 2023-10-17 09:32:28
>> preparing matrix for body region with no flank extension... 2023-10-17 09:32:28
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:32:28
>> binning method is used...2023-10-17 09:32:33
>> preparing body regions by gene... 2023-10-17 09:32:33
>> preparing tag matrix by binning... 2023-10-17 09:32:33
>> preparing matrix for body region with no flank extension... 2023-10-17 09:32:33
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:32:34
>> binning method is used...2023-10-17 09:32:38
>> preparing body regions by gene... 2023-10-17 09:32:38
>> preparing tag matrix by binning... 2023-10-17 09:32:38
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-10-17 09:32:38
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:32:39
>> binning method is used...2023-10-17 09:32:50
>> preparing body regions by gene... 2023-10-17 09:32:50
>> preparing tag matrix by binning... 2023-10-17 09:32:50
>> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-10-17 09:32:50
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:32:50
>> binning method is used...2023-10-17 09:33:04
>> preparing body regions by gene... 2023-10-17 09:33:04
>> preparing tag matrix by binning... 2023-10-17 09:33:04
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2023-10-17 09:33:04
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:33:05
>> binning method is used...2023-10-17 09:33:10
>> preparing body regions by gene... 2023-10-17 09:33:10
>> preparing tag matrix by binning... 2023-10-17 09:33:10
>> preparing matrix with flank extension from (TSS-1000bp)~(TTS+1000bp)... 2023-10-17 09:33:10
>> 0 peaks(0%), having lengths smaller than 800bp, are filtered... 2023-10-17 09:33:10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 45 ]
>
> proc.time()
user system elapsed
947.520 34.894 1463.953
ChIPseeker.Rcheck/ChIPseeker-Ex.timings
| name | user | system | elapsed | |
| annotatePeak | 0.000 | 0.001 | 0.001 | |
| dotFun | 0.000 | 0.001 | 0.002 | |
| plotAnnoPie | 0.000 | 0.001 | 0.000 | |
| plotDistToTSS.data.frame | 0 | 0 | 0 | |
| readPeakFile | 0.151 | 0.003 | 0.236 | |
| seq2gene | 0 | 0 | 0 | |
| vennplot | 0 | 0 | 0 | |