Zheng Wei
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/pipeFrame |
| git_branch: RELEASE_3_16 |
| git_last_commit: 6bfd083 |
| git_last_commit_date: 2022-11-01 11:19:48 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:20 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the pipeFrame package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pipeFrame.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1489/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pipeFrame 1.14.0 (landing page) Zheng Wei
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: pipeFrame |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pipeFrame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pipeFrame_1.14.0.tar.gz |
| StartedAt: 2023-04-10 21:52:43 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:56:15 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 212.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pipeFrame.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pipeFrame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pipeFrame_1.14.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/pipeFrame.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pipeFrame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeFrame’ version ‘1.14.0’
* 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 ‘pipeFrame’ 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 ... NOTE
Namespace in Imports field not imported from: ‘rmarkdown’
All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Step-class 4.823 0.848 5.724
* 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-3.16-bioc/meat/pipeFrame.Rcheck/00check.log’
for details.
pipeFrame.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pipeFrame ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘pipeFrame’ ... ** using staged installation ** R ** 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 (pipeFrame)
pipeFrame.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(pipeFrame)
>
> test_check("pipeFrame")
[1] "2023-04-10 21:56:03 EDT"
[1] "2023-04-10 21:56:03 EDT"
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[1] "/Users/biocbuild/bbs-3.16-bioc/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_01_pipe_OverlappedRandomRegion/test.bed"
[1] "2023-04-10 21:56:04 EDT"
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[1] "/Users/biocbuild/bbs-3.16-bioc/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_00_pipe_RandomRegionOnGenome/random.bed"
[1] "2023-04-10 21:56:04 EDT"
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[1] "/Users/biocbuild/bbs-3.16-bioc/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_01_pipe_OverlappedRandomRegion/test.bed"
[1] "2023-04-10 21:56:06 EDT"
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[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]
[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
16.250 1.356 17.686
pipeFrame.Rcheck/pipeFrame-Ex.timings
| name | user | system | elapsed | |
| Step-class | 4.823 | 0.848 | 5.724 | |
| Utils | 0.001 | 0.001 | 0.003 | |
| getObjsInPipe | 0.008 | 0.003 | 0.011 | |
| graphMng | 0.068 | 0.017 | 0.085 | |
| ignoreCheck | 0.000 | 0.001 | 0.001 | |
| initPipeFrame | 0 | 0 | 0 | |
| loadConfig | 0.001 | 0.001 | 0.001 | |
| loadStep | 0.001 | 0.001 | 0.002 | |
| runWithFinishCheck | 0.001 | 0.000 | 0.000 | |
| setGenome | 0.001 | 0.000 | 0.000 | |
| setJobName | 0 | 0 | 0 | |
| setPipeName | 0.001 | 0.001 | 0.000 | |
| setRefDir | 0.001 | 0.000 | 0.001 | |
| setThreads | 0.003 | 0.005 | 0.017 | |
| setTmpDir | 0.000 | 0.000 | 0.001 | |