Zheng Wei
| Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/pipeFrame |
| git_branch: devel |
| git_last_commit: e97ea2e |
| git_last_commit_date: 2024-04-30 11:14:26 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-08 11:45 -0400 (Mon, 08 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 1527/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pipeFrame 1.21.0 (landing page) Zheng Wei
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | OK | OK | ||||||||||
|
To the developers/maintainers of the pipeFrame package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: pipeFrame |
| Version: 1.21.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:pipeFrame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pipeFrame_1.21.0.tar.gz |
| StartedAt: 2024-07-06 07:19:59 -0000 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 07:25:12 -0000 (Sat, 06 Jul 2024) |
| EllapsedTime: 312.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pipeFrame.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:pipeFrame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pipeFrame_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/pipeFrame.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pipeFrame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeFrame’ version ‘1.21.0’
* 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 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 ... 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
* 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
‘/home/biocbuild/bbs-3.20-bioc/meat/pipeFrame.Rcheck/00check.log’
for details.
pipeFrame.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL pipeFrame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(pipeFrame)
>
> test_check("pipeFrame")
[1] "2024-07-06 07:25:05 UTC"
[1] "2024-07-06 07:25:05 UTC"
[1] "2024-07-06 07:25:05 UTC"
[1] "2024-07-06 07:25:05 UTC"
[1] "2024-07-06 07:25:05 UTC"
[1] "2024-07-06 07:25:05 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:06 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "/home/biocbuild/bbs-3.20-bioc/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_01_pipe_OverlappedRandomRegion/test.bed"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "/home/biocbuild/bbs-3.20-bioc/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_00_pipe_RandomRegionOnGenome/random.bed"
[1] "2024-07-06 07:25:07 UTC"
[1] "2024-07-06 07:25:07 UTC"
[1] "/home/biocbuild/bbs-3.20-bioc/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_01_pipe_OverlappedRandomRegion/test.bed"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[1] "2024-07-06 07:25:09 UTC"
[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]
[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
20.711 1.386 22.129
pipeFrame.Rcheck/pipeFrame-Ex.timings
| name | user | system | elapsed | |
| Step-class | 4.217 | 0.180 | 4.409 | |
| Utils | 0.003 | 0.000 | 0.002 | |
| getObjsInPipe | 0.009 | 0.000 | 0.010 | |
| graphMng | 0.107 | 0.004 | 0.113 | |
| ignoreCheck | 0 | 0 | 0 | |
| initPipeFrame | 0.000 | 0.001 | 0.000 | |
| loadConfig | 0.000 | 0.001 | 0.001 | |
| loadStep | 0.002 | 0.000 | 0.003 | |
| runWithFinishCheck | 0.001 | 0.000 | 0.001 | |
| setGenome | 0.001 | 0.000 | 0.001 | |
| setJobName | 0 | 0 | 0 | |
| setPipeName | 0 | 0 | 0 | |
| setRefDir | 0 | 0 | 0 | |
| setThreads | 0.007 | 0.000 | 0.005 | |
| setTmpDir | 0 | 0 | 0 | |