Zheng Wei
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/pipeFrame |
| git_branch: RELEASE_3_17 |
| git_last_commit: 89b7f04 |
| git_last_commit_date: 2023-04-25 11:09:55 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:09 -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 1524/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pipeFrame 1.16.0 (landing page) Zheng Wei
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the pipeFrame 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: pipeFrame |
| Version: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2023-10-18 14:54:05 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 15:00:50 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 404.7 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pipeFrame.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 ‘pipeFrame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeFrame’ version ‘1.16.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Step-class 5.271 0.825 9.175
* 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/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/4.3-arm64/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 4.3.1 (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(pipeFrame)
>
> test_check("pipeFrame")
[1] "2023-10-18 15:00:30 EDT"
[1] "2023-10-18 15:00:30 EDT"
[1] "2023-10-18 15:00:30 EDT"
[1] "2023-10-18 15:00:30 EDT"
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[1] "2023-10-18 15:00:30 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
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[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_01_pipe_OverlappedRandomRegion/test.bed"
[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
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[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_00_pipe_RandomRegionOnGenome/random.bed"
[1] "2023-10-18 15:00:32 EDT"
[1] "2023-10-18 15:00:32 EDT"
[1] "/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pipeFrame.Rcheck/tests/testthat/testJobName/Step_01_pipe_OverlappedRandomRegion/test.bed"
[1] "2023-10-18 15:00:35 EDT"
[1] "2023-10-18 15:00:35 EDT"
[1] "2023-10-18 15:00:35 EDT"
[1] "2023-10-18 15:00:35 EDT"
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[1] "2023-10-18 15:00:35 EDT"
[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]
[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
18.668 1.474 28.830
pipeFrame.Rcheck/pipeFrame-Ex.timings
| name | user | system | elapsed | |
| Step-class | 5.271 | 0.825 | 9.175 | |
| Utils | 0.003 | 0.002 | 0.005 | |
| getObjsInPipe | 0.009 | 0.003 | 0.017 | |
| graphMng | 0.109 | 0.025 | 0.169 | |
| ignoreCheck | 0.001 | 0.000 | 0.001 | |
| initPipeFrame | 0.001 | 0.000 | 0.001 | |
| loadConfig | 0.002 | 0.001 | 0.004 | |
| loadStep | 0.002 | 0.001 | 0.004 | |
| runWithFinishCheck | 0.001 | 0.001 | 0.003 | |
| setGenome | 0.000 | 0.000 | 0.001 | |
| setJobName | 0.001 | 0.000 | 0.001 | |
| setPipeName | 0.001 | 0.000 | 0.000 | |
| setRefDir | 0.001 | 0.000 | 0.001 | |
| setThreads | 0.004 | 0.006 | 0.033 | |
| setTmpDir | 0.000 | 0.000 | 0.001 | |