Ziyi Li
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/RegionalST |
| git_branch: RELEASE_3_18 |
| git_last_commit: b918b10 |
| git_last_commit_date: 2023-10-24 11:50:26 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:09 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1710/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RegionalST 1.0.0 (landing page) Ziyi Li
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the RegionalST package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RegionalST.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: RegionalST |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings RegionalST_1.0.0.tar.gz |
| StartedAt: 2023-11-02 13:34:21 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 13:39:54 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 332.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RegionalST.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:RegionalST.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings RegionalST_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RegionalST.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘RegionalST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RegionalST’ version ‘1.0.0’
* 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 ‘RegionalST’ 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GetOneRadiusEntropy 9.837 0.259 10.126
DoGSEA 5.604 0.626 6.087
GetCrossRegionalDE_raw 5.683 0.215 5.932
* 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: OK
RegionalST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL RegionalST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘RegionalST’ ... ** 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 (RegionalST)
RegionalST.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-unknown-linux-gnu (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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(RegionalST)
>
> test_check("RegionalST")
Processing to cell type:CAFs
Processing to cell type:Myeloid
Processing to cell type:T-cells
Processing to cell type:Cancer Epithelial
Processing to cell type:Normal Epithelial
Processing to cell type:Endothelial
Processing to Radius = 5
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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
30.487 1.008 31.551
RegionalST.Rcheck/RegionalST-Ex.timings
| name | user | system | elapsed | |
| DoGSEA | 5.604 | 0.626 | 6.087 | |
| DrawDotplot | 2.483 | 0.741 | 3.063 | |
| DrawRegionProportion | 0.627 | 0.092 | 0.721 | |
| DrawRegionProportion_withProp | 0.625 | 0.012 | 0.638 | |
| FindRegionalCells | 0 | 0 | 0 | |
| GetCrossRegionalDE_raw | 5.683 | 0.215 | 5.932 | |
| GetCrossRegionalDE_withProp | 4.012 | 0.299 | 4.327 | |
| GetOneRadiusEntropy | 9.837 | 0.259 | 10.126 | |
| GetOneRadiusEntropy_withProp | 2.810 | 0.024 | 2.840 | |
| ManualSelectCenter | 0.750 | 0.008 | 0.761 | |
| PlotOneSelectedCenter | 2.023 | 0.052 | 2.079 | |
| RankCenterByEntropy | 4.367 | 0.036 | 4.469 | |
| RankCenterByEntropy_withProp | 4.117 | 0.076 | 4.201 | |
| exampleRes | 0.003 | 0.000 | 0.002 | |
| example_sce | 0.003 | 0.004 | 0.006 | |
| getProportion | 0 | 0 | 0 | |
| mySpatialPreprocess | 0.727 | 0.000 | 0.729 | |
| pathways_hallmark | 0.011 | 0.000 | 0.011 | |
| pathways_kegg | 0.018 | 0.000 | 0.018 | |
| pathways_reactome | 0.153 | 0.000 | 0.154 | |