Peiying Cai
| Snapshot Date: 2025-04-18 13:00 -0400 (Fri, 18 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/DESpace |
| git_branch: devel |
| git_last_commit: d0e41b7 |
| git_last_commit_date: 2025-04-15 13:11:56 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-04-20 11:59 -0400 (Sun, 20 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4496 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4351 |
| 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 560/2302 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DESpace 2.1.0 (landing page) Peiying Cai
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the DESpace package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DESpace.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. |
| Package: DESpace |
| Version: 2.1.0 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DESpace.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings DESpace_2.1.0.tar.gz |
| StartedAt: 2025-04-19 00:51:28 -0400 (Sat, 19 Apr 2025) |
| EndedAt: 2025-04-19 01:01:53 -0400 (Sat, 19 Apr 2025) |
| EllapsedTime: 626.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DESpace.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DESpace.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings DESpace_2.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/DESpace.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DESpace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DESpace' version '2.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 whether package 'DESpace' 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 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
dsp_test 23.28 3.10 28.48
individual_dsp 21.80 2.26 24.20
svg_test 18.28 0.53 18.80
individual_svg 8.89 0.20 9.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testhat.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: OK
DESpace.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL DESpace ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'DESpace' ... ** this is package 'DESpace' version '2.1.0' ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (DESpace)
DESpace.Rcheck/tests/testhat.Rout
R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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(DESpace)
> test_check("DESpace")
(Intercept) condition20DPI condition2DPI cluster_id1 cluster_id2
2DPI_1_0 1 0 1 0 0
2DPI_2_0 1 0 1 0 0
cluster_id3 cluster_id4 condition20DPI:cluster_id1
2DPI_1_0 0 0 0
2DPI_2_0 0 0 0
condition2DPI:cluster_id1 condition20DPI:cluster_id2
2DPI_1_0 0 0
2DPI_2_0 0 0
condition2DPI:cluster_id2 condition20DPI:cluster_id3
2DPI_1_0 0 0
2DPI_2_0 0 0
condition2DPI:cluster_id3 condition20DPI:cluster_id4
2DPI_1_0 0 0
2DPI_2_0 0 0
condition2DPI:cluster_id4
2DPI_1_0 0
2DPI_2_0 0
(Intercept) condition20DPI condition2DPI cluster_id0
2DPI_1_Other 1 0 1 0
2DPI_2_Other 1 0 1 0
condition20DPI:cluster_id0 condition2DPI:cluster_id0
2DPI_1_Other 0 0
2DPI_2_Other 0 0
(Intercept) condition20DPI condition2DPI cluster_id1
2DPI_1_Other 1 0 1 0
2DPI_2_Other 1 0 1 0
condition20DPI:cluster_id1 condition2DPI:cluster_id1
2DPI_1_Other 0 0
2DPI_2_Other 0 0
(Intercept) condition20DPI condition2DPI cluster_id2
2DPI_1_Other 1 0 1 0
2DPI_2_Other 1 0 1 0
condition20DPI:cluster_id2 condition2DPI:cluster_id2
2DPI_1_Other 0 0
2DPI_2_Other 0 0
(Intercept) condition20DPI condition2DPI cluster_id3
2DPI_1_Other 1 0 1 0
2DPI_2_Other 1 0 1 0
condition20DPI:cluster_id3 condition2DPI:cluster_id3
2DPI_1_Other 0 0
2DPI_2_Other 0 0
(Intercept) condition20DPI condition2DPI cluster_id4
2DPI_1_Other 1 0 1 0
2DPI_2_Other 1 0 1 0
condition20DPI:cluster_id4 condition2DPI:cluster_id4
2DPI_1_Other 0 0
2DPI_2_Other 0 0
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
90.01 7.98 192.09
DESpace.Rcheck/DESpace-Ex.timings
| name | user | system | elapsed | |
| FeaturePlot | 2.37 | 0.08 | 2.45 | |
| LIBD_subset | 0 | 0 | 0 | |
| dsp_test | 23.28 | 3.10 | 28.48 | |
| individual_dsp | 21.80 | 2.26 | 24.20 | |
| individual_svg | 8.89 | 0.20 | 9.09 | |
| results_individual_svg | 0 | 0 | 0 | |
| results_svg_test | 0 | 0 | 0 | |
| svg_test | 18.28 | 0.53 | 18.80 | |
| top_results | 0.47 | 0.04 | 0.51 | |