Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-04-20 11:59 -0400 (Sun, 20 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4496
palomino8Windows Server 2022 Datacenterx644.5.0 (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 560/2302HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DESpace 2.1.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES


CHECK results for DESpace on palomino8

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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


Installation output

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)

Tests output

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 

Example timings

DESpace.Rcheck/DESpace-Ex.timings

nameusersystemelapsed
FeaturePlot2.370.082.45
LIBD_subset000
dsp_test23.28 3.1028.48
individual_dsp21.80 2.2624.20
individual_svg8.890.209.09
results_individual_svg000
results_svg_test000
svg_test18.28 0.5318.80
top_results0.470.040.51