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This page was generated on 2024-03-27 11:37:14 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 2038/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPOTlight 1.6.7  (landing page)
Marc Elosua-Bayes
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/SPOTlight
git_branch: RELEASE_3_18
git_last_commit: e9de3a6
git_last_commit_date: 2024-01-15 09:42:55 -0400 (Mon, 15 Jan 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for SPOTlight on palomino4


To the developers/maintainers of the SPOTlight package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPOTlight.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: SPOTlight
Version: 1.6.7
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPOTlight.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SPOTlight_1.6.7.tar.gz
StartedAt: 2024-03-26 05:36:22 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 05:42:50 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 387.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SPOTlight.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPOTlight.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SPOTlight_1.6.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SPOTlight.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SPOTlight/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SPOTlight' version '1.6.7'
* 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 whether package 'SPOTlight' 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 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 ... NOTE
.set_groups_if_null: no visible global function definition for 'Idents'
Undefined global functions or variables:
  Idents
* 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
SPOTlight         8.92   0.17    9.10
plotTopicProfiles 8.83   0.18    9.00
runDeconvolution  7.93   0.11    8.04
trainNMF          6.57   0.11    6.67
data              5.25   0.05    5.30
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/SPOTlight.Rcheck/00check.log'
for details.



Installation output

SPOTlight.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SPOTlight
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'SPOTlight' ...
** 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 (SPOTlight)

Tests output

SPOTlight.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> set.seed(321)
> library(testthat)
> library(SPOTlight)
> # plotImage() ----
> test_check("SPOTlight")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 354 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 354 ]
> 
> proc.time()
   user  system elapsed 
 117.09    6.31  146.62 

Example timings

SPOTlight.Rcheck/SPOTlight-Ex.timings

nameusersystemelapsed
SPOTlight8.920.179.10
data5.250.055.30
plotCorrelationMatrix0.820.010.85
plotImage2.280.032.33
plotInteractions1.110.001.12
plotSpatialScatterpie0.750.060.84
plotTopicProfiles8.830.189.00
runDeconvolution7.930.118.04
trainNMF6.570.116.67