Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1956/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
smoothclust 1.1.1  (landing page)
Lukas M. Weber
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/smoothclust
git_branch: devel
git_last_commit: b5d195c
git_last_commit_date: 2024-05-08 11:15:43 -0400 (Wed, 08 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino6Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  


CHECK results for smoothclust on palomino6

To the developers/maintainers of the smoothclust package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/smoothclust.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: smoothclust
Version: 1.1.1
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:smoothclust.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings smoothclust_1.1.1.tar.gz
StartedAt: 2024-07-16 04:26:12 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 04:37:44 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 691.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: smoothclust.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:smoothclust.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings smoothclust_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/smoothclust.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'smoothclust/DESCRIPTION' ... OK
* this is package 'smoothclust' version '1.1.1'
* 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 'smoothclust' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
smoothness_metric 134.56  33.70  170.81
smoothclust        31.44   7.05   41.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ── Error ('test_non_SPE_inputs.R:8:1'): (code run outside of `test_that()`) ────
  <Rcpp::exception/C++Error/error/condition>
  Error: The values in cols must be between 1 and ncol: 0
  Backtrace:
      ▆
   1. └─smoothclust::smoothclust(input, spatial_coords = spatial_coords) at test_non_SPE_inputs.R:8:1
   2.   ├─MatrixGenerics::rowMeans2(vals, cols = neigh[[i]])
   3.   └─sparseMatrixStats::rowMeans2(vals, cols = neigh[[i]])
   4.     └─sparseMatrixStats (local) .local(x, rows, cols, na.rm, ..., useNames)
   5.       ├─sparseMatrixStats:::set_result_names_t(...)
   6.       └─sparseMatrixStats:::dgCMatrix_rowMeans2_int_col_select(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/smoothclust.Rcheck/00check.log'
for details.


Installation output

smoothclust.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL smoothclust
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'smoothclust' ...
** 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 (smoothclust)

Tests output

smoothclust.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 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(smoothclust)
> 
> test_check("smoothclust")

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List of 2
 $ n_discordant   : num [1:3639] 0 0 0 0 0 2 0 3 0 2 ...
 $ mean_discordant: num 0.554
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_non_SPE_inputs.R:8:1'): (code run outside of `test_that()`) ────
<Rcpp::exception/C++Error/error/condition>
Error: The values in cols must be between 1 and ncol: 0
Backtrace:
    ▆
 1. └─smoothclust::smoothclust(input, spatial_coords = spatial_coords) at test_non_SPE_inputs.R:8:1
 2.   ├─MatrixGenerics::rowMeans2(vals, cols = neigh[[i]])
 3.   └─sparseMatrixStats::rowMeans2(vals, cols = neigh[[i]])
 4.     └─sparseMatrixStats (local) .local(x, rows, cols, na.rm, ..., useNames)
 5.       ├─sparseMatrixStats:::set_result_names_t(...)
 6.       └─sparseMatrixStats:::dgCMatrix_rowMeans2_int_col_select(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted

Example timings

smoothclust.Rcheck/smoothclust-Ex.timings

nameusersystemelapsed
smoothclust31.44 7.0541.79
smoothness_metric134.56 33.70170.81