| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (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 1956/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| smoothclust 1.1.1 (landing page) Lukas M. Weber
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
|
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. |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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)
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
smoothclust.Rcheck/smoothclust-Ex.timings
| name | user | system | elapsed | |
| smoothclust | 31.44 | 7.05 | 41.79 | |
| smoothness_metric | 134.56 | 33.70 | 170.81 | |