Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-22 11:36:28 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
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 1999/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpotClean 1.7.0 (landing page) Zijian Ni
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SpotClean package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpotClean.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: SpotClean |
Version: 1.7.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SpotClean.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SpotClean_1.7.0.tar.gz |
StartedAt: 2024-05-21 03:15:39 -0400 (Tue, 21 May 2024) |
EndedAt: 2024-05-21 03:29:43 -0400 (Tue, 21 May 2024) |
EllapsedTime: 844.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SpotClean.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SpotClean.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SpotClean_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SpotClean.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘SpotClean/DESCRIPTION’ ... OK * this is package ‘SpotClean’ version ‘1.7.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘SpotClean’ 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 loading without being on the library search path ... 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 ... NOTE checkRd: (-1) SpotClean.Rd:59: Lost braces; missing escapes or markup? 59 | Default: {c(5, 10, 15, 20, 25, 30)}} | ^ * 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 SpotClean 144.011 56.197 200.221 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-convert_to_seurat.R:36:5'): Consistent slide metadata ────────── Error in `factor(seurat_obj@images$slice1@coordinates$tissue)`: no slot of name "coordinates" for this object of class "VisiumV2" Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-convert_to_seurat.R:36:5 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::factor(seurat_obj@images$slice1@coordinates$tissue) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/SpotClean.Rcheck/00check.log’ for details.
SpotClean.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SpotClean ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘SpotClean’ ... ** using staged installation ** R ** data ** 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 (SpotClean)
SpotClean.Rcheck/tests/spelling.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.167 0.016 0.173
SpotClean.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(SpotClean) > > test_check("SpotClean") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-convert_to_seurat.R:36:5'): Consistent slide metadata ────────── Error in `factor(seurat_obj@images$slice1@coordinates$tissue)`: no slot of name "coordinates" for this object of class "VisiumV2" Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-convert_to_seurat.R:36:5 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::factor(seurat_obj@images$slice1@coordinates$tissue) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ] Error: Test failures Execution halted
SpotClean.Rcheck/SpotClean-Ex.timings
name | user | system | elapsed | |
ARCScore | 0.432 | 0.016 | 0.448 | |
ConvertToSeurat | 1.484 | 0.080 | 1.564 | |
CreateSlide | 0.352 | 0.008 | 0.359 | |
KeepHighGene | 1.224 | 0.060 | 1.283 | |
Read10x | 1.415 | 0.040 | 1.454 | |
SpotClean | 144.011 | 56.197 | 200.221 | |
VisualizeHeatmap | 0.655 | 0.032 | 0.686 | |
VisualizeLabel | 0.709 | 0.012 | 0.722 | |
VisualizeSlide | 0.482 | 0.020 | 0.502 | |
mbrain_raw | 0.208 | 0.008 | 0.216 | |