Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:39:36 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 1390/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
muscat 1.18.0 (landing page) Helena L. Crowell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the muscat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/muscat.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: muscat |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:muscat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings muscat_1.18.0.tar.gz |
StartedAt: 2024-05-03 23:33:30 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 23:41:25 -0400 (Fri, 03 May 2024) |
EllapsedTime: 474.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: muscat.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:muscat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings muscat_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/muscat.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘muscat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘muscat’ version ‘1.18.0’ * 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 ‘muscat’ 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 ... NOTE pbHeatmap: no visible binding for global variable ‘gene’ pbHeatmap: no visible binding for global variable ‘p_adj.loc’ pbHeatmap: no visible binding for global variable ‘logFC’ Undefined global functions or variables: gene logFC p_adj.loc * 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 simData 9.260 0.290 9.614 mmDS 8.991 0.150 9.227 pbHeatmap 8.264 0.137 8.471 prepSim 5.595 0.181 5.819 * 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: 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─muscat::pbDS(pbs, verbose = FALSE, min_cells = 0, filter = "none") 10. ├─BiocParallel::bplapply(...) 11. └─BiocParallel::bplapply(...) 12. └─BiocParallel:::.bpinit(...) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 552 ] 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/muscat.Rcheck/00check.log’ for details.
muscat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL muscat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘muscat’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning in checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.10 Current TMB version is 1.9.11 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.10 Current TMB version is 1.9.11 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** testing if installed package can be loaded from final location Warning in checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.10 Current TMB version is 1.9.11 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** testing if installed package keeps a record of temporary installation path * DONE (muscat)
muscat.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(muscat) Warning message: In checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.10 Current TMB version is 1.9.11 Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information) > > test_check("muscat") [ FAIL 1 | WARN 1 | SKIP 0 | PASS 552 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pbDS.R:99:3'): pbDS() filtering ──────────────────────────────── <bplist_error/bperror/error/condition> Error: BiocParallel errors 1 remote errors, element index: 5 0 unevaluated and other errors first remote error: Error in glmFit.default(sely, design, offset = seloffset, dispersion = 0.05, : Design matrix not of full rank. The following coefficients not estimable: g2 Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-pbDS.R:99:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─muscat::pbDS(pbs, verbose = FALSE, min_cells = 0, filter = "none") 10. ├─BiocParallel::bplapply(...) 11. └─BiocParallel::bplapply(...) 12. └─BiocParallel:::.bpinit(...) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 552 ] Error: Test failures Execution halted
muscat.Rcheck/muscat-Ex.timings
name | user | system | elapsed | |
aggregateData | 2.613 | 0.146 | 2.785 | |
calcExprFreqs | 0.652 | 0.036 | 0.694 | |
data | 0 | 0 | 0 | |
mmDS | 8.991 | 0.150 | 9.227 | |
pbDS | 2.702 | 0.051 | 2.774 | |
pbFlatten | 1.142 | 0.036 | 1.186 | |
pbHeatmap | 8.264 | 0.137 | 8.471 | |
pbMDS | 1.022 | 0.026 | 1.059 | |
prepSCE | 0.920 | 0.045 | 0.978 | |
prepSim | 5.595 | 0.181 | 5.819 | |
resDS | 3.441 | 0.069 | 3.536 | |
simData | 9.260 | 0.290 | 9.614 | |