Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:39 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1680/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rawDiag 1.0.0 (landing page) Christian Panse
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the rawDiag package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rawDiag.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: rawDiag |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rawDiag.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rawDiag_1.0.0.tar.gz |
StartedAt: 2024-06-24 02:53:37 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 02:55:50 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 133.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: rawDiag.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rawDiag.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rawDiag_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/rawDiag.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘rawDiag/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rawDiag’ version ‘1.0.0’ * 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 ‘rawDiag’ 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 ... 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 * 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: 38. ├─base::withCallingHandlers(...) 39. ├─base::withVisible(.func()) 40. └─shiny (local) .func() 41. ├─shiny::..stacktraceon..(`<reactive>`(...)) 42. └─rawDiag (local) `<reactive>`(...) 43. ├─base::Reduce(...) 44. ├─BiocParallel::bplapply(...) 45. └─BiocParallel::bplapply(...) 46. ├─BiocParallel::bplapply(...) 47. └─BiocParallel::bplapply(...) 48. └─BiocParallel:::.bpinit(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] 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 See ‘/home/biocbuild/bbs-3.19-bioc/meat/rawDiag.Rcheck/00check.log’ for details.
rawDiag.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL rawDiag ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘rawDiag’ ... ** 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 (rawDiag)
rawDiag.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24) -- "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. > #R > > library(testthat) > > suppressPackageStartupMessages(library(rawDiag)) > > test_check("rawDiag") Cannot open assembly '/home/biocbuild/.cache/R/rawrr/rawrrassembly/rawrr.exe': File does not contain a valid CIL image. [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-rawDiag.R:7:1'): (code run outside of `test_that()`) ─────────── Error in `.checkRawFileReaderDLLs(FUN)`: 'ThermoFisher.CommonCore.*.dll' files are not available on the system. Run 'rawrr::installRawFileReaderDLLs()' or setenv MONO_PATH to the location where the assemblies are located. For more information, type '?ThermoFisher'. Backtrace: ▆ 1. └─rawDiag::readRaw(rawrr::sampleFilePath()) at test-rawDiag.R:7:1 2. └─rawrr::readIndex(rawfile) 3. └─rawrr:::.isAssemblyWorking() 4. └─rawrr:::.checkRawFileReaderDLLs(FUN) ── Error ('test-rawDiagServerModule.R:10:3'): (code run outside of `test_that()`) ── <bplist_error/bperror/error/condition> Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in if (rvs != "No RAW file specified!") {: argument is of length zero Backtrace: ▆ 1. ├─shiny::testServer(...) at test-rawDiagServerModule.R:5:1 2. │ ├─shiny:::withMockContext(...) 3. │ │ ├─shiny::isolate(...) 4. │ │ │ ├─shiny::..stacktraceoff..(...) 5. │ │ │ └─ctx$run(...) 6. │ │ │ ├─promises::with_promise_domain(...) 7. │ │ │ │ └─domain$wrapSync(expr) 8. │ │ │ ├─shiny::withReactiveDomain(...) 9. │ │ │ │ └─promises::with_promise_domain(...) 10. │ │ │ │ └─domain$wrapSync(expr) 11. │ │ │ │ └─base::force(expr) 12. │ │ │ └─env$runWith(self, func) 13. │ │ │ └─shiny (local) contextFunc() 14. │ │ │ └─shiny::..stacktraceon..(expr) 15. │ │ ├─shiny::withReactiveDomain(...) 16. │ │ │ └─promises::with_promise_domain(...) 17. │ │ │ └─domain$wrapSync(expr) 18. │ │ │ └─base::force(expr) 19. │ │ └─withr::with_options(...) 20. │ │ └─base::force(code) 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env()) 22. ├─testthat::expect_true(is.data.frame(data())) at test-rawDiagServerModule.R:10:3 23. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 24. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 25. ├─base::is.data.frame(data()) 26. └─shiny (local) data() 27. ├─shiny::..stacktraceoff..(self$.updateValue()) 28. └─self$.updateValue() 29. └─ctx$run(...) 30. ├─promises::with_promise_domain(...) 31. │ └─domain$wrapSync(expr) 32. ├─shiny::withReactiveDomain(...) 33. │ └─promises::with_promise_domain(...) 34. │ └─domain$wrapSync(expr) 35. │ └─base::force(expr) 36. └─env$runWith(self, func) 37. └─shiny (local) contextFunc() 38. ├─base::withCallingHandlers(...) 39. ├─base::withVisible(.func()) 40. └─shiny (local) .func() 41. ├─shiny::..stacktraceon..(`<reactive>`(...)) 42. └─rawDiag (local) `<reactive>`(...) 43. ├─base::Reduce(...) 44. ├─BiocParallel::bplapply(...) 45. └─BiocParallel::bplapply(...) 46. ├─BiocParallel::bplapply(...) 47. └─BiocParallel::bplapply(...) 48. └─BiocParallel:::.bpinit(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted
rawDiag.Rcheck/rawDiag-Ex.timings
name | user | system | elapsed | |
buildRawDiagShinyApp | 0.000 | 0.000 | 0.001 | |
dot-fillNAgaps | 0.000 | 0.000 | 0.001 | |
is.rawDiag | 2.308 | 0.664 | 2.638 | |
plotChargeState | 3.741 | 0.943 | 4.362 | |
plotCycleLoad | 2.972 | 0.603 | 3.284 | |
plotCycleTime | 2.346 | 0.495 | 2.568 | |
plotInjectionTime | 2.528 | 0.424 | 2.708 | |
plotLockMassCorrection | 2.425 | 0.588 | 2.742 | |
plotMassDistribution | 2.432 | 0.380 | 2.551 | |
plotMzDistribution | 2.350 | 0.570 | 2.654 | |
plotPrecursorHeatmap | 2.623 | 0.626 | 2.977 | |
plotScanTime | 2.517 | 0.474 | 2.738 | |
plotTicBasepeak | 2.493 | 0.475 | 2.706 | |
rawDiagServer | 0.000 | 0.000 | 0.001 | |
rawDiagUI | 0.000 | 0.001 | 0.000 | |
readRaw | 2.162 | 0.444 | 2.369 | |