Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-23 11:41 -0400 (Tue, 23 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" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 1311/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsBackendRawFileReader 1.11.3 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | 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 | ERROR | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the MsBackendRawFileReader package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendRawFileReader.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: MsBackendRawFileReader |
Version: 1.11.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendRawFileReader_1.11.3.tar.gz |
StartedAt: 2024-07-22 22:44:49 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 22:49:27 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 278.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MsBackendRawFileReader.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendRawFileReader_1.11.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendRawFileReader.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘MsBackendRawFileReader/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MsBackendRawFileReader’ version ‘1.11.3’ * 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 ‘MsBackendRawFileReader’ 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 whether startup messages can be suppressed ... 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 ioBenchmark 50.281 13.292 20.762 MsBackendRawFileReader 10.185 4.411 15.935 MsBackendRawFileReader-class 4.384 1.556 6.729 hidden_aliases 3.305 1.461 5.314 * 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: ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_variables.R:262:1' ── Failed tests ──────────────────────────────────────────────────────────────── Failure ('test_peaks_variables.R:16:5'): peaksData columns and peaksVariables match colnames(res[[1L]]) not equal to peaksVariables(be). Lengths differ: 5 is not 2 Failure ('test_spectra_variables.R:205:5'): peaksData colnames(m) not equal to c("mz", "intensity"). Lengths differ: 5 is not 2 [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2381 ] 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 See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendRawFileReader.Rcheck/00check.log’ for details.
MsBackendRawFileReader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MsBackendRawFileReader’ ... ** 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 (MsBackendRawFileReader)
MsBackendRawFileReader.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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("MsBackendRawFileReader") Loading required package: Spectra Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: BiocParallel Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth > library("Spectra") > > > sample_raw_file <- file.path(system.file(package = "rawrr"), + 'extdata', 'sample.raw') > > sample_mzXML_file <- file.path(path.package(package = 'MsBackendRawFileReader'), + 'extdata', 'sample.mzXML') > > > sample_raw <- backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(), files = sample_raw_file) > > > #sample_mzr <- backendInitialize(MsBackendMzR(), files = sample_mzXML_file) > > > mgf_file <- file.path(system.file(package = "MsBackendRawFileReader"), + 'extdata', '3159619b11ed_4590_9594.mgf') > > > rv <- lapply(1:2, function(x){ + file.copy(from = sample_raw_file, to = tempfile(fileext='.raw'))}) > > > register(SnowParam(workers = 1, type = "SOCK") , default = TRUE); > sample_raw_2 <- backendInitialize(MsBackendRawFileReader(), + files = file.path(tempdir(), + list.files(path = tempdir(), pattern = 'raw$'))) > > > test_check("MsBackendRawFileReader") [ FAIL 0 | WARN 1 | SKIP 2 | PASS 21 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • isFALSE(file.exists(sample_mzXML_file)) is TRUE (1): 'test_MsBackendMzR_MsBackendRawFileReader.R:1:1' • isFALSE(require(MsBackendRawMgf)) is TRUE (1): 'test_top_n_mgf.R:1:1' [ FAIL 0 | WARN 1 | SKIP 2 | PASS 21 ] > > > be <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(), + files = c(sample_raw_file)) > > ## Run the MsBackend spectra variable test suite > test_suite <- system.file("test_backends", "test_MsBackend", + package = "Spectra") > > #res <- test_file(paste0(test_suite, "/test_spectra_variables.R"), > # reporter = check_reporter(), stop_on_failure = TRUE) > > > ## Run the whole suite. > res <- test_dir(test_suite, stop_on_failure = TRUE) ✔ | F W S OK | Context ⠏ | 0 | peaks_variables ⠙ | 2 | peaks_variables ⠸ | 1 3 | peaks_variables ✖ | 1 3 | peaks_variables [5.9s] ──────────────────────────────────────────────────────────────────────────────── Failure ('test_peaks_variables.R:16:5'): peaksData columns and peaksVariables match colnames(res[[1L]]) not equal to peaksVariables(be). Lengths differ: 5 is not 2 ──────────────────────────────────────────────────────────────────────────────── ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠹ | 13 | spectra_subsetting ⠹ | 23 | spectra_subsetting ⠸ | 34 | spectra_subsetting ⠴ | 46 | spectra_subsetting ⠧ | 58 | spectra_subsetting ⠇ | 69 | spectra_subsetting ⠇ | 79 | spectra_subsetting ⠋ | 91 | spectra_subsetting ⠹ | 103 | spectra_subsetting ⠼ | 115 | spectra_subsetting ⠼ | 125 | spectra_subsetting ⠴ | 136 | spectra_subsetting ⠴ | 146 | spectra_subsetting ⠦ | 157 | spectra_subsetting ⠴ | 166 | spectra_subsetting ⠦ | 177 | spectra_subsetting ⠴ | 186 | spectra_subsetting ⠴ | 196 | spectra_subsetting ⠧ | 208 | spectra_subsetting ⠸ | 214 | spectra_subsetting ⠸ | 224 | spectra_subsetting ⠼ | 235 | spectra_subsetting ⠦ | 247 | spectra_subsetting ⠦ | 257 | spectra_subsetting ⠧ | 268 | spectra_subsetting ⠧ | 278 | spectra_subsetting ⠴ | 286 | spectra_subsetting ⠧ | 298 | spectra_subsetting ⠏ | 310 | spectra_subsetting ⠙ | 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spectra_subsetting ⠹ | 2263 | spectra_subsetting ⠼ | 2265 | spectra_subsetting ⠦ | 2267 | spectra_subsetting ⠇ | 2269 | spectra_subsetting ⠋ | 2271 | spectra_subsetting ⠹ | 2273 | spectra_subsetting ⠼ | 2275 | spectra_subsetting ⠦ | 2277 | spectra_subsetting ⠇ | 2279 | spectra_subsetting ⠋ | 2281 | spectra_subsetting ⠹ | 2283 | spectra_subsetting ⠼ | 2285 | spectra_subsetting ⠦ | 2287 | spectra_subsetting ⠇ | 2289 | spectra_subsetting ⠋ | 2291 | spectra_subsetting ⠹ | 2293 | spectra_subsetting ⠼ | 2295 | spectra_subsetting ⠦ | 2297 | spectra_subsetting ⠇ | 2299 | spectra_subsetting ⠹ | 2303 | spectra_subsetting ⠇ | 2309 | spectra_subsetting ⠸ | 2314 | spectra_subsetting ⠦ | 2317 | spectra_subsetting ✔ | 2317 | spectra_subsetting [59.6s] ⠏ | 0 | spectra_variables ⠙ | 12 | spectra_variables ⠸ | 14 | spectra_variables ⠴ | 16 | spectra_variables ⠦ | 27 | spectra_variables ⠇ | 29 | spectra_variables ⠋ | 31 | spectra_variables ⠹ | 43 | spectra_variables ⠸ | 1 53 | spectra_variables ✖ | 1 1 61 | spectra_variables [22.3s] ──────────────────────────────────────────────────────────────────────────────── Failure ('test_spectra_variables.R:205:5'): peaksData colnames(m) not equal to c("mz", "intensity"). Lengths differ: 5 is not 2 ──────────────────────────────────────────────────────────────────────────────── ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 87.9 s ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_variables.R:262:1' ── Failed tests ──────────────────────────────────────────────────────────────── Failure ('test_peaks_variables.R:16:5'): peaksData columns and peaksVariables match colnames(res[[1L]]) not equal to peaksVariables(be). Lengths differ: 5 is not 2 Failure ('test_spectra_variables.R:205:5'): peaksData colnames(m) not equal to c("mz", "intensity"). Lengths differ: 5 is not 2 [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2381 ] Error: Test failures Execution halted
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
name | user | system | elapsed | |
MsBackendRawFileReader-class | 4.384 | 1.556 | 6.729 | |
MsBackendRawFileReader | 10.185 | 4.411 | 15.935 | |
hidden_aliases | 3.305 | 1.461 | 5.314 | |
ioBenchmark | 50.281 | 13.292 | 20.762 | |