Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-06 12:05 -0400 (Mon, 06 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 1368/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsBackendRawFileReader 1.15.1 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | 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: 1.15.1 |
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_1.15.1.tar.gz |
StartedAt: 2025-10-05 23:00:55 -0400 (Sun, 05 Oct 2025) |
EndedAt: 2025-10-05 23:04:52 -0400 (Sun, 05 Oct 2025) |
EllapsedTime: 237.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MsBackendRawFileReader.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MsBackendRawFileReader.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MsBackendRawFileReader’ version ‘1.15.1’ * 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 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 29.574 11.604 18.389 MsBackendRawFileReader 7.939 3.266 11.692 MsBackendRawFileReader-class 3.679 1.152 5.227 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: OK
MsBackendRawFileReader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘MsBackendRawFileReader’ ... ** this is package ‘MsBackendRawFileReader’ version ‘1.15.1’ ** 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
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 > 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 ⠸ | 4 | peaks_variables ✔ | 4 | peaks_variables [5.0s] ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠹ | 13 | spectra_subsetting ⠼ | 25 | spectra_subsetting ⠦ | 37 | spectra_subsetting ⠇ | 49 | spectra_subsetting ⠇ | 59 | spectra_subsetting ⠏ | 70 | spectra_subsetting ⠙ | 82 | spectra_subsetting ⠸ | 94 | spectra_subsetting ⠹ | 103 | spectra_subsetting ⠼ | 115 | spectra_subsetting ⠦ | 127 | spectra_subsetting ⠧ | 138 | spectra_subsetting ⠧ | 148 | spectra_subsetting ⠏ | 160 | spectra_subsetting ⠙ | 172 | spectra_subsetting ⠸ | 184 | spectra_subsetting ⠴ | 196 | spectra_subsetting ⠴ | 206 | spectra_subsetting ⠴ | 216 | spectra_subsetting ⠦ | 227 | spectra_subsetting ⠇ | 239 | spectra_subsetting ⠏ | 250 | spectra_subsetting ⠙ | 262 | spectra_subsetting ⠸ | 274 | spectra_subsetting ⠼ | 285 | spectra_subsetting ⠼ | 295 | spectra_subsetting ⠦ | 307 | spectra_subsetting ⠇ | 319 | spectra_subsetting ⠋ | 331 | spectra_subsetting ⠹ | 343 | spectra_subsetting ⠼ | 355 | spectra_subsetting ⠦ | 367 | spectra_subsetting ⠇ | 379 | spectra_subsetting ⠋ | 391 | spectra_subsetting ⠹ | 403 | spectra_subsetting ⠼ | 415 | spectra_subsetting ⠦ | 427 | spectra_subsetting ⠇ | 439 | spectra_subsetting ⠋ | 451 | spectra_subsetting ⠹ | 463 | spectra_subsetting ⠼ | 475 | spectra_subsetting ⠦ | 487 | spectra_subsetting ⠇ | 499 | spectra_subsetting ⠋ | 511 | spectra_subsetting ⠹ | 523 | spectra_subsetting ⠼ | 535 | spectra_subsetting ⠼ | 545 | spectra_subsetting ⠦ | 557 | spectra_subsetting ⠧ | 568 | spectra_subsetting ⠏ | 580 | spectra_subsetting ⠙ | 592 | spectra_subsetting ⠹ | 603 | spectra_subsetting ⠏ | 610 | spectra_subsetting ⠙ | 622 | spectra_subsetting ⠸ | 634 | spectra_subsetting ⠴ | 646 | spectra_subsetting ⠼ | 655 | spectra_subsetting ⠦ | 667 | spectra_subsetting ⠇ | 679 | spectra_subsetting ⠇ | 689 | spectra_subsetting ⠏ | 700 | spectra_subsetting ⠙ | 712 | spectra_subsetting ⠙ | 722 | spectra_subsetting ⠹ | 733 | spectra_subsetting ⠼ | 745 | spectra_subsetting ⠦ | 757 | spectra_subsetting ⠴ | 766 | spectra_subsetting ⠧ | 778 | spectra_subsetting ⠏ | 790 | spectra_subsetting ⠙ | 802 | spectra_subsetting ⠼ | 815 | spectra_subsetting ⠦ | 827 | spectra_subsetting ⠧ | 838 | spectra_subsetting ⠋ | 851 | spectra_subsetting ⠙ | 862 | spectra_subsetting ⠙ | 872 | spectra_subsetting ⠸ | 884 | spectra_subsetting ⠴ | 896 | spectra_subsetting ⠦ | 907 | spectra_subsetting ⠇ | 919 | spectra_subsetting ⠋ | 931 | spectra_subsetting ⠋ | 941 | spectra_subsetting ⠙ | 952 | spectra_subsetting ⠸ | 964 | spectra_subsetting ⠴ | 976 | spectra_subsetting ⠧ | 988 | spectra_subsetting ⠏ | 1000 | spectra_subsetting ⠙ | 1012 | spectra_subsetting ⠸ | 1024 | spectra_subsetting ⠴ | 1036 | spectra_subsetting ⠧ | 1048 | spectra_subsetting ⠇ | 1059 | spectra_subsetting ⠏ | 1070 | spectra_subsetting ⠋ | 1081 | spectra_subsetting ⠋ | 1091 | spectra_subsetting ⠹ | 1103 | spectra_subsetting ⠸ | 1114 | spectra_subsetting ⠼ | 1125 | spectra_subsetting ⠴ | 1136 | spectra_subsetting ⠦ | 1147 | spectra_subsetting ⠇ | 1159 | spectra_subsetting ⠋ | 1171 | spectra_subsetting ⠹ | 1183 | spectra_subsetting ⠼ | 1195 | spectra_subsetting ⠦ | 1207 | spectra_subsetting ⠇ | 1219 | spectra_subsetting ⠋ | 1231 | spectra_subsetting ⠹ | 1243 | spectra_subsetting ⠼ | 1255 | spectra_subsetting ⠦ | 1267 | spectra_subsetting ⠇ | 1279 | spectra_subsetting ⠋ | 1291 | spectra_subsetting ⠹ | 1303 | spectra_subsetting ⠋ | 1311 | spectra_subsetting ⠸ | 1324 | spectra_subsetting ⠴ | 1336 | spectra_subsetting ⠧ | 1348 | spectra_subsetting ⠋ | 1361 | spectra_subsetting ⠙ | 1372 | spectra_subsetting ⠹ | 1383 | spectra_subsetting ⠸ | 1394 | spectra_subsetting ⠼ | 1405 | spectra_subsetting ⠦ | 1417 | spectra_subsetting ⠇ | 1429 | spectra_subsetting ⠋ | 1441 | spectra_subsetting ⠹ | 1453 | spectra_subsetting ⠼ | 1465 | spectra_subsetting ⠦ | 1477 | spectra_subsetting ⠦ | 1487 | spectra_subsetting ⠧ | 1498 | spectra_subsetting ⠏ | 1510 | spectra_subsetting ⠋ | 1521 | spectra_subsetting ⠧ | 1528 | spectra_subsetting ⠏ | 1540 | 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spectra_subsetting ⠸ | 2334 | spectra_subsetting ✔ | 2342 | spectra_subsetting [51.0s] ⠏ | 0 | spectra_variables ⠙ | 12 | spectra_variables ⠸ | 14 | spectra_variables ⠴ | 16 | spectra_variables ⠦ | 27 | spectra_variables ⠇ | 29 | spectra_variables ⠋ | 31 | spectra_variables ⠋ | 41 | spectra_variables ⠹ | 43 | spectra_variables ⠸ | 54 | spectra_variables ✔ | 1 62 | spectra_variables [20.0s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 76.0 s ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_variables.R:262:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2408 ] > > proc.time() user system elapsed 97.762 13.935 115.493
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
name | user | system | elapsed | |
MsBackendRawFileReader-class | 3.679 | 1.152 | 5.227 | |
MsBackendRawFileReader | 7.939 | 3.266 | 11.692 | |
hidden_aliases | 2.602 | 1.110 | 3.918 | |
ioBenchmark | 29.574 | 11.604 | 18.389 | |