Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 1352/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsBackendRawFileReader 1.15.1 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MsBackendRawFileReader_1.15.1.tar.gz |
StartedAt: 2025-08-09 00:31:55 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 00:36:41 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 286.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MsBackendRawFileReader.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MsBackendRawFileReader_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MsBackendRawFileReader.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 30.863 6.117 11.487 MsBackendRawFileReader 6.411 2.142 9.077 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
MsBackendRawFileReader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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("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 [3.8s] ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠴ | 16 | spectra_subsetting ⠇ | 29 | spectra_subsetting ⠹ | 43 | spectra_subsetting ⠧ | 58 | spectra_subsetting ⠏ | 70 | spectra_subsetting ⠼ | 85 | spectra_subsetting ⠏ | 100 | spectra_subsetting ⠼ | 115 | spectra_subsetting ⠏ | 130 | spectra_subsetting ⠼ | 145 | spectra_subsetting ⠏ | 160 | spectra_subsetting ⠼ | 175 | spectra_subsetting ⠧ | 188 | spectra_subsetting ⠙ | 202 | spectra_subsetting ⠼ | 215 | spectra_subsetting ⠇ | 229 | spectra_subsetting ⠸ | 244 | spectra_subsetting ⠇ | 259 | spectra_subsetting ⠸ | 274 | spectra_subsetting ⠇ | 289 | spectra_subsetting ⠸ | 304 | spectra_subsetting ⠇ | 319 | spectra_subsetting ⠸ | 334 | spectra_subsetting ⠇ | 349 | spectra_subsetting ⠸ | 364 | spectra_subsetting ⠏ | 380 | spectra_subsetting ⠼ | 395 | spectra_subsetting ⠇ | 409 | spectra_subsetting ⠸ | 424 | spectra_subsetting ⠇ | 439 | spectra_subsetting ⠸ | 454 | spectra_subsetting ⠇ | 469 | spectra_subsetting ⠸ | 484 | 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spectra_subsetting ⠹ | 973 | spectra_subsetting ⠴ | 986 | spectra_subsetting ⠏ | 1000 | spectra_subsetting ⠼ | 1015 | spectra_subsetting ⠏ | 1030 | spectra_subsetting ⠼ | 1045 | spectra_subsetting ⠏ | 1060 | spectra_subsetting ⠼ | 1075 | spectra_subsetting ⠏ | 1090 | spectra_subsetting ⠼ | 1105 | spectra_subsetting ⠏ | 1120 | spectra_subsetting ⠼ | 1135 | spectra_subsetting ⠏ | 1150 | spectra_subsetting ⠼ | 1165 | spectra_subsetting ⠏ | 1180 | spectra_subsetting ⠼ | 1195 | spectra_subsetting ⠦ | 1207 | spectra_subsetting ⠙ | 1222 | spectra_subsetting ⠦ | 1237 | spectra_subsetting ⠙ | 1252 | spectra_subsetting ⠦ | 1267 | spectra_subsetting ⠏ | 1280 | spectra_subsetting ⠸ | 1294 | spectra_subsetting ⠴ | 1306 | spectra_subsetting ⠦ | 1317 | spectra_subsetting ⠏ | 1330 | spectra_subsetting ⠼ | 1345 | spectra_subsetting ⠏ | 1360 | spectra_subsetting ⠼ | 1375 | spectra_subsetting ⠏ | 1390 | spectra_subsetting ⠼ | 1405 | spectra_subsetting ⠏ | 1420 | spectra_subsetting ⠼ | 1435 | 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spectra_subsetting ⠹ | 2283 | spectra_subsetting ⠴ | 2286 | spectra_subsetting ⠇ | 2289 | spectra_subsetting ⠙ | 2292 | spectra_subsetting ⠼ | 2295 | spectra_subsetting ⠧ | 2298 | spectra_subsetting ⠙ | 2302 | spectra_subsetting ⠴ | 2306 | spectra_subsetting ⠸ | 2314 | spectra_subsetting ⠙ | 2322 | spectra_subsetting ⠋ | 2331 | spectra_subsetting ⠸ | 2334 | spectra_subsetting ✔ | 2342 | spectra_subsetting [42.7s] ⠏ | 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 62 | spectra_variables ✔ | 1 62 | spectra_variables [14.2s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 60.8 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 82.390 7.974 92.929
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
name | user | system | elapsed | |
MsBackendRawFileReader-class | 3.058 | 0.770 | 4.037 | |
MsBackendRawFileReader | 6.411 | 2.142 | 9.077 | |
hidden_aliases | 2.131 | 0.723 | 3.032 | |
ioBenchmark | 30.863 | 6.117 | 11.487 | |