Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 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" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 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 1343/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsBackendRawFileReader 1.10.0 (landing page) Christian Panse
| 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 | OK | 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: 1.10.0 |
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_1.10.0.tar.gz |
StartedAt: 2024-06-05 21:46:19 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 21:50:30 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 250.3 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MsBackendRawFileReader.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.10.0’ * 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 ‘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 ... NOTE filterScan,MsBackendRawFileReader : <anonymous>: no visible global function definition for ‘scanIndex’ peaksData,MsBackendRawFileReader: no visible global function definition for ‘scanIndex’ Undefined global functions or variables: scanIndex * 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 51.510 13.169 25.446 MsBackendRawFileReader 6.653 2.732 10.183 MsBackendRawFileReader-class 4.237 1.366 6.166 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-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
R version 4.4.0 (2024-04-24) -- "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("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 ⠸ | 4 | peaks_variables ✔ | 4 | peaks_variables [6.2s] ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠏ | 10 | spectra_subsetting ⠙ | 22 | spectra_subsetting ⠙ | 32 | spectra_subsetting ⠹ | 43 | spectra_subsetting ⠼ | 55 | spectra_subsetting ⠼ | 65 | spectra_subsetting ⠋ | 71 | spectra_subsetting ⠏ | 80 | spectra_subsetting ⠋ | 91 | spectra_subsetting ⠋ | 101 | spectra_subsetting ⠇ | 109 | spectra_subsetting ⠋ | 121 | spectra_subsetting ⠹ | 133 | spectra_subsetting ⠙ | 142 | spectra_subsetting ⠙ | 152 | spectra_subsetting ⠹ | 163 | spectra_subsetting ⠹ | 173 | spectra_subsetting ⠋ | 181 | spectra_subsetting ⠋ | 191 | spectra_subsetting ⠙ | 202 | spectra_subsetting ⠋ | 211 | spectra_subsetting ⠏ | 220 | spectra_subsetting ⠏ | 230 | spectra_subsetting ⠋ | 241 | spectra_subsetting ⠏ | 250 | spectra_subsetting ⠏ | 260 | spectra_subsetting ⠋ | 271 | spectra_subsetting ⠋ | 281 | spectra_subsetting ⠇ | 289 | spectra_subsetting ⠧ | 298 | spectra_subsetting ⠏ | 310 | spectra_subsetting ⠏ | 320 | spectra_subsetting ⠇ | 329 | spectra_subsetting ⠏ | 340 | spectra_subsetting ⠋ | 351 | spectra_subsetting ⠧ | 358 | spectra_subsetting ⠧ | 368 | spectra_subsetting ⠇ | 379 | spectra_subsetting ⠇ | 389 | spectra_subsetting ⠦ | 397 | spectra_subsetting ⠴ | 406 | spectra_subsetting ⠴ | 416 | spectra_subsetting ⠦ | 427 | spectra_subsetting ⠴ | 436 | spectra_subsetting ⠧ | 448 | spectra_subsetting ⠧ | 458 | spectra_subsetting ⠴ | 466 | spectra_subsetting ⠴ | 476 | spectra_subsetting ⠧ | 488 | spectra_subsetting ⠇ | 499 | spectra_subsetting ⠧ | 508 | spectra_subsetting ⠏ | 520 | spectra_subsetting ⠙ | 532 | spectra_subsetting ⠋ | 541 | spectra_subsetting ⠏ | 550 | spectra_subsetting ⠙ | 562 | spectra_subsetting ⠋ | 571 | spectra_subsetting ⠹ | 583 | spectra_subsetting ⠼ | 595 | spectra_subsetting ⠦ | 607 | spectra_subsetting ⠴ | 616 | spectra_subsetting ⠧ | 628 | spectra_subsetting ⠸ | 634 | spectra_subsetting ⠹ | 643 | spectra_subsetting ⠹ | 653 | spectra_subsetting ⠸ | 664 | spectra_subsetting ⠴ | 676 | spectra_subsetting ⠼ | 685 | spectra_subsetting ⠦ | 697 | 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spectra_variables ⠴ | 16 | spectra_variables ⠼ | 35 | spectra_variables ⠹ | 43 | spectra_variables ⠸ | 54 | spectra_variables ✔ | 1 62 | spectra_variables [12.5s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 73.2 s ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_variables.R:262:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2383 ] > > proc.time() user system elapsed 100.191 14.584 121.764
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
name | user | system | elapsed | |
MsBackendRawFileReader-class | 4.237 | 1.366 | 6.166 | |
MsBackendRawFileReader | 6.653 | 2.732 | 10.183 | |
hidden_aliases | 0.047 | 0.025 | 4.704 | |
ioBenchmark | 51.510 | 13.169 | 25.446 | |