Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1333/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsBackendRawFileReader 1.12.0 (landing page) Christian Panse
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.12.0 |
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_1.12.0.tar.gz |
StartedAt: 2024-12-21 02:21:08 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 02:24:48 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 219.9 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendRawFileReader.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MsBackendRawFileReader’ version ‘1.12.0’ * 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 ... 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 41.555 9.929 19.565 hidden_aliases 5.910 2.367 4.212 MsBackendRawFileReader 5.615 2.283 12.002 MsBackendRawFileReader-class 4.036 1.241 5.618 * 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/4.4-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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, saveRDS, 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 > 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 [5.1s] ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠸ | 14 | spectra_subsetting ⠧ | 28 | spectra_subsetting ⠹ | 43 | spectra_subsetting ⠼ | 55 | spectra_subsetting ⠏ | 70 | spectra_subsetting ⠼ | 85 | spectra_subsetting ⠦ | 97 | spectra_subsetting ⠙ | 112 | spectra_subsetting ⠦ | 127 | spectra_subsetting ⠙ | 142 | spectra_subsetting ⠦ | 157 | spectra_subsetting ⠇ | 169 | spectra_subsetting ⠸ | 184 | spectra_subsetting ⠇ | 199 | spectra_subsetting ⠸ | 214 | spectra_subsetting ⠇ | 229 | spectra_subsetting ⠸ | 244 | spectra_subsetting ⠇ | 259 | spectra_subsetting ⠸ | 274 | spectra_subsetting ⠇ | 289 | spectra_subsetting ⠸ | 304 | spectra_subsetting ⠇ | 319 | spectra_subsetting ⠼ | 335 | spectra_subsetting ⠇ | 349 | spectra_subsetting ⠸ | 364 | spectra_subsetting ⠇ | 379 | spectra_subsetting ⠙ | 392 | spectra_subsetting ⠴ | 406 | spectra_subsetting ⠋ | 421 | spectra_subsetting ⠴ | 436 | spectra_subsetting ⠋ | 451 | spectra_subsetting ⠴ | 466 | spectra_subsetting ⠙ | 482 | spectra_subsetting ⠴ | 496 | spectra_subsetting ⠙ | 512 | spectra_subsetting ⠦ | 527 | spectra_subsetting ⠋ | 541 | spectra_subsetting ⠴ | 556 | spectra_subsetting ⠋ | 571 | spectra_subsetting ⠴ | 586 | spectra_subsetting ⠋ | 601 | spectra_subsetting ⠴ | 616 | spectra_subsetting ⠋ | 631 | spectra_subsetting ⠹ | 643 | spectra_subsetting ⠧ | 658 | spectra_subsetting ⠹ | 673 | spectra_subsetting ⠧ | 688 | spectra_subsetting ⠹ | 703 | spectra_subsetting ⠧ | 718 | spectra_subsetting ⠹ | 733 | spectra_subsetting ⠧ | 748 | spectra_subsetting ⠹ | 763 | spectra_subsetting ⠧ | 778 | spectra_subsetting ⠏ | 790 | spectra_subsetting ⠼ | 805 | spectra_subsetting ⠏ | 820 | spectra_subsetting ⠼ | 835 | spectra_subsetting ⠏ | 850 | spectra_subsetting ⠙ | 862 | spectra_subsetting ⠦ | 877 | spectra_subsetting ⠙ | 892 | spectra_subsetting ⠦ | 907 | spectra_subsetting ⠙ | 922 | spectra_subsetting ⠦ | 937 | spectra_subsetting ⠹ | 953 | spectra_subsetting ⠦ | 967 | spectra_subsetting ⠙ | 982 | spectra_subsetting ⠦ | 997 | spectra_subsetting ⠇ | 1009 | spectra_subsetting ⠸ | 1024 | spectra_subsetting ⠇ | 1039 | spectra_subsetting ⠸ | 1054 | spectra_subsetting ⠇ | 1069 | spectra_subsetting ⠙ | 1082 | spectra_subsetting ⠦ | 1097 | spectra_subsetting ⠋ | 1111 | spectra_subsetting ⠴ | 1126 | spectra_subsetting ⠋ | 1141 | spectra_subsetting ⠸ | 1154 | spectra_subsetting ⠏ | 1170 | spectra_subsetting ⠹ | 1183 | spectra_subsetting ⠧ | 1198 | spectra_subsetting ⠹ | 1213 | spectra_subsetting ⠧ | 1228 | spectra_subsetting ⠹ | 1243 | spectra_subsetting ⠧ | 1258 | spectra_subsetting ⠹ | 1273 | spectra_subsetting ⠧ | 1288 | spectra_subsetting ⠋ | 1301 | spectra_subsetting ⠴ | 1316 | spectra_subsetting ⠏ | 1330 | spectra_subsetting ⠼ | 1345 | spectra_subsetting ⠋ | 1361 | spectra_subsetting ⠼ | 1375 | spectra_subsetting ⠏ | 1390 | spectra_subsetting ⠸ | 1404 | spectra_subsetting ⠦ | 1417 | spectra_subsetting ⠙ | 1432 | spectra_subsetting ⠸ | 1444 | spectra_subsetting ⠏ | 1460 | spectra_subsetting ⠸ | 1474 | spectra_subsetting ⠏ | 1490 | spectra_subsetting ⠼ | 1505 | spectra_subsetting ⠇ | 1519 | spectra_subsetting ⠸ | 1534 | spectra_subsetting ⠴ | 1546 | spectra_subsetting ⠋ | 1561 | spectra_subsetting ⠴ | 1576 | spectra_subsetting ⠧ | 1588 | spectra_subsetting ⠸ | 1604 | spectra_subsetting ⠧ | 1618 | spectra_subsetting ⠹ | 1633 | spectra_subsetting ⠧ | 1648 | spectra_subsetting ⠏ | 1660 | spectra_subsetting ⠼ | 1675 | spectra_subsetting ⠏ | 1690 | spectra_subsetting ⠼ | 1705 | spectra_subsetting ⠏ | 1720 | spectra_subsetting ⠦ | 1727 | spectra_subsetting ⠇ | 1729 | spectra_subsetting ⠋ | 1731 | spectra_subsetting ⠹ | 1733 | spectra_subsetting ⠼ | 1735 | spectra_subsetting ⠧ | 1738 | spectra_subsetting ⠋ | 1741 | spectra_subsetting ⠹ | 1743 | spectra_subsetting ⠴ | 1746 | spectra_subsetting ⠧ | 1748 | spectra_subsetting ⠏ | 1750 | spectra_subsetting ⠙ | 1752 | spectra_subsetting ⠼ | 1755 | spectra_subsetting ⠦ | 1757 | spectra_subsetting ⠇ | 1759 | spectra_subsetting ⠙ | 1762 | spectra_subsetting ⠸ | 1764 | spectra_subsetting ⠴ | 1766 | spectra_subsetting ⠧ | 1768 | spectra_subsetting ⠋ | 1771 | 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spectra_subsetting ⠙ | 2112 | spectra_subsetting ⠼ | 2115 | spectra_subsetting ⠦ | 2117 | spectra_subsetting ⠇ | 2119 | spectra_subsetting ⠋ | 2121 | spectra_subsetting ⠹ | 2123 | spectra_subsetting ⠴ | 2126 | spectra_subsetting ⠧ | 2128 | spectra_subsetting ⠋ | 2131 | spectra_subsetting ⠹ | 2133 | spectra_subsetting ⠴ | 2136 | spectra_subsetting ⠇ | 2139 | spectra_subsetting ⠙ | 2142 | spectra_subsetting ⠼ | 2145 | spectra_subsetting ⠧ | 2148 | spectra_subsetting ⠋ | 2151 | spectra_subsetting ⠸ | 2154 | spectra_subsetting ⠦ | 2157 | spectra_subsetting ⠏ | 2160 | spectra_subsetting ⠙ | 2162 | spectra_subsetting ⠼ | 2165 | spectra_subsetting ⠦ | 2167 | spectra_subsetting ⠏ | 2170 | spectra_subsetting ⠙ | 2172 | spectra_subsetting ⠼ | 2175 | spectra_subsetting ⠧ | 2178 | spectra_subsetting ⠏ | 2180 | spectra_subsetting ⠙ | 2182 | spectra_subsetting ⠸ | 2184 | spectra_subsetting ⠦ | 2187 | spectra_subsetting ⠏ | 2190 | spectra_subsetting ⠹ | 2193 | spectra_subsetting ⠴ | 2196 | spectra_subsetting ⠇ | 2199 | spectra_subsetting ⠋ | 2201 | spectra_subsetting ⠹ | 2203 | spectra_subsetting ⠴ | 2206 | spectra_subsetting ⠇ | 2209 | spectra_subsetting ⠙ | 2212 | spectra_subsetting ⠼ | 2215 | spectra_subsetting ⠧ | 2218 | spectra_subsetting ⠋ | 2221 | spectra_subsetting ⠸ | 2224 | spectra_subsetting ⠦ | 2227 | spectra_subsetting ⠏ | 2230 | spectra_subsetting ⠹ | 2233 | spectra_subsetting ⠼ | 2235 | spectra_subsetting ⠧ | 2238 | spectra_subsetting ⠋ | 2241 | spectra_subsetting ⠸ | 2244 | spectra_subsetting ⠴ | 2246 | spectra_subsetting ⠧ | 2248 | spectra_subsetting ⠋ | 2251 | spectra_subsetting ⠸ | 2254 | spectra_subsetting ⠴ | 2256 | spectra_subsetting ⠇ | 2259 | spectra_subsetting ⠙ | 2262 | spectra_subsetting ⠸ | 2264 | spectra_subsetting ⠦ | 2267 | spectra_subsetting ⠇ | 2269 | spectra_subsetting ⠙ | 2272 | spectra_subsetting ⠼ | 2275 | spectra_subsetting ⠦ | 2277 | spectra_subsetting ⠏ | 2280 | spectra_subsetting ⠙ | 2282 | spectra_subsetting ⠼ | 2285 | spectra_subsetting ⠧ | 2288 | spectra_subsetting ⠋ | 2291 | spectra_subsetting ⠸ | 2294 | spectra_subsetting ⠦ | 2297 | spectra_subsetting ⠇ | 2299 | spectra_subsetting ⠹ | 2303 | spectra_subsetting ⠋ | 2311 | spectra_subsetting ⠇ | 2319 | spectra_subsetting ⠸ | 2324 | spectra_subsetting ✔ | 2324 | spectra_subsetting [42.5s] ⠏ | 0 | spectra_variables ⠙ | 12 | spectra_variables ⠸ | 14 | spectra_variables ⠴ | 16 | spectra_variables ⠦ | 27 | spectra_variables ⠇ | 29 | spectra_variables ⠋ | 31 | spectra_variables ⠹ | 43 | spectra_variables ⠼ | 55 | spectra_variables ✔ | 1 62 | spectra_variables [18.1s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 65.7 s ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_variables.R:262:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2390 ] > > proc.time() user system elapsed 92.901 13.730 106.805
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
name | user | system | elapsed | |
MsBackendRawFileReader-class | 4.036 | 1.241 | 5.618 | |
MsBackendRawFileReader | 5.615 | 2.283 | 12.002 | |
hidden_aliases | 5.910 | 2.367 | 4.212 | |
ioBenchmark | 41.555 | 9.929 | 19.565 | |