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 12:04 -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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendRawFileReader_1.12.0.tar.gz |
StartedAt: 2024-12-20 03:09:55 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:18:30 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 514.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MsBackendRawFileReader.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendRawFileReader_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MsBackendRawFileReader.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 68.190 4.145 11.811 MsBackendRawFileReader 7.063 1.703 7.784 * 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-3.20-bioc/R/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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: 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 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 [4.0s] ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠇ | 19 | spectra_subsetting ⠦ | 37 | spectra_subsetting ⠙ | 52 | spectra_subsetting ⠏ | 70 | spectra_subsetting ⠧ | 88 | spectra_subsetting ⠋ | 101 | spectra_subsetting ⠼ | 115 | spectra_subsetting ⠹ | 133 | spectra_subsetting ⠴ | 146 | spectra_subsetting ⠹ | 163 | spectra_subsetting ⠋ | 181 | spectra_subsetting ⠴ | 196 | spectra_subsetting ⠸ | 214 | spectra_subsetting ⠙ | 232 | spectra_subsetting ⠦ | 247 | spectra_subsetting ⠼ | 265 | spectra_subsetting ⠙ | 282 | spectra_subsetting ⠼ | 295 | spectra_subsetting ⠹ | 313 | spectra_subsetting ⠋ | 331 | spectra_subsetting ⠸ | 334 | spectra_subsetting ⠙ | 352 | spectra_subsetting ⠏ | 370 | spectra_subsetting ⠧ | 388 | spectra_subsetting ⠴ | 406 | spectra_subsetting ⠸ | 424 | spectra_subsetting ⠙ | 442 | spectra_subsetting ⠏ | 460 | spectra_subsetting ⠧ | 478 | spectra_subsetting ⠴ | 496 | spectra_subsetting ⠸ | 514 | spectra_subsetting ⠙ | 532 | spectra_subsetting ⠏ | 550 | spectra_subsetting ⠧ | 568 | spectra_subsetting ⠴ | 586 | spectra_subsetting ⠸ | 604 | spectra_subsetting ⠙ | 622 | spectra_subsetting ⠏ | 640 | spectra_subsetting ⠧ | 658 | spectra_subsetting ⠴ | 676 | spectra_subsetting ⠸ | 694 | spectra_subsetting ⠙ | 712 | spectra_subsetting ⠏ | 730 | spectra_subsetting ⠴ | 746 | spectra_subsetting ⠹ | 763 | spectra_subsetting ⠏ | 780 | spectra_subsetting ⠴ | 796 | spectra_subsetting ⠸ | 814 | spectra_subsetting ⠙ | 832 | spectra_subsetting ⠏ | 850 | spectra_subsetting ⠧ | 868 | spectra_subsetting ⠴ | 886 | spectra_subsetting ⠸ | 904 | spectra_subsetting ⠙ | 922 | spectra_subsetting ⠏ | 940 | spectra_subsetting ⠧ | 958 | spectra_subsetting ⠴ | 976 | spectra_subsetting ⠸ | 994 | spectra_subsetting ⠙ | 1012 | spectra_subsetting ⠏ | 1030 | spectra_subsetting ⠧ | 1048 | spectra_subsetting ⠴ | 1066 | spectra_subsetting ⠸ | 1084 | spectra_subsetting ⠙ | 1102 | spectra_subsetting ⠏ | 1120 | spectra_subsetting ⠧ | 1138 | spectra_subsetting ⠴ | 1156 | spectra_subsetting ⠸ | 1174 | spectra_subsetting ⠙ | 1192 | spectra_subsetting ⠏ | 1210 | spectra_subsetting ⠧ | 1228 | spectra_subsetting ⠴ | 1246 | spectra_subsetting ⠸ | 1264 | spectra_subsetting ⠙ | 1282 | spectra_subsetting ⠏ | 1300 | spectra_subsetting ⠧ | 1318 | spectra_subsetting ⠴ | 1336 | spectra_subsetting ⠸ | 1354 | spectra_subsetting ⠙ | 1372 | spectra_subsetting ⠏ | 1390 | spectra_subsetting ⠧ | 1408 | spectra_subsetting ⠴ | 1426 | spectra_subsetting ⠸ | 1444 | spectra_subsetting ⠋ | 1461 | spectra_subsetting ⠦ | 1477 | spectra_subsetting ⠼ | 1495 | spectra_subsetting ⠹ | 1513 | spectra_subsetting ⠋ | 1531 | spectra_subsetting ⠇ | 1549 | spectra_subsetting ⠦ | 1567 | spectra_subsetting ⠼ | 1585 | spectra_subsetting ⠹ | 1603 | spectra_subsetting ⠋ | 1621 | spectra_subsetting ⠇ | 1639 | spectra_subsetting ⠋ | 1651 | spectra_subsetting ⠇ | 1669 | spectra_subsetting ⠦ | 1687 | spectra_subsetting ⠼ | 1705 | spectra_subsetting ⠹ | 1723 | spectra_subsetting ⠧ | 1728 | spectra_subsetting ⠋ | 1731 | spectra_subsetting ⠸ | 1734 | spectra_subsetting ⠦ | 1737 | spectra_subsetting ⠏ | 1740 | spectra_subsetting ⠹ | 1743 | spectra_subsetting ⠴ | 1746 | spectra_subsetting ⠇ | 1749 | spectra_subsetting ⠙ | 1752 | spectra_subsetting ⠼ | 1755 | spectra_subsetting ⠧ | 1758 | spectra_subsetting ⠋ | 1761 | spectra_subsetting ⠸ | 1764 | spectra_subsetting ⠦ | 1767 | spectra_subsetting ⠏ | 1770 | spectra_subsetting ⠙ | 1772 | spectra_subsetting ⠸ | 1774 | spectra_subsetting ⠦ | 1777 | spectra_subsetting ⠏ | 1780 | spectra_subsetting ⠹ | 1783 | spectra_subsetting ⠴ | 1786 | spectra_subsetting ⠇ | 1789 | spectra_subsetting ⠙ | 1792 | spectra_subsetting ⠼ | 1795 | spectra_subsetting ⠧ | 1798 | spectra_subsetting ⠋ | 1801 | spectra_subsetting ⠸ | 1804 | spectra_subsetting ⠦ | 1807 | spectra_subsetting ⠏ | 1810 | spectra_subsetting ⠹ | 1813 | spectra_subsetting ⠴ | 1816 | spectra_subsetting ⠇ | 1819 | spectra_subsetting ⠙ | 1822 | spectra_subsetting ⠼ | 1825 | spectra_subsetting ⠧ | 1828 | spectra_subsetting ⠋ | 1831 | spectra_subsetting ⠸ | 1834 | spectra_subsetting ⠦ | 1837 | 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spectra_subsetting ⠦ | 1937 | spectra_subsetting ⠏ | 1940 | spectra_subsetting ⠹ | 1943 | spectra_subsetting ⠴ | 1946 | spectra_subsetting ⠇ | 1949 | spectra_subsetting ⠙ | 1952 | spectra_subsetting ⠸ | 1954 | spectra_subsetting ⠦ | 1957 | spectra_subsetting ⠏ | 1960 | spectra_subsetting ⠹ | 1963 | spectra_subsetting ⠴ | 1966 | spectra_subsetting ⠇ | 1969 | spectra_subsetting ⠙ | 1972 | spectra_subsetting ⠼ | 1975 | spectra_subsetting ⠧ | 1978 | spectra_subsetting ⠋ | 1981 | spectra_subsetting ⠸ | 1984 | spectra_subsetting ⠦ | 1987 | spectra_subsetting ⠏ | 1990 | spectra_subsetting ⠹ | 1993 | spectra_subsetting ⠴ | 1996 | spectra_subsetting ⠇ | 1999 | spectra_subsetting ⠙ | 2002 | spectra_subsetting ⠼ | 2005 | spectra_subsetting ⠧ | 2008 | spectra_subsetting ⠋ | 2011 | spectra_subsetting ⠸ | 2014 | spectra_subsetting ⠦ | 2017 | spectra_subsetting ⠏ | 2020 | spectra_subsetting ⠹ | 2023 | spectra_subsetting ⠴ | 2026 | spectra_subsetting ⠇ | 2029 | spectra_subsetting ⠙ | 2032 | spectra_subsetting ⠼ | 2035 | spectra_subsetting ⠧ | 2038 | spectra_subsetting ⠋ | 2041 | spectra_subsetting ⠸ | 2044 | spectra_subsetting ⠦ | 2047 | spectra_subsetting ⠏ | 2050 | spectra_subsetting ⠹ | 2053 | spectra_subsetting ⠴ | 2056 | spectra_subsetting ⠇ | 2059 | spectra_subsetting ⠙ | 2062 | spectra_subsetting ⠼ | 2065 | spectra_subsetting ⠧ | 2068 | spectra_subsetting ⠋ | 2071 | spectra_subsetting ⠸ | 2074 | spectra_subsetting ⠦ | 2077 | spectra_subsetting ⠏ | 2080 | spectra_subsetting ⠹ | 2083 | spectra_subsetting ⠴ | 2086 | spectra_subsetting ⠇ | 2089 | spectra_subsetting ⠙ | 2092 | spectra_subsetting ⠼ | 2095 | spectra_subsetting ⠧ | 2098 | spectra_subsetting ⠋ | 2101 | spectra_subsetting ⠸ | 2104 | spectra_subsetting ⠦ | 2107 | spectra_subsetting ⠏ | 2110 | spectra_subsetting ⠹ | 2113 | spectra_subsetting ⠴ | 2116 | spectra_subsetting ⠇ | 2119 | spectra_subsetting ⠙ | 2122 | spectra_subsetting ⠼ | 2125 | spectra_subsetting ⠧ | 2128 | spectra_subsetting ⠋ | 2131 | spectra_subsetting ⠸ | 2134 | spectra_subsetting ⠦ | 2137 | spectra_subsetting ⠏ | 2140 | spectra_subsetting ⠹ | 2143 | spectra_subsetting ⠴ | 2146 | spectra_subsetting ⠇ | 2149 | spectra_subsetting ⠙ | 2152 | spectra_subsetting ⠼ | 2155 | spectra_subsetting ⠧ | 2158 | spectra_subsetting ⠋ | 2161 | spectra_subsetting ⠸ | 2164 | spectra_subsetting ⠦ | 2167 | spectra_subsetting ⠏ | 2170 | spectra_subsetting ⠹ | 2173 | spectra_subsetting ⠴ | 2176 | spectra_subsetting ⠇ | 2179 | spectra_subsetting ⠙ | 2182 | spectra_subsetting ⠼ | 2185 | spectra_subsetting ⠧ | 2188 | spectra_subsetting ⠋ | 2191 | spectra_subsetting ⠸ | 2194 | spectra_subsetting ⠦ | 2197 | spectra_subsetting ⠏ | 2200 | 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 ⠴ | 2236 | spectra_subsetting ⠇ | 2239 | spectra_subsetting ⠙ | 2242 | spectra_subsetting ⠼ | 2245 | spectra_subsetting ⠧ | 2248 | spectra_subsetting ⠋ | 2251 | spectra_subsetting ⠹ | 2253 | spectra_subsetting ⠴ | 2256 | spectra_subsetting ⠇ | 2259 | spectra_subsetting ⠙ | 2262 | spectra_subsetting ⠼ | 2265 | spectra_subsetting ⠧ | 2268 | spectra_subsetting ⠋ | 2271 | spectra_subsetting ⠸ | 2274 | spectra_subsetting ⠦ | 2277 | spectra_subsetting ⠏ | 2280 | spectra_subsetting ⠹ | 2283 | spectra_subsetting ⠴ | 2286 | spectra_subsetting ⠇ | 2289 | spectra_subsetting ⠙ | 2292 | spectra_subsetting ⠼ | 2295 | spectra_subsetting ⠧ | 2298 | spectra_subsetting ⠙ | 2302 | spectra_subsetting ⠼ | 2305 | spectra_subsetting ⠴ | 2316 | spectra_subsetting ⠹ | 2323 | spectra_subsetting ✔ | 2324 | spectra_subsetting [38.3s] ⠏ | 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 [14.4s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 56.6 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 82.735 6.108 86.199
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
name | user | system | elapsed | |
MsBackendRawFileReader-class | 3.115 | 0.572 | 3.397 | |
MsBackendRawFileReader | 7.063 | 1.703 | 7.784 | |
hidden_aliases | 2.340 | 0.565 | 2.593 | |
ioBenchmark | 68.190 | 4.145 | 11.811 | |