Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-18 11:43 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
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 1325/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsBackendRawFileReader 1.11.6 (landing page) Christian Panse
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.11.6 |
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_1.11.6.tar.gz |
StartedAt: 2024-10-18 03:38:31 -0400 (Fri, 18 Oct 2024) |
EndedAt: 2024-10-18 03:42:36 -0400 (Fri, 18 Oct 2024) |
EllapsedTime: 245.3 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_1.11.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MsBackendRawFileReader.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘1.11.6’ * 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 24.742 4.822 10.479 MsBackendRawFileReader 5.101 2.004 6.669 * 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 ‘/media/volume/teran2_disk/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 4.4.1 (2024-06-14) -- "Race for Your Life" 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 [2.8s] ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠹ | 23 | spectra_subsetting ⠹ | 43 | spectra_subsetting ⠸ | 64 | spectra_subsetting ⠴ | 86 | spectra_subsetting ⠴ | 106 | spectra_subsetting ⠧ | 128 | spectra_subsetting ⠦ | 147 | spectra_subsetting ⠇ | 169 | spectra_subsetting ⠏ | 190 | spectra_subsetting ⠋ | 211 | spectra_subsetting ⠸ | 234 | spectra_subsetting ⠹ | 253 | spectra_subsetting ⠼ | 275 | spectra_subsetting ⠼ | 295 | spectra_subsetting ⠦ | 317 | spectra_subsetting ⠸ | 334 | spectra_subsetting ⠧ | 358 | spectra_subsetting ⠙ | 382 | spectra_subsetting ⠴ | 406 | spectra_subsetting ⠏ | 430 | spectra_subsetting ⠸ | 454 | spectra_subsetting ⠧ | 478 | spectra_subsetting ⠙ | 502 | spectra_subsetting ⠴ | 526 | spectra_subsetting ⠏ | 550 | spectra_subsetting ⠸ | 574 | spectra_subsetting ⠦ | 597 | spectra_subsetting ⠇ | 619 | spectra_subsetting ⠹ | 643 | spectra_subsetting ⠼ | 665 | spectra_subsetting ⠧ | 688 | spectra_subsetting ⠙ | 712 | spectra_subsetting ⠴ | 736 | spectra_subsetting ⠏ | 760 | spectra_subsetting ⠸ | 784 | spectra_subsetting ⠧ | 808 | spectra_subsetting ⠙ | 832 | spectra_subsetting ⠴ | 856 | spectra_subsetting ⠏ | 880 | spectra_subsetting ⠸ | 904 | spectra_subsetting ⠧ | 928 | spectra_subsetting ⠙ | 952 | spectra_subsetting ⠼ | 975 | spectra_subsetting ⠦ | 997 | spectra_subsetting ⠋ | 1021 | spectra_subsetting ⠹ | 1043 | spectra_subsetting ⠴ | 1066 | spectra_subsetting ⠏ | 1090 | spectra_subsetting ⠸ | 1114 | spectra_subsetting ⠧ | 1138 | spectra_subsetting ⠋ | 1161 | spectra_subsetting ⠹ | 1183 | spectra_subsetting ⠦ | 1207 | spectra_subsetting ⠋ | 1231 | spectra_subsetting ⠼ | 1255 | spectra_subsetting ⠇ | 1279 | spectra_subsetting ⠹ | 1303 | spectra_subsetting ⠴ | 1326 | spectra_subsetting ⠼ | 1345 | spectra_subsetting ⠦ | 1367 | spectra_subsetting ⠧ | 1388 | spectra_subsetting ⠧ | 1408 | spectra_subsetting ⠙ | 1432 | spectra_subsetting ⠴ | 1456 | spectra_subsetting ⠦ | 1477 | spectra_subsetting ⠋ | 1501 | spectra_subsetting ⠼ | 1525 | spectra_subsetting ⠴ | 1546 | spectra_subsetting ⠏ | 1570 | spectra_subsetting ⠙ | 1592 | spectra_subsetting ⠼ | 1615 | spectra_subsetting ⠧ | 1638 | spectra_subsetting ⠸ | 1654 | spectra_subsetting ⠼ | 1675 | spectra_subsetting ⠦ | 1697 | spectra_subsetting ⠦ | 1717 | spectra_subsetting ⠦ | 1727 | spectra_subsetting ⠏ | 1730 | spectra_subsetting ⠹ | 1733 | spectra_subsetting ⠴ | 1736 | spectra_subsetting ⠇ | 1739 | spectra_subsetting ⠙ | 1742 | spectra_subsetting ⠼ | 1745 | spectra_subsetting ⠧ | 1748 | spectra_subsetting ⠋ | 1751 | spectra_subsetting ⠸ | 1754 | spectra_subsetting ⠦ | 1757 | spectra_subsetting ⠏ | 1760 | spectra_subsetting ⠹ | 1763 | spectra_subsetting ⠴ | 1766 | spectra_subsetting ⠇ | 1769 | spectra_subsetting ⠙ | 1772 | spectra_subsetting ⠼ | 1775 | spectra_subsetting ⠧ | 1778 | spectra_subsetting ⠋ | 1781 | spectra_subsetting ⠸ | 1784 | spectra_subsetting ⠦ | 1787 | spectra_subsetting ⠏ | 1790 | spectra_subsetting ⠹ | 1793 | spectra_subsetting ⠴ | 1796 | spectra_subsetting ⠇ | 1799 | spectra_subsetting ⠙ | 1802 | spectra_subsetting ⠼ | 1805 | spectra_subsetting ⠧ | 1808 | spectra_subsetting ⠋ | 1811 | spectra_subsetting ⠸ | 1814 | spectra_subsetting ⠦ | 1817 | spectra_subsetting ⠏ | 1820 | spectra_subsetting ⠹ | 1823 | spectra_subsetting ⠴ | 1826 | spectra_subsetting ⠏ | 1830 | spectra_subsetting ⠹ | 1833 | spectra_subsetting ⠦ | 1837 | spectra_subsetting ⠏ | 1840 | spectra_subsetting ⠹ | 1843 | spectra_subsetting ⠴ | 1846 | spectra_subsetting ⠇ | 1849 | spectra_subsetting ⠙ | 1852 | spectra_subsetting ⠼ | 1855 | spectra_subsetting ⠧ | 1858 | spectra_subsetting ⠋ | 1861 | spectra_subsetting ⠸ | 1864 | spectra_subsetting ⠧ | 1868 | spectra_subsetting ⠋ | 1871 | spectra_subsetting ⠸ | 1874 | spectra_subsetting ⠦ | 1877 | spectra_subsetting ⠏ | 1880 | spectra_subsetting ⠹ | 1883 | spectra_subsetting ⠦ | 1887 | spectra_subsetting ⠏ | 1890 | spectra_subsetting ⠹ | 1893 | spectra_subsetting ⠴ | 1896 | spectra_subsetting ⠇ | 1899 | spectra_subsetting ⠙ | 1902 | spectra_subsetting ⠼ | 1905 | spectra_subsetting ⠧ | 1908 | spectra_subsetting ⠋ | 1911 | spectra_subsetting ⠸ | 1914 | spectra_subsetting ⠦ | 1917 | spectra_subsetting ⠏ | 1920 | spectra_subsetting ⠹ | 1923 | spectra_subsetting ⠴ | 1926 | spectra_subsetting ⠇ | 1929 | spectra_subsetting ⠙ | 1932 | spectra_subsetting ⠼ | 1935 | spectra_subsetting ⠧ | 1938 | spectra_subsetting ⠋ | 1941 | spectra_subsetting ⠸ | 1944 | spectra_subsetting ⠦ | 1947 | spectra_subsetting ⠏ | 1950 | spectra_subsetting ⠹ | 1953 | spectra_subsetting ⠴ | 1956 | spectra_subsetting ⠇ | 1959 | spectra_subsetting ⠙ | 1962 | spectra_subsetting ⠼ | 1965 | spectra_subsetting ⠧ | 1968 | spectra_subsetting ⠙ | 1972 | spectra_subsetting ⠼ | 1975 | spectra_subsetting ⠇ | 1979 | spectra_subsetting ⠙ | 1982 | spectra_subsetting ⠼ | 1985 | spectra_subsetting ⠧ | 1988 | spectra_subsetting ⠋ | 1991 | spectra_subsetting ⠸ | 1994 | spectra_subsetting ⠦ | 1997 | spectra_subsetting ⠏ | 2000 | spectra_subsetting ⠹ | 2003 | spectra_subsetting ⠴ | 2006 | spectra_subsetting ⠇ | 2009 | spectra_subsetting ⠙ | 2012 | spectra_subsetting ⠼ | 2015 | spectra_subsetting ⠧ | 2018 | spectra_subsetting ⠋ | 2021 | spectra_subsetting ⠸ | 2024 | spectra_subsetting ⠦ | 2027 | spectra_subsetting ⠏ | 2030 | spectra_subsetting ⠹ | 2033 | spectra_subsetting ⠴ | 2036 | spectra_subsetting ⠇ | 2039 | spectra_subsetting ⠙ | 2042 | spectra_subsetting ⠼ | 2045 | spectra_subsetting ⠧ | 2048 | spectra_subsetting ⠋ | 2051 | spectra_subsetting ⠸ | 2054 | spectra_subsetting ⠧ | 2058 | spectra_subsetting ⠋ | 2061 | 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 ⠼ | 2165 | spectra_subsetting ⠧ | 2168 | spectra_subsetting ⠋ | 2171 | spectra_subsetting ⠸ | 2174 | spectra_subsetting ⠦ | 2177 | spectra_subsetting ⠏ | 2180 | spectra_subsetting ⠹ | 2183 | spectra_subsetting ⠴ | 2186 | spectra_subsetting ⠇ | 2189 | spectra_subsetting ⠙ | 2192 | spectra_subsetting ⠼ | 2195 | spectra_subsetting ⠧ | 2198 | spectra_subsetting ⠙ | 2202 | spectra_subsetting ⠼ | 2205 | spectra_subsetting ⠧ | 2208 | spectra_subsetting ⠋ | 2211 | spectra_subsetting ⠸ | 2214 | spectra_subsetting ⠦ | 2217 | spectra_subsetting ⠏ | 2220 | spectra_subsetting ⠹ | 2223 | spectra_subsetting ⠴ | 2226 | spectra_subsetting ⠏ | 2230 | spectra_subsetting ⠹ | 2233 | spectra_subsetting ⠦ | 2237 | spectra_subsetting ⠏ | 2240 | spectra_subsetting ⠹ | 2243 | spectra_subsetting ⠴ | 2246 | spectra_subsetting ⠇ | 2249 | spectra_subsetting ⠙ | 2252 | spectra_subsetting ⠼ | 2255 | 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 ⠏ | 2290 | spectra_subsetting ⠹ | 2293 | spectra_subsetting ⠴ | 2296 | spectra_subsetting ⠇ | 2299 | spectra_subsetting ⠼ | 2305 | spectra_subsetting ⠇ | 2319 | spectra_subsetting ✔ | 2324 | spectra_subsetting [30.5s] ⠏ | 0 | spectra_variables ⠙ | 12 | spectra_variables ⠸ | 14 | spectra_variables ⠴ | 16 | spectra_variables ⠦ | 27 | spectra_variables ⠇ | 29 | spectra_variables ⠋ | 31 | spectra_variables ⠹ | 43 | spectra_variables ✔ | 1 62 | spectra_variables [10.7s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 44.0 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 61.743 6.783 67.151
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
name | user | system | elapsed | |
MsBackendRawFileReader-class | 2.537 | 0.658 | 3.240 | |
MsBackendRawFileReader | 5.101 | 2.004 | 6.669 | |
hidden_aliases | 1.656 | 0.641 | 2.130 | |
ioBenchmark | 24.742 | 4.822 | 10.479 | |