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 1330/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsBackendMetaboLights 1.0.0 (landing page) Johannes Rainer
| 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 MsBackendMetaboLights package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMetaboLights.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: MsBackendMetaboLights |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendMetaboLights_1.0.0.tar.gz |
StartedAt: 2024-12-20 03:07:20 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:17:19 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 599.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MsBackendMetaboLights.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendMetaboLights_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MsBackendMetaboLights.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 ‘MsBackendMetaboLights/DESCRIPTION’ ... OK * this is package ‘MsBackendMetaboLights’ version ‘1.0.0’ * 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 ‘MsBackendMetaboLights’ 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 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 MsBackendMetaboLights 10.075 1.571 96.547 MetaboLights-utils 0.368 0.013 6.918 * 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
MsBackendMetaboLights.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MsBackendMetaboLights ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘MsBackendMetaboLights’ ... ** using staged installation ** R ** 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 (MsBackendMetaboLights)
MsBackendMetaboLights.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. > #' MetaboLights ID: MTBLS8735 > #' ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8735 > > library(testthat) > library(MsBackendMetaboLights) 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 > > test_check("MsBackendMetaboLights") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 67 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 67 ] > > ## Run tests with the unit test suite defined in the Spectra package to ensure > ## compliance with the definitions of the MsBackend interface/class. > be <- backendInitialize(MsBackendMetaboLights(), mtblsId = "MTBLS39", + filePattern = "63A.cdf", offline = TRUE) > > library(Spectra) > test_suite <- system.file("test_backends", "test_MsBackend", + package = "Spectra") > 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 ⠏ | 0 | spectra_subsetting ⠋ | 1 | spectra_subsetting ⠹ | 13 | spectra_subsetting ⠼ | 25 | spectra_subsetting ⠧ | 38 | spectra_subsetting ⠇ | 49 | spectra_subsetting ⠙ | 62 | spectra_subsetting ⠹ | 73 | spectra_subsetting ⠼ | 85 | 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spectra_subsetting ⠦ | 2037 | spectra_subsetting ⠧ | 2038 | spectra_subsetting ⠇ | 2039 | spectra_subsetting ⠏ | 2040 | spectra_subsetting ⠋ | 2041 | spectra_subsetting ⠙ | 2042 | spectra_subsetting ⠹ | 2043 | spectra_subsetting ⠸ | 2044 | spectra_subsetting ⠼ | 2045 | spectra_subsetting ⠴ | 2046 | spectra_subsetting ⠦ | 2047 | spectra_subsetting ⠧ | 2048 | spectra_subsetting ⠇ | 2049 | spectra_subsetting ⠏ | 2050 | spectra_subsetting ⠋ | 2051 | spectra_subsetting ⠙ | 2052 | spectra_subsetting ⠹ | 2053 | spectra_subsetting ⠸ | 2054 | spectra_subsetting ⠼ | 2055 | spectra_subsetting ⠴ | 2056 | spectra_subsetting ⠦ | 2057 | spectra_subsetting ⠧ | 2058 | spectra_subsetting ⠇ | 2059 | spectra_subsetting ⠏ | 2060 | spectra_subsetting ⠋ | 2061 | spectra_subsetting ⠙ | 2062 | spectra_subsetting ⠹ | 2063 | spectra_subsetting ⠸ | 2064 | spectra_subsetting ⠼ | 2065 | spectra_subsetting ⠴ | 2066 | spectra_subsetting ⠦ | 2067 | spectra_subsetting ⠧ | 2068 | spectra_subsetting ⠇ | 2069 | spectra_subsetting ⠏ | 2070 | spectra_subsetting ⠋ | 2071 | spectra_subsetting ⠙ | 2072 | spectra_subsetting ⠹ | 2073 | spectra_subsetting ⠸ | 2074 | spectra_subsetting ⠼ | 2075 | spectra_subsetting ⠴ | 2076 | spectra_subsetting ⠦ | 2077 | spectra_subsetting ⠧ | 2078 | spectra_subsetting ⠇ | 2079 | spectra_subsetting ⠏ | 2080 | spectra_subsetting ⠋ | 2081 | spectra_subsetting ⠙ | 2082 | spectra_subsetting ⠹ | 2083 | spectra_subsetting ⠸ | 2084 | spectra_subsetting ⠼ | 2085 | spectra_subsetting ⠴ | 2086 | spectra_subsetting ⠦ | 2087 | spectra_subsetting ⠧ | 2088 | spectra_subsetting ⠇ | 2089 | spectra_subsetting ⠏ | 2090 | spectra_subsetting ⠋ | 2091 | spectra_subsetting ⠙ | 2092 | spectra_subsetting ⠹ | 2093 | spectra_subsetting ⠸ | 2094 | spectra_subsetting ⠼ | 2095 | spectra_subsetting ⠴ | 2096 | spectra_subsetting ⠦ | 2097 | spectra_subsetting ⠧ | 2098 | spectra_subsetting ⠇ | 2099 | spectra_subsetting ⠏ | 2100 | spectra_subsetting ⠋ | 2101 | spectra_subsetting ⠙ | 2102 | spectra_subsetting ⠹ | 2103 | spectra_subsetting ⠸ | 2104 | spectra_subsetting ⠼ | 2105 | spectra_subsetting ⠴ | 2106 | spectra_subsetting ⠦ | 2107 | spectra_subsetting ⠧ | 2108 | spectra_subsetting ⠇ | 2109 | spectra_subsetting ⠏ | 2110 | spectra_subsetting ⠋ | 2111 | spectra_subsetting ⠙ | 2112 | spectra_subsetting ⠹ | 2113 | spectra_subsetting ⠸ | 2114 | spectra_subsetting ⠼ | 2115 | spectra_subsetting ⠴ | 2116 | spectra_subsetting ⠦ | 2117 | spectra_subsetting ⠧ | 2118 | spectra_subsetting ⠇ | 2119 | spectra_subsetting ⠏ | 2120 | spectra_subsetting ⠋ | 2121 | spectra_subsetting ⠙ | 2122 | spectra_subsetting ⠹ | 2123 | spectra_subsetting ⠸ | 2124 | spectra_subsetting ⠼ | 2125 | spectra_subsetting ⠴ | 2126 | spectra_subsetting ⠦ | 2127 | spectra_subsetting ⠧ | 2128 | spectra_subsetting ⠇ | 2129 | spectra_subsetting ⠏ | 2130 | spectra_subsetting ⠋ | 2131 | spectra_subsetting ⠙ | 2132 | spectra_subsetting ⠹ | 2133 | spectra_subsetting ⠸ | 2134 | spectra_subsetting ⠼ | 2135 | spectra_subsetting ⠴ | 2136 | spectra_subsetting ⠦ | 2137 | spectra_subsetting ⠧ | 2138 | spectra_subsetting ⠇ | 2139 | spectra_subsetting ⠏ | 2140 | spectra_subsetting ⠋ | 2141 | spectra_subsetting ⠙ | 2142 | spectra_subsetting ⠹ | 2143 | spectra_subsetting ⠸ | 2144 | spectra_subsetting ⠼ | 2145 | spectra_subsetting ⠴ | 2146 | spectra_subsetting ⠦ | 2147 | spectra_subsetting ⠧ | 2148 | spectra_subsetting ⠇ | 2149 | spectra_subsetting ⠏ | 2150 | spectra_subsetting ⠋ | 2151 | spectra_subsetting ⠙ | 2152 | spectra_subsetting ⠹ | 2153 | spectra_subsetting ⠸ | 2154 | spectra_subsetting ⠼ | 2155 | spectra_subsetting ⠴ | 2156 | spectra_subsetting ⠦ | 2157 | spectra_subsetting ⠧ | 2158 | spectra_subsetting ⠇ | 2159 | spectra_subsetting ⠏ | 2160 | spectra_subsetting ⠋ | 2161 | spectra_subsetting ⠙ | 2162 | spectra_subsetting ⠹ | 2163 | spectra_subsetting ⠸ | 2164 | spectra_subsetting ⠼ | 2165 | spectra_subsetting ⠴ | 2166 | spectra_subsetting ⠦ | 2167 | spectra_subsetting ⠧ | 2168 | spectra_subsetting ⠇ | 2169 | spectra_subsetting ⠏ | 2170 | spectra_subsetting ⠋ | 2171 | spectra_subsetting ⠙ | 2172 | spectra_subsetting ⠹ | 2173 | spectra_subsetting ⠸ | 2174 | spectra_subsetting ⠼ | 2175 | spectra_subsetting ⠴ | 2176 | spectra_subsetting ⠦ | 2177 | spectra_subsetting ⠧ | 2178 | spectra_subsetting ⠇ | 2179 | spectra_subsetting ⠏ | 2180 | spectra_subsetting ⠋ | 2181 | spectra_subsetting ⠙ | 2182 | spectra_subsetting ⠹ | 2183 | spectra_subsetting ⠸ | 2184 | spectra_subsetting ⠼ | 2185 | spectra_subsetting ⠴ | 2186 | spectra_subsetting ⠦ | 2187 | spectra_subsetting ⠧ | 2188 | spectra_subsetting ⠇ | 2189 | spectra_subsetting ⠏ | 2190 | spectra_subsetting ⠋ | 2191 | spectra_subsetting ⠙ | 2192 | spectra_subsetting ⠹ | 2193 | spectra_subsetting ⠸ | 2194 | spectra_subsetting ⠼ | 2195 | spectra_subsetting ⠴ | 2196 | spectra_subsetting ⠦ | 2197 | spectra_subsetting ⠧ | 2198 | spectra_subsetting ⠇ | 2199 | spectra_subsetting ⠏ | 2200 | spectra_subsetting ⠋ | 2201 | spectra_subsetting ⠙ | 2202 | spectra_subsetting ⠹ | 2203 | spectra_subsetting ⠸ | 2204 | spectra_subsetting ⠼ | 2205 | spectra_subsetting ⠴ | 2206 | spectra_subsetting ⠦ | 2207 | spectra_subsetting ⠧ | 2208 | spectra_subsetting ⠇ | 2209 | spectra_subsetting ⠏ | 2210 | spectra_subsetting ⠋ | 2211 | spectra_subsetting ⠙ | 2212 | spectra_subsetting ⠹ | 2213 | spectra_subsetting ⠸ | 2214 | spectra_subsetting ⠼ | 2215 | spectra_subsetting ⠴ | 2216 | spectra_subsetting ⠇ | 2219 | spectra_subsetting ⠋ | 2221 | spectra_subsetting ⠙ | 2232 | spectra_subsetting ⠧ | 2238 | spectra_subsetting ⠏ | 2240 | spectra_subsetting ✔ | 2240 | spectra_subsetting [95.5s] ⠏ | 0 | spectra_variables ⠙ | 12 | spectra_variables ⠸ | 14 | spectra_variables ⠴ | 16 | spectra_variables ⠦ | 27 | spectra_variables ⠇ | 29 | spectra_variables ⠋ | 31 | spectra_variables ⠹ | 43 | spectra_variables ⠸ | 54 | spectra_variables ✔ | 1 62 | spectra_variables [1.5s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 97.3 s ── Skipped tests (1) ─────────────────────────────────────────────────────────── • empty test (1): 'test_spectra_variables.R:262:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 2306 ] > > proc.time() user system elapsed 106.415 5.371 178.566
MsBackendMetaboLights.Rcheck/MsBackendMetaboLights-Ex.timings
name | user | system | elapsed | |
MetaboLights-utils | 0.368 | 0.013 | 6.918 | |
MsBackendMetaboLights | 10.075 | 1.571 | 96.547 | |