Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 2069/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpectriPy 0.99.12 (landing page) Johannes Rainer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the SpectriPy package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpectriPy.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: SpectriPy |
Version: 0.99.12 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpectriPy.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpectriPy_0.99.12.tar.gz |
StartedAt: 2025-09-27 04:36:15 -0400 (Sat, 27 Sep 2025) |
EndedAt: 2025-09-27 04:49:41 -0400 (Sat, 27 Sep 2025) |
EllapsedTime: 805.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpectriPy.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpectriPy.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpectriPy_0.99.12.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpectriPy.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘SpectriPy/DESCRIPTION’ ... OK * this is package ‘SpectriPy’ version ‘0.99.12’ * 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 ‘SpectriPy’ 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 ... NOTE Unexported object imported by a ':::' call: ‘Spectra:::.check_peaks_data_value’ See the note in ?`:::` about the use of this operator. * 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 MsBackendPy 5.781 0.883 6.49 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/SpectriPy.Rcheck/00check.log’ for details.
SpectriPy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SpectriPy ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘SpectriPy’ ... ** this is package ‘SpectriPy’ version ‘0.99.12’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (SpectriPy)
SpectriPy.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 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(Spectra) Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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(SpectriPy) Loading required package: reticulate > library(MsBackendMgf) > > fl <- system.file("extdata", "mgf", "test.mgf", package = "SpectriPy") > s <- Spectra(fl, source = MsBackendMgf()) Start data import from 1 files ... done > s <- setBackend(s, MsBackendPy(), pythonVariableName = "py_be") > > be <- s@backend > > test_check("SpectriPy") 2025-09-27 04:40:48,103:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,104:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,105:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,106:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,107:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,107:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,108:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,109:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,109:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,110:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,111:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,111:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,112:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,113:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,114:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,114:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata. 2025-09-27 04:40:48,115:WARNING:matchms:add_precursor_mz:No 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Processing spectra: 0%| | 0/4 [00:00<?, ?it/s] Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3464.22it/s] Processing spectra: 0%| | 0/4 [00:00<?, ?it/s] Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3818.21it/s] Processing spectra: 0%| | 0/4 [00:00<?, ?it/s] Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 4072.14it/s] Processing spectra: 0%| | 0/4 [00:00<?, ?it/s] Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 4137.41it/s] Processing spectra: 0%| | 0/4 [00:00<?, ?it/s] Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3771.86it/s] [ FAIL 0 | WARN 4 | SKIP 1 | PASS 592 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_zzz.R:16:1' [ FAIL 0 | WARN 4 | SKIP 1 | PASS 592 ] > > ## TODO: add tests from the Spectra unit test suite! > > ## ## Run the MsBackend spectra variable test suite > ## test_suite <- system.file("test_backends", "test_MsBackend", > ## package = "Spectra") > > ## ## Run single test file. > ## res <- test_dir(test_suite, stop_on_failure = TRUE) > > proc.time() user system elapsed 30.191 2.699 31.619
SpectriPy.Rcheck/SpectriPy-Ex.timings
name | user | system | elapsed | |
MsBackendPy | 5.781 | 0.883 | 6.490 | |
compareSpectriPy | 2.408 | 0.220 | 2.652 | |
conversion | 0.346 | 0.292 | 0.479 | |
filterSpectriPy | 0.180 | 0.015 | 0.196 | |