Johannes Rainer
| Snapshot Date: 2025-11-25 13:40 -0500 (Tue, 25 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SpectriPy |
| git_branch: devel |
| git_last_commit: 09e5773 |
| git_last_commit_date: 2025-10-29 11:36:52 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-26 11:38 -0500 (Wed, 26 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4830 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4609 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4569 |
| 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 2065/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpectriPy 1.1.0 (landing page) Johannes Rainer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
|
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: 1.1.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SpectriPy.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SpectriPy_1.1.0.tar.gz |
| StartedAt: 2025-11-26 04:25:59 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 04:39:06 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 787.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpectriPy.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SpectriPy.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SpectriPy_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SpectriPy.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.1.0’
* 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 ‘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 5.501 0.925 6.233
* 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-3.23-bioc/meat/SpectriPy.Rcheck/00check.log’
for details.
SpectriPy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SpectriPy ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘SpectriPy’ ... ** this is package ‘SpectriPy’ version ‘1.1.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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")
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2025-11-26 04:30:39,961:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-11-26 04:30:39,962:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
2025-11-26 04:30:39,962:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.
Processing spectra: 0%| | 0/4 [00:00<?, ?it/s]
Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3560.53it/s]
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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 3927.25it/s]
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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 4141.50it/s]
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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 4171.36it/s]
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Processing spectra: 100%|██████████| 4/4 [00:00<00:00, 4016.57it/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
28.690 2.839 30.860
SpectriPy.Rcheck/SpectriPy-Ex.timings
| name | user | system | elapsed | |
| MsBackendPy | 5.501 | 0.925 | 6.233 | |
| compareSpectriPy | 2.349 | 0.261 | 2.628 | |
| conversion | 0.338 | 0.256 | 0.457 | |
| filterSpectriPy | 0.173 | 0.024 | 0.197 | |