Johannes Rainer
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MsBackendMsp |
| git_branch: RELEASE_3_20 |
| git_last_commit: 6f0f4d6 |
| git_last_commit_date: 2024-10-29 11:08:36 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -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 1332/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendMsp 1.10.0 (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 MsBackendMsp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMsp.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: MsBackendMsp |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMsp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMsp_1.10.0.tar.gz |
| StartedAt: 2024-12-20 06:28:33 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 06:31:26 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 172.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendMsp.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMsp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMsp_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsBackendMsp.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendMsp/DESCRIPTION’ ... OK
* this is package ‘MsBackendMsp’ version ‘1.10.0’
* 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 ‘MsBackendMsp’ 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 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MsBackendMsp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendMsp ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MsBackendMsp’ ... ** 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 (MsBackendMsp)
MsBackendMsp.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-apple-darwin20
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(MsBackendMsp)
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
>
> ## Run specific (backend) package tests
> test_check("MsBackendMsp")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> ## Run additional tests from Spectra:
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
>
> fls <- system.file("extdata", "minimona.msp", package = "MsBackendMsp")
> be <- MsBackendMsp()
> be <- backendInitialize(
+ be, fls, mapping = spectraVariableMapping(MsBackendMsp(), "mona"))
>
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
⠋ | 1 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠦ | 7 | spectra_subsetting
⠹ | 13 | spectra_subsetting
⠇ | 19 | spectra_subsetting
⠼ | 25 | spectra_subsetting
⠋ | 31 | spectra_subsetting
⠦ | 37 | spectra_subsetting
⠹ | 43 | spectra_subsetting
⠇ | 49 | spectra_subsetting
⠼ | 55 | spectra_subsetting
⠋ | 61 | spectra_subsetting
⠦ | 67 | spectra_subsetting
⠹ | 73 | spectra_subsetting
⠇ | 79 | spectra_subsetting
⠼ | 85 | spectra_subsetting
⠋ | 91 | spectra_subsetting
⠼ | 95 | spectra_subsetting
⠴ | 96 | spectra_subsetting
⠦ | 97 | spectra_subsetting
⠇ | 99 | spectra_subsetting
⠏ | 100 | spectra_subsetting
⠙ | 102 | spectra_subsetting
⠹ | 103 | spectra_subsetting
⠸ | 104 | spectra_subsetting
⠼ | 105 | spectra_subsetting
⠴ | 106 | spectra_subsetting
⠧ | 108 | spectra_subsetting
⠏ | 110 | spectra_subsetting
⠋ | 111 | spectra_subsetting
⠙ | 112 | spectra_subsetting
⠸ | 114 | spectra_subsetting
⠴ | 116 | spectra_subsetting
⠧ | 118 | spectra_subsetting
⠇ | 119 | spectra_subsetting
⠏ | 120 | spectra_subsetting
⠋ | 121 | spectra_subsetting
⠙ | 122 | spectra_subsetting
⠸ | 124 | spectra_subsetting
⠦ | 127 | spectra_subsetting
⠇ | 129 | spectra_subsetting
⠼ | 135 | spectra_subsetting
⠏ | 140 | spectra_subsetting
⠹ | 143 | spectra_subsetting
⠧ | 148 | spectra_subsetting
✔ | 148 | spectra_subsetting [5.8s]
⠏ | 0 | spectra_variables
⠴ | 6 | spectra_variables
⠏ | 10 | spectra_variables
⠦ | 17 | spectra_variables
⠼ | 25 | spectra_variables
⠋ | 31 | spectra_variables
⠦ | 37 | spectra_variables
⠙ | 42 | spectra_variables
⠇ | 49 | spectra_variables
⠇ | 59 | spectra_variables
⠦ | 67 | spectra_variables
⠏ | 70 | spectra_variables
⠴ | 76 | spectra_variables
✔ | 78 | spectra_variables [1.9s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 8.0 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 230 ]
>
>
>
>
> proc.time()
user system elapsed
25.340 0.847 26.825
MsBackendMsp.Rcheck/MsBackendMsp-Ex.timings
| name | user | system | elapsed | |
| MsBackendMsp | 2.046 | 0.098 | 2.163 | |
| readMsp | 0.594 | 0.009 | 0.610 | |