| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-22 11:40 -0400 (Sat, 22 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 1342/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendMassbank 1.15.3 (landing page) RforMassSpectrometry Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the MsBackendMassbank package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMassbank.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: MsBackendMassbank |
| Version: 1.15.3 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MsBackendMassbank_1.15.3.tar.gz |
| StartedAt: 2025-03-22 00:24:23 -0400 (Sat, 22 Mar 2025) |
| EndedAt: 2025-03-22 00:26:05 -0400 (Sat, 22 Mar 2025) |
| EllapsedTime: 101.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendMassbank.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MsBackendMassbank_1.15.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MsBackendMassbank.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendMassbank/DESCRIPTION’ ... OK
* this is package ‘MsBackendMassbank’ version ‘1.15.3’
* 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 ‘MsBackendMassbank’ 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.extract_mb_ac’ ‘.extract_mb_ch’ ‘.extract_mb_comment’
‘.extract_mb_ms’ ‘.extract_mb_pk’ ‘.extract_mb_record’
‘.extract_mb_sp’ ‘.extract_mb_spectrum’
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/MsBackendMassbank.Rcheck/00check.log’
for details.
MsBackendMassbank.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MsBackendMassbank ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘MsBackendMassbank’ ... ** this is package ‘MsBackendMassbank’ version ‘1.15.3’ ** 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 (MsBackendMassbank)
MsBackendMassbank.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-13 r87965) -- "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(MsBackendMassbank)
Loading required package: 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(RSQLite)
> dbc <- dbConnect(SQLite(), system.file("sql", "minimassbank.sqlite",
+ package = "MsBackendMassbank"))
>
> test_check("MsBackendMassbank")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 392 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_MsBackendMassbankSql.R:616:1'
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 392 ]
>
> ## Run additional tests from Spectra:
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
>
> ## Test MsBackendMassbank:
> fls <- dir(system.file("extdata", package = "MsBackendMassbank"),
+ full.names = TRUE, pattern = "^RP.*txt$")
> be <- MsBackendMassbank()
> be <- backendInitialize(be, fls)
Start data import from 7 files ... done
Merging results ...done
>
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠹ | 13 | spectra_subsetting
⠼ | 25 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠙ | 32 | spectra_subsetting
⠋ | 41 | spectra_subsetting
⠏ | 50 | spectra_subsetting
⠇ | 59 | spectra_subsetting
⠴ | 66 | spectra_subsetting
✔ | 74 | spectra_subsetting
⠏ | 0 | spectra_variables
⠏ | 10 | spectra_variables
⠴ | 26 | spectra_variables
⠦ | 37 | spectra_variables
⠋ | 51 | spectra_variables
⠙ | 62 | spectra_variables
⠋ | 71 | spectra_variables
✔ | 78 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.7 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 156 ]
>
> ## Test MsBackendMassbankSql
> be <- MsBackendMassbankSql()
> be <- backendInitialize(be, dbc)
>
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠼ | 25 | spectra_subsetting
⠼ | 55 | spectra_subsetting
⠴ | 86 | spectra_subsetting
⠦ | 117 | spectra_subsetting
⠹ | 143 | spectra_subsetting
⠹ | 173 | spectra_subsetting
⠦ | 197 | spectra_subsetting
⠼ | 215 | spectra_subsetting
⠦ | 217 | spectra_subsetting
⠇ | 219 | spectra_subsetting
⠋ | 221 | spectra_subsetting
⠹ | 223 | spectra_subsetting
⠸ | 224 | spectra_subsetting
⠴ | 226 | spectra_subsetting
⠧ | 228 | spectra_subsetting
⠏ | 230 | spectra_subsetting
⠙ | 232 | spectra_subsetting
⠸ | 234 | spectra_subsetting
⠴ | 236 | spectra_subsetting
⠧ | 238 | spectra_subsetting
⠏ | 240 | spectra_subsetting
⠙ | 242 | spectra_subsetting
⠸ | 244 | spectra_subsetting
⠴ | 246 | spectra_subsetting
⠧ | 248 | spectra_subsetting
⠏ | 250 | spectra_subsetting
⠙ | 252 | spectra_subsetting
⠸ | 254 | spectra_subsetting
⠴ | 256 | spectra_subsetting
⠧ | 258 | spectra_subsetting
⠏ | 260 | spectra_subsetting
⠙ | 262 | spectra_subsetting
⠸ | 264 | spectra_subsetting
⠴ | 266 | spectra_subsetting
⠧ | 268 | spectra_subsetting
⠇ | 269 | spectra_subsetting
⠏ | 270 | spectra_subsetting
⠙ | 272 | spectra_subsetting
⠸ | 274 | spectra_subsetting
⠴ | 276 | spectra_subsetting
⠦ | 277 | spectra_subsetting
⠧ | 278 | spectra_subsetting
⠏ | 280 | spectra_subsetting
⠙ | 282 | spectra_subsetting
⠹ | 283 | spectra_subsetting
⠦ | 287 | spectra_subsetting
⠏ | 290 | spectra_subsetting
⠋ | 301 | spectra_subsetting
⠇ | 309 | spectra_subsetting
⠦ | 317 | spectra_subsetting
⠹ | 1 322 | spectra_subsetting
✔ | 1 325 | spectra_subsetting [8.4s]
⠏ | 0 | spectra_variables
⠸ | 14 | spectra_variables
⠇ | 29 | spectra_variables
⠧ | 48 | spectra_variables
⠏ | 60 | spectra_variables
✔ | 64 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 8.9 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_subsetting.R:131:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 393 ]
>
> proc.time()
user system elapsed
22.986 2.752 24.383
MsBackendMassbank.Rcheck/MsBackendMassbank-Ex.timings
| name | user | system | elapsed | |
| MsBackendMassbank | 1.776 | 0.536 | 1.467 | |
| MsBackendMassbankSql | 0.528 | 0.058 | 0.586 | |
| metaDataBlocks | 0.002 | 0.000 | 0.002 | |