| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-03 11:41 -0400 (Thu, 03 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 1318/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendMassbank 1.13.1 (landing page) RforMassSpectrometry Package Maintainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.13.1 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendMassbank_1.13.1.tar.gz |
| StartedAt: 2024-10-02 23:33:15 -0400 (Wed, 02 Oct 2024) |
| EndedAt: 2024-10-02 23:35:08 -0400 (Wed, 02 Oct 2024) |
| EllapsedTime: 112.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendMassbank.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MsBackendMassbank_1.13.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MsBackendMassbank.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘MsBackendMassbank/DESCRIPTION’ ... OK
* this is package ‘MsBackendMassbank’ version ‘1.13.1’
* 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 ... 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
MsBackendMassbank 7.976 1.606 3.889
* 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
MsBackendMassbank.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MsBackendMassbank ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘MsBackendMassbank’ ... ** 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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.
> library(testthat)
> library(MsBackendMassbank)
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
>
> library(RSQLite)
> dbc <- dbConnect(SQLite(), system.file("sql", "minimassbank.sqlite",
+ package = "MsBackendMassbank"))
>
> test_check("MsBackendMassbank")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 353 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_MsBackendMassbankSql.R:592:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 353 ]
>
> ## 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 6 files ... 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
⠹ | 23 | spectra_subsetting
⠦ | 27 | spectra_subsetting
⠹ | 33 | spectra_subsetting
⠸ | 44 | spectra_subsetting
⠙ | 52 | spectra_subsetting
✔ | 52 | spectra_subsetting
⠏ | 0 | spectra_variables
⠇ | 9 | spectra_variables
⠋ | 21 | spectra_variables
⠸ | 34 | spectra_variables
⠼ | 45 | spectra_variables
⠙ | 62 | spectra_variables
⠋ | 71 | spectra_variables
✔ | 78 | spectra_variables
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.4 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> ## 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
⠧ | 58 | spectra_subsetting
⠋ | 91 | spectra_subsetting
⠸ | 124 | spectra_subsetting
⠸ | 154 | spectra_subsetting
⠦ | 187 | spectra_subsetting
⠼ | 215 | spectra_subsetting
⠴ | 216 | spectra_subsetting
⠦ | 217 | spectra_subsetting
⠧ | 218 | spectra_subsetting
⠇ | 219 | spectra_subsetting
⠏ | 220 | spectra_subsetting
⠋ | 221 | spectra_subsetting
⠙ | 222 | spectra_subsetting
⠹ | 223 | spectra_subsetting
⠸ | 224 | spectra_subsetting
⠼ | 225 | spectra_subsetting
⠴ | 226 | spectra_subsetting
⠦ | 227 | spectra_subsetting
⠧ | 228 | spectra_subsetting
⠇ | 229 | spectra_subsetting
⠏ | 230 | spectra_subsetting
⠋ | 231 | spectra_subsetting
⠙ | 232 | spectra_subsetting
⠹ | 233 | spectra_subsetting
⠸ | 234 | spectra_subsetting
⠼ | 235 | spectra_subsetting
⠴ | 236 | spectra_subsetting
⠦ | 237 | spectra_subsetting
⠧ | 238 | spectra_subsetting
⠇ | 239 | spectra_subsetting
⠏ | 240 | spectra_subsetting
⠋ | 241 | spectra_subsetting
⠙ | 242 | spectra_subsetting
⠹ | 243 | spectra_subsetting
⠸ | 244 | spectra_subsetting
⠼ | 245 | spectra_subsetting
⠴ | 246 | spectra_subsetting
⠦ | 247 | spectra_subsetting
⠧ | 248 | spectra_subsetting
⠇ | 249 | spectra_subsetting
⠏ | 250 | spectra_subsetting
⠋ | 251 | spectra_subsetting
⠙ | 252 | spectra_subsetting
⠹ | 253 | spectra_subsetting
⠸ | 254 | spectra_subsetting
⠼ | 255 | spectra_subsetting
⠴ | 256 | spectra_subsetting
⠦ | 257 | spectra_subsetting
⠧ | 258 | spectra_subsetting
⠇ | 259 | spectra_subsetting
⠏ | 260 | spectra_subsetting
⠋ | 261 | spectra_subsetting
⠙ | 262 | spectra_subsetting
⠹ | 263 | spectra_subsetting
⠸ | 264 | spectra_subsetting
⠼ | 265 | spectra_subsetting
⠴ | 266 | spectra_subsetting
⠦ | 267 | spectra_subsetting
⠧ | 268 | spectra_subsetting
⠇ | 269 | spectra_subsetting
⠏ | 270 | spectra_subsetting
⠋ | 271 | spectra_subsetting
⠙ | 272 | spectra_subsetting
⠹ | 273 | spectra_subsetting
⠸ | 274 | spectra_subsetting
⠼ | 275 | spectra_subsetting
⠴ | 276 | spectra_subsetting
⠦ | 277 | spectra_subsetting
⠧ | 278 | spectra_subsetting
⠇ | 279 | spectra_subsetting
⠏ | 280 | spectra_subsetting
⠋ | 281 | spectra_subsetting
⠙ | 282 | spectra_subsetting
⠹ | 283 | spectra_subsetting
⠸ | 284 | spectra_subsetting
⠦ | 287 | spectra_subsetting
⠇ | 289 | spectra_subsetting
⠋ | 301 | spectra_subsetting
✔ | 1 307 | spectra_subsetting [10.8s]
⠏ | 0 | spectra_variables
⠦ | 3 4 | spectra_variables
⠇ | 3 16 | spectra_variables
⠸ | 3 31 | spectra_variables
⠹ | 3 50 | spectra_variables
⠙ | 3 59 | spectra_variables
✔ | 3 64 | spectra_variables
────────────────────────────────────────────────────────────────────────────────
Warning ('test_spectra_variables.R:18:5'): backend is valid
cannot create dir '/tmp/Rtmp5xATH6/file1619a6791c824e', reason 'No space left on device'
Backtrace:
▆
1. └─testthat::expect_true(validObject(be)) at test_spectra_variables.R:18:5
2. └─testthat:::expect_waldo_constant(act, TRUE, info = info)
3. └─testthat:::waldo_compare(...)
4. └─testthat:::local_reporter_output()
5. └─reporter$local_user_output(.env)
6. └─testthat::local_reproducible_output(...)
7. └─withr::local_language(lang, .local_envir = .env)
8. └─withr:::reset_gettext_cache()
9. ├─base::bindtextdomain("reset", local_tempdir())
10. └─withr::local_tempdir()
11. └─base::dir.create(path, recursive = TRUE)
Warning ('test_spectra_variables.R:18:5'): backend is valid
cannot create dir '/tmp/Rtmp5xATH6/file1619a67d77eefd', reason 'No space left on device'
Backtrace:
▆
1. ├─testthat::expect_true(validObject(be)) at test_spectra_variables.R:18:5
2. │ └─testthat:::expect_waldo_constant(act, TRUE, info = info)
3. │ └─testthat:::waldo_compare(...)
4. │ └─withr (local) `<fn>`()
5. └─withr:::reset_gettext_cache()
6. ├─base::bindtextdomain("reset", local_tempdir())
7. └─withr::local_tempdir()
8. └─base::dir.create(path, recursive = TRUE)
Warning ('test_spectra_variables.R:17:1'): (code run outside of `test_that()`)
cannot create dir '/tmp/Rtmp5xATH6/file1619a63b8ab95b', reason 'No space left on device'
Backtrace:
▆
1. └─testthat::test_dir(test_suite, stop_on_failure = TRUE)
2. └─testthat:::test_files(...)
3. └─testthat:::test_files_serial(...)
4. ├─testthat::with_reporter(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─base::lapply(...)
10. └─testthat (local) FUN(X[[i]], ...)
11. └─testthat::source_file(path, env = env(env), desc = desc, error_call = error_call)
12. └─testthat:::test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
13. ├─base::tryCatch(...)
14. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ ├─base (local) tryCatchOne(...)
16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
18. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. ├─base::withCallingHandlers(...)
21. └─base::eval(code, test_env)
22. └─base::eval(code, test_env)
23. └─testthat::test_that(...) at test_spectra_variables.R:17:1
24. └─testthat:::test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
25. └─testthat:::testthat_state_condition(before, after, call = sys.call(-1))
26. └─testthat:::waldo_compare(before, after, x_arg = "before", y_arg = "after")
27. └─testthat:::local_reporter_output()
28. └─reporter$local_user_output(.env)
29. └─testthat::local_reproducible_output(...)
30. └─withr::local_language(lang, .local_envir = .env)
31. └─withr:::reset_gettext_cache()
32. ├─base::bindtextdomain("reset", local_tempdir())
33. └─withr::local_tempdir()
34. └─base::dir.create(path, recursive = TRUE)
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 11.6 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_subsetting.R:108:1'
[ FAIL 0 | WARN 3 | SKIP 1 | PASS 375 ]
>
> proc.time()
user system elapsed
32.606 3.077 33.056
MsBackendMassbank.Rcheck/MsBackendMassbank-Ex.timings
| name | user | system | elapsed | |
| MsBackendMassbank | 7.976 | 1.606 | 3.889 | |
| MsBackendMassbankSql | 0.524 | 0.017 | 0.541 | |
| metaDataBlocks | 0.002 | 0.000 | 0.002 | |