| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1294/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendMassbank 1.8.0 (landing page) RforMassSpectrometry Package Maintainer
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the MsBackendMassbank package: - 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: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMassbank_1.8.0.tar.gz |
| StartedAt: 2023-10-18 09:26:39 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 09:29:51 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 191.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendMassbank.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMassbank_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MsBackendMassbank.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendMassbank/DESCRIPTION’ ... OK
* this is package ‘MsBackendMassbank’ version ‘1.8.0’
* 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 ‘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 R 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MsBackendMassbank 9.859 1.242 8.445
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MsBackendMassbank.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendMassbank ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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, setdiff, sort, 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
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
>
> library(RSQLite)
> dbc <- dbConnect(SQLite(), system.file("sql", "minimassbank.sqlite",
+ package = "MsBackendMassbank"))
>
> test_check("MsBackendMassbank")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 348 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_MsBackendMassbankSql.R:578:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 348 ]
>
> ## 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 | spectra_subsetting
⠸ | 4 | spectra_subsetting
⠋ | 11 | spectra_subsetting
⠦ | 17 | spectra_subsetting
⠙ | 22 | spectra_subsetting
⠸ | 24 | spectra_subsetting
⠴ | 26 | spectra_subsetting
⠧ | 28 | spectra_subsetting
⠋ | 31 | spectra_subsetting
⠦ | 37 | spectra_subsetting
⠏ | 40 | spectra_subsetting
⠼ | 45 | spectra_subsetting
✔ | 45 | spectra_subsetting [1.4s]
⠏ | 0 | spectra_variables
⠴ | 6 | spectra_variables
⠏ | 10 | spectra_variables
⠦ | 17 | spectra_variables
⠼ | 25 | spectra_variables
⠋ | 31 | spectra_variables
⠦ | 37 | spectra_variables
⠸ | 44 | spectra_variables
⠏ | 50 | spectra_variables
⠇ | 59 | spectra_variables
⠦ | 67 | spectra_variables
⠋ | 71 | spectra_variables
✔ | 78 | spectra_variables [1.4s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 2.9 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
>
> ## Test MsBackendMassbankSql
> be <- MsBackendMassbankSql()
> be <- backendInitialize(be, dbc)
>
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | spectra_subsetting
⠏ | 10 | spectra_subsetting
⠼ | 25 | spectra_subsetting
⠏ | 40 | spectra_subsetting
⠼ | 55 | spectra_subsetting
⠏ | 70 | spectra_subsetting
⠼ | 85 | spectra_subsetting
⠏ | 100 | spectra_subsetting
⠼ | 115 | spectra_subsetting
⠏ | 130 | spectra_subsetting
⠹ | 143 | spectra_subsetting
⠦ | 157 | spectra_subsetting
⠏ | 170 | spectra_subsetting
⠸ | 184 | spectra_subsetting
⠇ | 199 | spectra_subsetting
⠸ | 214 | 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
⠧ | 288 | spectra_subsetting
⠇ | 289 | spectra_subsetting
⠸ | 294 | spectra_subsetting
⠏ | 300 | spectra_subsetting
✔ | 1 300 | spectra_subsetting [24.4s]
⠏ | 0 | spectra_variables
⠴ | 6 | spectra_variables
⠙ | 12 | spectra_variables
⠴ | 16 | spectra_variables
⠼ | 25 | spectra_variables
⠇ | 29 | spectra_variables
⠦ | 37 | spectra_variables
⠧ | 48 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 64 | spectra_variables [1.1s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 25.6 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_subsetting.R:90:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 364 ]
>
> proc.time()
user system elapsed
43.910 2.745 67.564
MsBackendMassbank.Rcheck/MsBackendMassbank-Ex.timings
| name | user | system | elapsed | |
| MsBackendMassbank | 9.859 | 1.242 | 8.445 | |
| MsBackendMassbankSql | 0.687 | 0.062 | 1.148 | |
| metaDataBlocks | 0.003 | 0.001 | 0.005 | |