Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:37:16 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1294/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendMassbank 1.8.0  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MsBackendMassbank
git_branch: RELEASE_3_17
git_last_commit: 8b032ac
git_last_commit_date: 2023-04-25 11:26:59 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for MsBackendMassbank on merida1


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.

raw results


Summary

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: 2023-10-16 04:16:21 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 04:21:19 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 298.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendMassbank.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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/meat/MsBackendMassbank.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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 20.662  4.043   11.52
* 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


Installation output

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-x86_64/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)

Tests output

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: x86_64-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                                             
⠋ |          1 | spectra_subsetting                                             
⠼ |          5 | spectra_subsetting                                             
⠏ |         10 | spectra_subsetting                                             
⠹ |         13 | spectra_subsetting                                             
⠦ |         17 | spectra_subsetting                                             
⠋ |         21 | spectra_subsetting                                             
⠹ |         23 | spectra_subsetting                                             
⠸ |         24 | spectra_subsetting                                             
⠼ |         25 | spectra_subsetting                                             
⠴ |         26 | spectra_subsetting                                             
⠧ |         28 | spectra_subsetting                                             
⠋ |         31 | spectra_subsetting                                             
⠹ |         33 | spectra_subsetting                                             
⠦ |         37 | spectra_subsetting                                             
⠧ |         38 | spectra_subsetting                                             
⠋ |         41 | spectra_subsetting                                             
⠸ |         44 | spectra_subsetting                                             
⠼ |         45 | spectra_subsetting                                             
✔ |         45 | spectra_subsetting [2.4s]

⠏ |          0 | spectra_variables                                              
⠹ |          3 | spectra_variables                                              
⠴ |          6 | spectra_variables                                              
⠧ |          8 | spectra_variables                                              
⠋ |         11 | spectra_variables                                              
⠦ |         17 | spectra_variables                                              
⠸ |         24 | spectra_variables                                              
⠧ |         28 | spectra_variables                                              
⠋ |         31 | spectra_variables                                              
⠸ |         34 | spectra_variables                                              
⠦ |         37 | spectra_variables                                              
⠇ |         39 | spectra_variables                                              
⠼ |         45 | spectra_variables                                              
⠸ |         54 | spectra_variables                                              
⠇ |         59 | spectra_variables                                              
⠙ |         62 | spectra_variables                                              
⠦ |         67 | spectra_variables                                              
⠏ |         70 | spectra_variables                                              
⠹ |         73 | spectra_variables                                              
⠧ |         78 | spectra_variables                                              
✔ |         78 | spectra_variables [2.5s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 4.9 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                                             
⠸ |          4 | spectra_subsetting                                             
⠹ |         13 | spectra_subsetting                                             
⠙ |         22 | spectra_subsetting                                             
⠋ |         31 | spectra_subsetting                                             
⠏ |         40 | spectra_subsetting                                             
⠇ |         49 | spectra_subsetting                                             
⠦ |         57 | spectra_subsetting                                             
⠼ |         65 | spectra_subsetting                                             
⠹ |         73 | spectra_subsetting                                             
⠋ |         81 | spectra_subsetting                                             
⠇ |         89 | spectra_subsetting                                             
⠦ |         97 | spectra_subsetting                                             
⠴ |        106 | spectra_subsetting                                             
⠹ |        113 | spectra_subsetting                                             
⠙ |        122 | spectra_subsetting                                             
⠋ |        131 | spectra_subsetting                                             
⠏ |        140 | spectra_subsetting                                             
⠧ |        148 | spectra_subsetting                                             
⠦ |        157 | spectra_subsetting                                             
⠴ |        166 | spectra_subsetting                                             
⠼ |        175 | spectra_subsetting                                             
⠸ |        184 | spectra_subsetting                                             
⠹ |        193 | spectra_subsetting                                             
⠙ |        202 | spectra_subsetting                                             
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⠇ |        219 | spectra_subsetting                                             
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⠇ |        229 | spectra_subsetting                                             
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⠙ |        232 | spectra_subsetting                                             
⠹ |        233 | spectra_subsetting                                             
⠸ |        234 | spectra_subsetting                                             
⠼ |        235 | spectra_subsetting                                             
⠴ |        236 | spectra_subsetting                                             
⠦ |        237 | spectra_subsetting                                             
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⠇ |        239 | spectra_subsetting                                             
⠏ |        240 | spectra_subsetting                                             
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⠙ |        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                                             
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⠴ |        266 | spectra_subsetting                                             
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⠧ |        268 | spectra_subsetting                                             
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⠋ |        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                                             
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⠦ |        287 | spectra_subsetting                                             
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⠇ |        289 | spectra_subsetting                                             
⠸ |        294 | spectra_subsetting                                             
⠧ |        298 | spectra_subsetting                                             
⠋ |      1 300 | spectra_subsetting                                             
✔ |      1 300 | spectra_subsetting [39.8s]

⠏ |          0 | spectra_variables                                              
⠸ |          4 | spectra_variables                                              
⠧ |          8 | spectra_variables                                              
⠙ |         12 | spectra_variables                                              
⠸ |         14 | spectra_variables                                              
⠦ |         17 | spectra_variables                                              
⠙ |         22 | spectra_variables                                              
⠦ |         27 | spectra_variables                                              
⠏ |         30 | spectra_variables                                              
⠙ |         32 | spectra_variables                                              
⠇ |         39 | spectra_variables                                              
⠹ |         43 | spectra_variables                                              
⠧ |         48 | spectra_variables                                              
⠸ |         54 | spectra_variables                                              
⠙ |         62 | spectra_variables                                              
✔ |         64 | spectra_variables [2.2s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 42.0 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 
 85.303   7.717 111.749 

Example timings

MsBackendMassbank.Rcheck/MsBackendMassbank-Ex.timings

nameusersystemelapsed
MsBackendMassbank20.662 4.04311.520
MsBackendMassbankSql1.2740.0871.666
metaDataBlocks0.0040.0020.006