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This page was generated on 2022-10-19 13:20:33 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for MsBackendMassbank on nebbiolo1


To the developers/maintainers of the MsBackendMassbank package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1244/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendMassbank 1.4.0  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MsBackendMassbank
git_branch: RELEASE_3_15
git_last_commit: 5b15c06
git_last_commit_date: 2022-04-26 12:13:12 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MsBackendMassbank
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MsBackendMassbank_1.4.0.tar.gz
StartedAt: 2022-10-18 20:43:26 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:45:01 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 94.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendMassbank.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MsBackendMassbank.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MsBackendMassbank_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MsBackendMassbank.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendMassbank/DESCRIPTION’ ... OK
* this is package ‘MsBackendMassbank’ version ‘1.4.0’
* 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 11.173  1.736   4.633
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MsBackendMassbank
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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 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


Attaching package: 'Spectra'

The following object is masked from 'package:ProtGenerics':

    addProcessing

> 
> library(RSQLite)
> dbc <- dbConnect(SQLite(), system.file("sql", "minimassbank.sqlite",
+                                        package = "MsBackendMassbank"))
> 
> test_check("MsBackendMassbank")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 346 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 346 ]
> 
> ## 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
> 
> res <- test_file(paste0(test_suite, "/test_spectra_variables.R"),
+                  reporter = check_reporter(), stop_on_failure = TRUE)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 75 ]
> 
> ## Test MsBackendMassbankSql
> be <- MsBackendMassbankSql()
> be <- backendInitialize(be, dbc)
> res <- test_file(paste0(test_suite, "/test_spectra_variables.R"),
+                  reporter = check_reporter(), stop_on_failure = TRUE)
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 61 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 61 ]
> 
> proc.time()
   user  system elapsed 
 27.628   3.158  27.437 

Example timings

MsBackendMassbank.Rcheck/MsBackendMassbank-Ex.timings

nameusersystemelapsed
MsBackendMassbank11.173 1.736 4.633
MsBackendMassbankSql0.7060.0320.738
metaDataBlocks0.0030.0000.003