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This page was generated on 2023-03-01 07:38:45 -0000 (Wed, 01 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4266
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CHECK results for MsBackendMsp on kunpeng1


To the developers/maintainers of the MsBackendMsp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMsp.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 1257/2171HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendMsp 1.3.1  (landing page)
Johannes Rainer
Snapshot Date: 2023-02-27 07:53:22 -0000 (Mon, 27 Feb 2023)
git_url: https://git.bioconductor.org/packages/MsBackendMsp
git_branch: master
git_last_commit: 4d11132
git_last_commit_date: 2023-01-18 12:07:47 -0000 (Wed, 18 Jan 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: MsBackendMsp
Version: 1.3.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MsBackendMsp.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MsBackendMsp_1.3.1.tar.gz
StartedAt: 2023-02-28 09:04:45 -0000 (Tue, 28 Feb 2023)
EndedAt: 2023-02-28 09:06:26 -0000 (Tue, 28 Feb 2023)
EllapsedTime: 101.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendMsp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MsBackendMsp.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MsBackendMsp_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MsBackendMsp.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendMsp/DESCRIPTION’ ... OK
* this is package ‘MsBackendMsp’ version ‘1.3.1’
* 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 ‘MsBackendMsp’ 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
* 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 ...
  ‘MsBackendMsp.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

MsBackendMsp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MsBackendMsp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘MsBackendMsp’ ...
** 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 (MsBackendMsp)

Tests output

MsBackendMsp.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(MsBackendMsp)
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 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

> 
> ## Run specific (backend) package tests
> test_check("MsBackendMsp")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 55 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 55 ]
> 
> ## Run additional tests from Spectra:
> test_suite <- system.file("test_backends", "test_MsBackend",
+                           package = "Spectra")
> 
> fls <- system.file("extdata", "minimona.msp", package = "MsBackendMsp")
> be <- MsBackendMsp()
> be <- backendInitialize(
+     be, fls, mapping = spectraVariableMapping(MsBackendMsp(), "mona"))
Start data import from 1 files ... done
> 
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S  OK | Context

⠏ |         0 | spectra_subsetting                                              
⠋ |         1 | spectra_subsetting                                              
⠋ |        11 | spectra_subsetting                                              
⠏ |        20 | spectra_subsetting                                              
⠇ |        29 | spectra_subsetting                                              
⠏ |        40 | spectra_subsetting                                              
⠇ |        49 | spectra_subsetting                                              
⠋ |        61 | spectra_subsetting                                              
⠹ |        73 | spectra_subsetting                                              
⠼ |        85 | spectra_subsetting                                              
⠸ |        94 | spectra_subsetting                                              
⠴ |        96 | spectra_subsetting                                              
⠧ |        98 | spectra_subsetting                                              
⠏ |       100 | spectra_subsetting                                              
⠙ |       102 | spectra_subsetting                                              
⠸ |       104 | spectra_subsetting                                              
⠴ |       106 | spectra_subsetting                                              
⠧ |       108 | spectra_subsetting                                              
⠏ |       110 | spectra_subsetting                                              
⠙ |       112 | spectra_subsetting                                              
⠸ |       114 | spectra_subsetting                                              
⠴ |       116 | spectra_subsetting                                              
⠧ |       118 | spectra_subsetting                                              
⠏ |       120 | spectra_subsetting                                              
⠙ |       122 | spectra_subsetting                                              
⠸ |       124 | spectra_subsetting                                              
⠧ |       128 | spectra_subsetting                                              
⠸ |       134 | spectra_subsetting                                              
⠋ |       141 | spectra_subsetting                                              
✔ |       141 | spectra_subsetting [3.5s]

⠏ |         0 | spectra_variables                                               
⠦ |         7 | spectra_variables                                               
⠧ |        18 | spectra_variables                                               
⠋ |        31 | spectra_variables                                               
⠦ |        37 | spectra_variables                                               
⠼ |        45 | spectra_variables                                               
⠇ |        59 | spectra_variables                                               
⠧ |        68 | spectra_variables                                               
⠴ |        76 | spectra_variables                                               
✔ |        78 | spectra_variables [1.0s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 4.5 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 219 ]
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
 14.664   1.827  15.813

Example timings

MsBackendMsp.Rcheck/MsBackendMsp-Ex.timings

nameusersystemelapsed
MsBackendMsp2.3930.4262.769
readMsp0.2980.0280.326