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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1295/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendMgf 1.8.0  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MsBackendMgf
git_branch: RELEASE_3_17
git_last_commit: 2709cce
git_last_commit_date: 2023-04-25 11:27:26 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for MsBackendMgf on kjohnson2


To the developers/maintainers of the MsBackendMgf 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.

raw results


Summary

Package: MsBackendMgf
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMgf.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMgf_1.8.0.tar.gz
StartedAt: 2023-10-18 09:27:19 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 09:29:45 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 146.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendMgf.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMgf.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMgf_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MsBackendMgf.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 ‘MsBackendMgf/DESCRIPTION’ ... OK
* this is package ‘MsBackendMgf’ 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 ‘MsBackendMgf’ 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
MsBackendMgf 3.002  0.057   5.111
* 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

MsBackendMgf.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendMgf
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘MsBackendMgf’ ...
** 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 (MsBackendMgf)

Tests output

MsBackendMgf.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(MsBackendMgf)
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

> 
> test_check("MsBackendMgf")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 56 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 56 ]
> 
> ## Run tests defined in test suites from the Spectra package.
> fls <- dir(system.file("extdata", package = "MsBackendMgf"),
+            full.names = TRUE, pattern = "mgf$")[1:2]
> be <- MsBackendMgf()
> be <- backendInitialize(be, fls)
Start data import from 2 files ... done
> 
> ## Run the MsBackend spectra variable test suite
> test_suite <- system.file("test_backends", "test_MsBackend",
+                           package = "Spectra")
> 
> ## Run single test file.
> res <- test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S  OK | Context

⠏ |         0 | spectra_subsetting                                              
⠸ |         4 | spectra_subsetting                                              
⠋ |        11 | spectra_subsetting                                              
⠇ |        19 | spectra_subsetting                                              
⠴ |        26 | spectra_subsetting                                              
⠧ |        28 | spectra_subsetting                                              
⠏ |        30 | spectra_subsetting                                              
⠙ |        32 | spectra_subsetting                                              
⠼ |        35 | spectra_subsetting                                              
⠋ |        41 | spectra_subsetting                                              
⠸ |        44 | spectra_subsetting                                              
⠇ |        49 | spectra_subsetting                                              
✔ |        49 | spectra_subsetting [1.6s]

⠏ |         0 | spectra_variables                                               
⠴ |         6 | spectra_variables                                               
⠏ |        10 | spectra_variables                                               
⠦ |        17 | spectra_variables                                               
⠴ |        26 | spectra_variables                                               
⠙ |        32 | spectra_variables                                               
⠦ |        37 | spectra_variables                                               
⠼ |        45 | spectra_variables                                               
⠇ |        59 | spectra_variables                                               
⠦ |        67 | spectra_variables                                               
⠏ |        70 | spectra_variables                                               
⠧ |        78 | spectra_variables                                               
✔ |        78 | spectra_variables [1.5s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 3.1 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 127 ]

Your tests are pioneering!
> 
> proc.time()
   user  system elapsed 
 10.730   1.279  18.101 

Example timings

MsBackendMgf.Rcheck/MsBackendMgf-Ex.timings

nameusersystemelapsed
MsBackendMgf3.0020.0575.111
readMgf0.1430.0020.219