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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 1341/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendMgf 1.12.0  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/MsBackendMgf
git_branch: RELEASE_3_19
git_last_commit: 923fb77
git_last_commit_date: 2024-04-30 11:31:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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


CHECK results for MsBackendMgf on nebbiolo1

To the developers/maintainers of the MsBackendMgf package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMgf.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: MsBackendMgf
Version: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MsBackendMgf.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MsBackendMgf_1.12.0.tar.gz
StartedAt: 2024-06-13 01:17:09 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 01:18:31 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 82.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendMgf.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MsBackendMgf.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MsBackendMgf_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MsBackendMgf.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendMgf/DESCRIPTION’ ... OK
* this is package ‘MsBackendMgf’ version ‘1.12.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MsBackendMgf.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MsBackendMgf
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, 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

> 
> fls <- dir(system.file("extdata", package = "MsBackendMgf"),
+            full.names = TRUE, pattern = "mgf$")[1:2]
> 
> test_check("MsBackendMgf")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 78 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 78 ]
> 
> ## 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 | peaks_variables                                                
✔ |          4 | peaks_variables

⠏ |          0 | spectra_subsetting                                             
⠹ |         13 | spectra_subsetting                                             
⠴ |         26 | spectra_subsetting                                             
⠏ |         30 | spectra_subsetting                                             
⠼ |         35 | spectra_subsetting                                             
⠙ |         42 | spectra_subsetting                                             
⠇ |         49 | spectra_subsetting                                             
✔ |         49 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠏ |         10 | spectra_variables                                              
⠧ |         28 | spectra_variables                                              
⠦ |         37 | spectra_variables                                              
⠸ |         54 | spectra_variables                                              
⠴ |         66 | spectra_variables                                              
⠋ |         71 | spectra_variables                                              
✔ |         78 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.5 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 131 ]

Your tests are pioneering!
> 
> proc.time()
   user  system elapsed 
  8.366   0.510   8.665 

Example timings

MsBackendMgf.Rcheck/MsBackendMgf-Ex.timings

nameusersystemelapsed
MsBackendMgf1.3400.0041.345
readMgf0.0440.0000.043