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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MsBackendMgf.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MsBackendMgf_1.15.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsBackendMgf.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendMgf/DESCRIPTION’ ... OK
* this is package ‘MsBackendMgf’ version ‘1.15.1’
* 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 ‘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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MsBackendMgf.Rd: MsBackendDataFrame, applyProcessing, SerialParam,
    Spectra
  readMgf.Rd: DataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MsBackendMgf.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL MsBackendMgf
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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)

R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
> 
> fls <- dir(system.file("extdata", package = "MsBackendMgf"),
+            full.names = TRUE, pattern = "mgf$")[1:2]
> 
> test_check("MsBackendMgf")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 86 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 86 ]
> 
> ## 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                                             
⠇ |         19 | spectra_subsetting                                             
⠇ |         29 | spectra_subsetting                                             
⠴ |         36 | spectra_subsetting                                             
⠋ |         51 | spectra_subsetting                                             
✔ |         56 | spectra_subsetting

⠏ |          0 | spectra_variables                                              
⠦ |         17 | spectra_variables                                              
⠦ |         37 | spectra_variables                                              
⠇ |         59 | spectra_variables                                              
⠴ |         76 | spectra_variables                                              
✔ |         78 | spectra_variables

══ Results ═════════════════════════════════════════════════════════════════════
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
> 
> proc.time()
   user  system elapsed 
  6.350   0.626   6.779