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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Chromatograms.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Chromatograms_0.99.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Chromatograms.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Chromatograms/DESCRIPTION’ ... OK
* this is package ‘Chromatograms’ version ‘0.99.7’
* 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 ‘Chromatograms’ 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:
  processingQueue.Rd: backendParallelFactor
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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ChromBackendSpectra 4.343  1.349   7.303
Chromatograms       2.059  1.149   5.665
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Chromatograms.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Chromatograms
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Chromatograms’ ...
** this is package ‘Chromatograms’ version ‘0.99.7’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (Chromatograms)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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(Chromatograms)
Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> library(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


Attaching package: 'Spectra'

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

    reset

> library(MsBackendMetaboLights) ## remove MsbackendMetaboLights dependency for test and examples
> 
> ### Test ChromBackendSpectra
> be <- backendInitialize(MsBackendMetaboLights(),
+     mtblsId = "MTBLS39",
+     filePattern = c("63B.cdf")
+ )
Used data files from the assay's column "Raw Spectral Data File" since none were available in column "Derived Spectral Data File".
> s <- Spectra(be)
> s <- setBackend(s, MsBackendMemory())
> be_empty <- new("ChromBackendSpectra")
> be <- backendInitialize(be_empty, s)
> test_suite <- system.file("test_backends", "test_ChromBackend",
+     package = "Chromatograms"
+ )
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | chromData                                                      
⠇ |          9 | chromData                                                      
⠋ |         31 | chromData                                                      
⠹ |         33 | chromData                                                      
⠧ |         38 | chromData                                                      
✔ |         48 | chromData

⠏ |          0 | peaksData                                                      
⠸ |          4 | peaksData                                                      
⠙ |         12 | peaksData                                                      
⠏ |         20 | peaksData                                                      
⠙ |         22 | peaksData                                                      
✔ |         23 | peaksData

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 1.1 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 71 ]
> be_sp <- be
> c_sp <- Chromatograms(be)
> 
> ### Test ChrombackendMzR
> # fetch files
> MRM_file <- system.file("proteomics", "MRM-standmix-5.mzML.gz",
+     package = "msdata"
+ )
> be_empty <- ChromBackendMzR()
> be <- backendInitialize(be_empty, files = MRM_file, BPPARAM = SerialParam())
> 
> test_suite <- system.file("test_backends", "test_ChromBackend",
+     package = "Chromatograms"
+ )
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | chromData                                                      
⠧ |         18 | chromData                                                      
⠋ |         31 | chromData                                                      
⠹ |         33 | chromData                                                      
⠸ |         34 | chromData                                                      
⠴ |         36 | chromData                                                      
✔ |         48 | chromData [1.2s]

⠏ |          0 | peaksData                                                      
⠋ |          1 | peaksData                                                      
⠸ |          4 | peaksData                                                      
⠦ |          7 | peaksData                                                      
⠙ |         12 | peaksData                                                      
⠦ |         17 | peaksData                                                      
⠇ |         19 | peaksData                                                      
⠏ |         20 | peaksData                                                      
⠙ |         22 | peaksData                                                      
✔ |         23 | peaksData [1.8s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 3.0 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 71 ]
> 
> be_mzr <- be
> c_mzr <- Chromatograms(be)
> 
> ### Test ChrombackendMemory
> cdata <- data.frame(
+     msLevel = c(1L, 1L, 1L),
+     mz = c(112.2, 123.3, 134.4),
+     dataOrigin = c("mem1", "mem2", "mem3")
+ )
> pdata <- list(
+     data.frame(
+         rtime = c(12.4, 12.8, 13.2, 14.6),
+         intensity = c(123.3, 153.6, 2354.3, 243.4)
+     ),
+     data.frame(
+         rtime = c(45.1, 46.2),
+         intensity = c(100, 80.1)
+     ),
+     data.frame(
+         rtime = c(12.4, 12.8, 13.2, 14.6),
+         intensity = c(123.3, 153.6, 2354.3, 243.4)
+     )
+ )
> 
> be_empty <- new("ChromBackendMemory")
> be_cd <- backendInitialize(be_empty, chromData = cdata)
> be <- backendInitialize(be_empty, chromData = cdata, peaksData = pdata)
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | chromData                                                      
⠼ |         15 | chromData                                                      
⠇ |         29 | chromData                                                      
⠙ |         42 | chromData                                                      
⠴ |         56 | chromData                                                      
✔ |         63 | chromData

⠏ |          0 | peaksData                                                      
⠏ |         20 | peaksData                                                      
⠏ |         30 | peaksData                                                      
✔ |         30 | peaksData

══ Results ═════════════════════════════════════════════════════════════════════
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 93 ]
> 
> c_empty <- Chromatograms()
> c_full <- Chromatograms(be)
> 
> test_check("Chromatograms")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 579 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test_Chromatograms-plot.R:5:5',
  'test_Chromatograms-plot.R:52:5', 'test_Chromatograms-plot.R:79:5'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 579 ]
Deleting unused snapshots:
• Chromatograms-plot/plot-single-chromatogram-color.svg
• Chromatograms-plot/plot-single-chromatogram-infinite-xlim.svg
• Chromatograms-plot/plot-single-chromatogram-infinite-ylim.svg
• Chromatograms-plot/plot-single-chromatogram-xlim.svg
• Chromatograms-plot/plotchromatograms-asp05.svg
• Chromatograms-plot/plotchromatograms-asp2.svg
• Chromatograms-plot/plotchromatograms-color.svg
• Chromatograms-plot/plotchromatograms-multiple.svg
• Chromatograms-plot/plotchromatograms-one-color.svg
• Chromatograms-plot/plotchromatograms-one-title.svg
• Chromatograms-plot/plotchromatograms-toomany-color.svg
• Chromatograms-plot/plotchromatograms-toomany-main.svg
• Chromatograms-plot/plotchromatogramsoverlay-main-title.svg
• Chromatograms-plot/plotchromatogramsoverlay-no-axes.svg
• Chromatograms-plot/plotchromatogramsoverlay-one-sample.svg
• Chromatograms-plot/plotchromatogramsoverlay-xlim.svg
> 
> proc.time()
   user  system elapsed 
 27.658   1.832  36.328