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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:QFeatures.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings QFeatures_1.17.5.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘QFeatures/DESCRIPTION’ ... OK
* this is package ‘QFeatures’ version ‘1.17.5’
* 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 ‘QFeatures’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’
  ‘MultiAssayExperiment:::.sampleMapFromData’
  See the note in ?`:::` about the use of this operator.
* 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:
  QFeatures-aggregate.Rd: sparseMatrix, adjacencyMatrix
  QFeatures-filtering.Rd: AnnotationFilter
  readQFeatures.Rd: SummarizedExperiment
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘QFeatures-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readQFeaturesFromDIANN
> ### Title: Read DIA-NN output as a QFeatures objects
> ### Aliases: readQFeaturesFromDIANN
> 
> ### ** Examples
> 
> 
> x <- read.delim(MsDataHub::benchmarkingDIA.tsv())
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
loading from cache
> x[["File.Name"]] <- x[["Run"]]
> 
> #################################
> ## Label-free multi-set case
> 
> ## using default arguments
> readQFeaturesFromDIANN(x)
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Splitting data in runs.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
An instance of class QFeatures containing 24 set(s):
 [1] RD139_Overlap_UPS1_0_1fmol_inj1: SummarizedExperiment with 28980 rows and 1 columns 
 [2] RD139_Overlap_UPS1_0_1fmol_inj2: SummarizedExperiment with 29495 rows and 1 columns 
 [3] RD139_Overlap_UPS1_0_1fmol_inj3: SummarizedExperiment with 29210 rows and 1 columns 
 ...
 [22] RD139_Overlap_UPS1_5fmol_inj1: SummarizedExperiment with 30941 rows and 1 columns 
 [23] RD139_Overlap_UPS1_5fmol_inj2: SummarizedExperiment with 30321 rows and 1 columns 
 [24] RD139_Overlap_UPS1_5fmol_inj3: SummarizedExperiment with 24168 rows and 1 columns 
> 
> ## use the precursor identifier as assay rownames
> readQFeaturesFromDIANN(x, fnames = "Precursor.Id") |>
+     rownames()
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Splitting data in runs.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
Setting assay rownames.
CharacterList of length 24
[["RD139_Overlap_UPS1_0_1fmol_inj1"]] AAAAIAGELGLEFK2 ... YYTETEGALR2
[["RD139_Overlap_UPS1_0_1fmol_inj2"]] AAAAEIAVK1 ... YYTETEGALR2
[["RD139_Overlap_UPS1_0_1fmol_inj3"]] AAAAIAGELGLEFK2 ... YYTETEGALR2
[["RD139_Overlap_UPS1_0_25fmol_inj1"]] AAAAEIAVK1 AAAAEIAVK2 ... YYTETEGALR2
[["RD139_Overlap_UPS1_0_25fmol_inj2"]] AAAAEIAVK1 ... YYTETEGALR2
[["RD139_Overlap_UPS1_0_25fmol_inj3"]] AAAAIAGELGLEFK2 ... YYTETEGALR2
[["RD139_Overlap_UPS1_10fmol_inj1"]] AAAAEIAVK1 AAAAIAGELGLEFK2 ... YYTLEEIQK2
[["RD139_Overlap_UPS1_10fmol_inj2"]] AAAAEIAVK1 AAAAIAGELGLEFK2 ... YYTLEEIQK2
[["RD139_Overlap_UPS1_10fmol_inj3"]] AAAAEIAVK1 AAAAIAGELGLEFK2 ... YYTLEEIQK2
[["RD139_Overlap_UPS1_1fmol_inj1"]] AAAAEIAVK1 AAAAIAGELGLEFK2 ... YYTETEGALR2
...
<14 more elements>
> 
> ## with a colData (and default arguments)
> cd <- data.frame(sampleInfo = LETTERS[1:24],
+                  quantCols = "Ms1.Area",
+                  runCol = unique(x[["File.Name"]]))
> readQFeaturesFromDIANN(x, colData = cd)
Checking arguments.
Loading data as a 'SummarizedExperiment' object.
Splitting data in runs.
Formatting sample annotations (colData).
Formatting data as a 'QFeatures' object.
An instance of class QFeatures containing 24 set(s):
 [1] RD139_Overlap_UPS1_0_1fmol_inj1: SummarizedExperiment with 28980 rows and 1 columns 
 [2] RD139_Overlap_UPS1_0_1fmol_inj2: SummarizedExperiment with 29495 rows and 1 columns 
 [3] RD139_Overlap_UPS1_0_1fmol_inj3: SummarizedExperiment with 29210 rows and 1 columns 
 ...
 [22] RD139_Overlap_UPS1_5fmol_inj1: SummarizedExperiment with 30941 rows and 1 columns 
 [23] RD139_Overlap_UPS1_5fmol_inj2: SummarizedExperiment with 30321 rows and 1 columns 
 [24] RD139_Overlap_UPS1_5fmol_inj3: SummarizedExperiment with 24168 rows and 1 columns 
> 
> #################################
> ## mTRAQ multi-set case
> 
> x2 <- read.delim(MsDataHub::Report.Derks2022.plexDIA.tsv())
see ?MsDataHub and browseVignettes('MsDataHub') for documentation
downloading 1 resources
retrieving 1 resource
Warning: download failed
  web resource path: ‘https://experimenthub.bioconductor.org/fetch/9552’
  local file path: ‘/home/rapidbuild/.cache/R/ExperimentHub/file6f2c142d9fd5d’
  reason: Failed writing received data to disk/application [zenodo.org]: Failure writing output to destination
Warning: bfcdownload() failed
  rid: BFC25
  file: ‘https://experimenthub.bioconductor.org/fetch/9552’
  reason: download failed
Warning: download failed
  hub path: ‘https://experimenthub.bioconductor.org/fetch/9552’
  cache resource: ‘EH9486 : 9552’
  reason: download failed; see warnings()
Error loading resource.
 attempting to re-download
downloading 1 resources
retrieving 1 resource
Warning: download failed
  hub path: ‘https://experimenthub.bioconductor.org/fetch/9552’
  cache resource: ‘EH9486 : 9552’
  reason: database or disk is full
Error: failed to load resource
  name: EH9486
  title: Report.Derks2022.plexDIA.tsv
  reason: 1 resources failed to download
Execution halted
* 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 ... ERROR
Error(s) in re-building vignettes:

--- re-building ‘QFeatures.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/QFeatures_files/figure-html/featuresplot-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/QFeatures_files/figure-html/plotstat3-1.png" but not available.
Write Error
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/QFeatures_files/figure-html/plotstat-1.png" but not available.
--- finished re-building ‘QFeatures.Rmd’

--- re-building ‘Visualization.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/plot2-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/plot_assay-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/hist_rowData-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/ggplot_rowData-1.png" but not available.
Write Error
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/ComplexHeatmap-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/ComplexHeatmap_annotations-1.png" but not available.
Write Error
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/vign_test/QFeatures/vignettes/Visualization_files/figure-html/longFormat-1.png" but not available.
Write Error
--- finished re-building ‘Visualization.Rmd’

--- re-building ‘read_QFeatures.Rmd’ using rmarkdown
--- finished re-building ‘read_QFeatures.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
!pdfTeX error: pdflatex: fwrite() failed
 ==> Fatal error occurred, no output PDF file produced!
* checking PDF version of manual without index ... ERROR
* DONE

Status: 3 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL QFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘QFeatures’ ...
** this is package ‘QFeatures’ version ‘1.17.5’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘sweep’ in package ‘QFeatures’
** 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 (QFeatures)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("QFeatures")
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
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

Loading required package: S4Vectors

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: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'QFeatures'

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

    sweep

> 
> test_check("QFeatures")
AssayLink for assay <foo>
[from:NA|fcol:NA|hits:0]
AssayLinks of length 0
names(0): 
A empty instance of class QFeatures 
An instance of class QFeatures containing 1 set(s):
 [1] psms: SummarizedExperiment with 10 rows and 2 columns 
[ FAIL 0 | WARN 44 | SKIP 0 | PASS 784 ]

[ FAIL 0 | WARN 44 | SKIP 0 | PASS 784 ]
> 
> proc.time()
   user  system elapsed 
 46.883   0.873  49.450