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### Running command:
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###   /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_1.17.4.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 ‘1.17.4’
* 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/file19fe1e5ebfd3e6’
  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
  web resource path: ‘https://experimenthub.bioconductor.org/fetch/9552’
  local file path: ‘/home/rapidbuild/.cache/R/ExperimentHub/file19fe1e65ed4304’
  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: 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’ ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking tests ... 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/QFeatures.Rcheck/00check.log’
for details.