##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scpdata.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scpdata_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scpdata.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘scpdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scpdata’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘scpdata’ 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 whether startup messages can be suppressed ... 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:
  brunner2022.Rd: QFeatures, SingleCellExperiment
  cong2020AC.Rd: QFeatures, SingleCellExperiment
  derks2022.Rd: QFeatures, SingleCellExperiment
  dou2019_boosting.Rd: QFeatures, SingleCellExperiment
  dou2019_lysates.Rd: QFeatures, SingleCellExperiment
  dou2019_mouse.Rd: QFeatures, SingleCellExperiment
  gregoire2023_mixCTRL.Rd: QFeatures, SingleCellExperiment
  guise2024.Rd: QFeatures, SingleCellExperiment
  khan2023.Rd: QFeatures, SingleCellExperiment
  leduc2022_pSCoPE.Rd: QFeatures, SingleCellExperiment
  leduc2022_plexDIA.Rd: QFeatures, SingleCellExperiment
  liang2020_hela.Rd: QFeatures, SingleCellExperiment
  petrosius2023_AstralAML.Rd: QFeatures, SingleCellExperiment
  petrosius2023_mES.Rd: QFeatures, SingleCellExperiment
  schoof2021.Rd: QFeatures, SingleCellExperiment
  scpdata.Rd: SingleCellExperiment, QFeatures
  specht2019v2.Rd: QFeatures, SingleCellExperiment
  specht2019v3.Rd: QFeatures, SingleCellExperiment
  williams2020_lfq.Rd: QFeatures, SingleCellExperiment, AssayLinks
  williams2020_tmt.Rd: QFeatures, SingleCellExperiment, AssayLinks
  woo2022_lung.Rd: QFeatures, SingleCellExperiment, AssayLinks
  woo2022_macrophage.Rd: QFeatures, SingleCellExperiment, AssayLinks
  zhu2018MCP.Rd: QFeatures, SingleCellExperiment
  zhu2018NC_hela.Rd: QFeatures, SingleCellExperiment
  zhu2018NC_islets.Rd: QFeatures, SingleCellExperiment
  zhu2018NC_lysates.Rd: QFeatures, SingleCellExperiment
  zhu2019EL.Rd: QFeatures, SingleCellExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘hu2023_K562’ ‘hu2023_oocyte’ ‘krull2024’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-datasets.R:27:9'): all datasets are available ────────────────
  is(ds, "QFeatures") is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-datasets.R:27:9'): all datasets are available ────────────────
  is(ds, "QFeatures") is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 32 ]
  Error: Test failures
  Execution halted
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scpdata.Rcheck/00check.log’
for details.