##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRNAseq_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scRNAseq.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 ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scRNAseq’ 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:
  AztekinTailData.Rd: reducedDims, SingleCellExperiment-class
  BachMammaryData.Rd: rowRanges, SingleCellExperiment-class
  BacherTCellData.Rd: colData, rowRanges, SingleCellExperiment-class
  BaronPancreasData.Rd: rowRanges, SingleCellExperiment-class
  BhaduriOrganoidData.Rd: rowRanges, SingleCellExperiment-class
  BuettnerESCData.Rd: altExps, rowRanges, SingleCellExperiment-class
  BunisHSPCData.Rd: colData, SingleCellExperiment-class
  CampbellBrainData.Rd: rowRanges, SingleCellExperiment-class
  ChenBrainData.Rd: rowRanges, SingleCellExperiment-class
  DarmanisBrainData.Rd: rowRanges, SingleCellExperiment-class
  ERCCSpikeInConcentrations.Rd: DataFrame-class
  ErnstSpermatogenesisData.Rd: rowRanges, SingleCellExperiment-class
  FletcherOlfactoryData.Rd: colData, rowRanges,
    SingleCellExperiment-class
  GiladiHSCData.Rd: colData, rowRanges, SingleCellExperiment-class
  GrunHSCData.Rd: rowRanges, SingleCellExperiment-class
  GrunPancreasData.Rd: altExps, rowRanges, SingleCellExperiment-class
  HeOrganAtlasData.Rd: rowRanges, SingleCellExperiment-class
  HermannSpermatogenesisData.Rd: SingleCellExperiment-class
  HuCortexData.Rd: rowRanges, SingleCellExperiment-class
  JessaBrainData.Rd: colData, rowRanges, SingleCellExperiment-class
  KolodziejczykESCData.Rd: altExps, rowRanges,
    SingleCellExperiment-class
  KotliarovPBMCData.Rd: rowRanges, SingleCellExperiment-class
  LaMannoBrainData.Rd: rowRanges, SingleCellExperiment-class
  LawlorPancreasData.Rd: SingleCellExperiment-class
  LedergorMyelomaData.Rd: rowRanges, SingleCellExperiment-class
  LengESCData.Rd: rowRanges, SingleCellExperiment-class
  LunSpikeInData.Rd: altExp, altExps, rowRanges,
    SingleCellExperiment-class
  MacoskoRetinaData.Rd: rowRanges, SingleCellExperiment-class
  MairPBMCData.Rd: rowRanges, SingleCellExperiment-class
  MarquesBrainData.Rd: rowRanges, SingleCellExperiment-class
  MessmerESCData.Rd: altExps, rowRanges, SingleCellExperiment-class
  MuraroPancreasData.Rd: altExps, rowRanges, SingleCellExperiment-class
  NestorowaHSCData.Rd: colData, reducedDims, altExps, rowRanges,
    SingleCellExperiment-class
  NowakowskiCortexData.Rd: rowRanges, SingleCellExperiment-class,
    reducedDims
  PaulHSCData.Rd: rowRanges, SingleCellExperiment-class
  PollenGliaData.Rd: rowRanges, SingleCellExperiment-class
  ReprocessedData.Rd: altExps, metadata, rowRanges,
    SingleCellExperiment-class
  RichardTCellData.Rd: altExps, rowRanges, SingleCellExperiment-class
  RomanovBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class
  SegerstolpePancreasData.Rd: altExps, rowData, rowRanges,
    SingleCellExperiment-class
  ShekharRetinaData.Rd: rowRanges, SingleCellExperiment-class
  StoeckiusHashingData.Rd: rowRanges, SingleCellExperiment-class
  TasicBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class
  UsoskinBrainData.Rd: rowRanges, SingleCellExperiment-class
  WuKidneyData.Rd: rowRanges, SingleCellExperiment-class
  XinPancreasData.Rd: rowRanges, SingleCellExperiment-class
  ZeiselBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class
  ZeiselNervousData.Rd: rowRanges, SingleCellExperiment-class
  ZhaoImmuneLiverData.Rd: rowRanges, colData,
    SingleCellExperiment-class
  ZhongPrefrontalData.Rd: rowRanges, SingleCellExperiment-class
  ZilionisLungData.Rd: rowRanges, colData, reducedDim,
    SingleCellExperiment-class
  countErccMolecules.Rd: DataFrame-class
  fetchDataset.Rd: ReloadedArray-class, dgCMatrix-class, readObject,
    SummarizedExperiment-class, uploadDirectory
  listDatasets.Rd: DataFrame-class
  polishDataset.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, altExp
  saveDataset.Rd: SummarizedExperiment-class, fetchMetadataSchema,
    uploadDirectory
  searchDatasets.Rd: gypsum.search.clause, fetchMetadataDatabase,
    DataFrame-class, translateTextQuery
  surveyDatasets.Rd: fetchMetadataDatabase, DataFrame-class
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
BhaduriOrganoidData      22.843  8.279  31.393
BacherTCellData          16.074  5.565  22.697
ZeiselNervousData        14.879  6.246  22.693
HeOrganAtlasData         12.230  6.627  19.366
ErnstSpermatogenesisData  9.789  4.272  15.265
JessaBrainData            8.651  4.038  13.785
StoeckiusHashingData      8.445  1.488  10.720
BachMammaryData           6.814  1.484   9.277
GiladiHSCData             4.692  2.324   7.600
LunSpikeInData            5.821  1.128   7.446
AztekinTailData           6.209  0.674   7.103
ZhaoImmuneLiverData       4.663  2.146   7.637
ZilionisLungData          4.094  1.220   5.911
NestorowaHSCData          4.125  0.903   5.443
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘scRNAseq’ ...
** 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 (scRNAseq)

R Under development (unstable) (2024-10-21 r87258) -- "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(scRNAseq)
Loading required package: SingleCellExperiment
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

> test_check("scRNAseq")
[ FAIL 0 | WARN 35 | SKIP 1 | PASS 176 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• is.null(gh_token) is TRUE (1): 'test-uploadDirectory.R:59:5'

[ FAIL 0 | WARN 35 | SKIP 1 | PASS 176 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
264.452  46.818 326.790