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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scAnnotatR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings scAnnotatR_1.10.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/scAnnotatR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scAnnotatR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scAnnotatR' version '1.10.0'
* 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 whether package 'scAnnotatR' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ape::where' by 'dplyr::where' when loading 'scAnnotatR'
See 'F:/biocbuild/bbs-3.19-bioc/meat/scAnnotatR.Rcheck/00install.out' for details.
* 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 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'scAnnotatR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plant_tree
> ### Title: Plant tree from list of models
> ### Aliases: plant_tree
> 
> ### ** Examples
> 
> 
> # to create the tree of classifiers 
> # (in this example, based on default classifiers)
> plant_tree()
downloading 1 resources
retrieving 1 resource
loading from cache
Warning: file '2414424e1006_102652' has magic number 'chain'
  Use of save versions prior to 2 is deprecated
Error: failed to load resource
  name: AH95906
  title: Pretrained models
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted
* 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:
       ▆
    1. └─scAnnotatR::load_models("default") at test_class.R:21:3
    2.   └─scAnnotatR:::download_data_file()
    3.     ├─query[["AH95906"]]
    4.     └─query[["AH95906"]]
    5.       └─AnnotationHub (local) .local(x, i, j = j, ...)
    6.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
    7.           └─base::tryCatch(...)
    8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.                 └─value[[3L]](cond)
  
  [ FAIL 3 | WARN 5 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING
See
  'F:/biocbuild/bbs-3.19-bioc/meat/scAnnotatR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL scAnnotatR
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'scAnnotatR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ape::where' by 'dplyr::where' when loading 'scAnnotatR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ape::where' by 'dplyr::where' when loading 'scAnnotatR'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ape::where' by 'dplyr::where' when loading 'scAnnotatR'
** testing if installed package keeps a record of temporary installation path
* DONE (scAnnotatR)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(scAnnotatR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp

Attaching package: 'SeuratObject'

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

    intersect, t

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

Attaching package: 'BiocGenerics'

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

    intersect

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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

Attaching package: 'IRanges'

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

    %over%

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

    windows

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: 'SummarizedExperiment'

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

    Assays

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

    Assays

Warning message:
replacing previous import 'ape::where' by 'dplyr::where' when loading 'scAnnotatR' 
> 
> test_check("scAnnotatR")
No model found in provided path to models[ FAIL 3 | WARN 5 | SKIP 0 | PASS 10 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_class.R:5:3'): Set cell type changes cell type ─────────────────
Error: failed to load resource
  name: AH95906
  title: Pretrained models
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─scAnnotatR::load_models("default") at test_class.R:5:3
  2.   └─scAnnotatR:::download_data_file()
  3.     ├─query[["AH95906"]]
  4.     └─query[["AH95906"]]
  5.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  7.           └─base::tryCatch(...)
  8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.                 └─value[[3L]](cond)
── Error ('test_class.R:13:3'): Set probability threshold changes probability threshold ──
Error: failed to load resource
  name: AH95906
  title: Pretrained models
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─scAnnotatR::load_models("default") at test_class.R:13:3
  2.   └─scAnnotatR:::download_data_file()
  3.     ├─query[["AH95906"]]
  4.     └─query[["AH95906"]]
  5.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  7.           └─base::tryCatch(...)
  8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.                 └─value[[3L]](cond)
── Error ('test_class.R:21:3'): Set classifier changes classifier and marker genes ──
Error: failed to load resource
  name: AH95906
  title: Pretrained models
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─scAnnotatR::load_models("default") at test_class.R:21:3
  2.   └─scAnnotatR:::download_data_file()
  3.     ├─query[["AH95906"]]
  4.     └─query[["AH95906"]]
  5.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  7.           └─base::tryCatch(...)
  8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.                 └─value[[3L]](cond)

[ FAIL 3 | WARN 5 | SKIP 0 | PASS 10 ]
Error: Test failures
Execution halted