##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:singleCellTK.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings singleCellTK_2.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 'singleCellTK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'singleCellTK' version '2.13.1'
* 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 'singleCellTK' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    shiny     2.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... NOTE
checkRd: (-1) dedupRowNames.Rd:10: Lost braces
    10 | \item{x}{A matrix like or /linkS4class{SingleCellExperiment} object, on which
       |                                       ^
checkRd: (-1) dedupRowNames.Rd:14: Lost braces
    14 | /linkS4class{SingleCellExperiment} object. When set to \code{TRUE}, will
       |             ^
checkRd: (-1) dedupRowNames.Rd:22: Lost braces
    22 | By default, a matrix or /linkS4class{SingleCellExperiment} object
       |                                     ^
checkRd: (-1) dedupRowNames.Rd:24: Lost braces
    24 | When \code{x} is a /linkS4class{SingleCellExperiment} and \code{as.rowData}
       |                                ^
checkRd: (-1) runEmptyDrops.Rd:66: Lost braces
    66 | provided \\linkS4class{SingleCellExperiment} object.
       |                       ^
checkRd: (-1) runSCMerge.Rd:44: Lost braces
    44 | construct pseudo-replicates. The length of code{kmeansK} needs to be the same
       |                                                ^
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'singleCellTK-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertSeuratToSCE
> ### Title: convertSeuratToSCE Converts the input seurat object to a sce
> ###   object
> ### Aliases: convertSeuratToSCE
> 
> ### ** Examples
> 
> data(scExample, package = "singleCellTK")
> seurat <- convertSCEToSeurat(sce)
> sce <- convertSeuratToSCE(seurat)
Error in normarg_assays(assays, as.null.if.no.assay = TRUE) : 
  no slot of name "counts" for this object of class "Assay5"
Calls: convertSeuratToSCE ... SingleCellExperiment -> SummarizedExperiment -> normarg_assays
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'spelling.R'
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   └─singleCellTK:::.updateAssaySCE(...)
   3.     └─methods::slot(...)
  ── Error ('test-trajectory.R:7:1'): (code run outside of `test_that()`) ────────
  Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), 
      seuratDataSlot)`: no slot of name "data" for this object of class "Assay5"
  Backtrace:
      ▆
   1. └─singleCellTK::runNormalization(...) at test-trajectory.R:7:1
   2.   └─singleCellTK::runSeuratNormalizeData(...)
   3.     └─singleCellTK:::.updateAssaySCE(...)
   4.       └─methods::slot(...)
  
  [ FAIL 7 | WARN 22 | SKIP 0 | PASS 143 ]
  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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'singleCellTK' ...
** using staged installation
** R
** data
** exec
** 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
Warning in fun(libname, pkgname) :
  Package 'singleCellTK' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'singleCellTK' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.15    0.09    0.25 

R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
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(singleCellTK)
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 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: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

Loading required package: SingleCellExperiment
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep


Attaching package: 'singleCellTK'

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

    plotPCA

Warning message:
In fun(libname, pkgname) :
  Package 'singleCellTK' is deprecated and will be removed from
  Bioconductor version 3.20
> 
> test_check("singleCellTK")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 0 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Uploading data to Enrichr... Done.
  Querying HDSigDB_Human_2021... Done.
Parsing results... Done.
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 7 | WARN 22 | SKIP 0 | PASS 143 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-computeHeatmap.R:8:3'): Testing computeHeatmap.R ───────────────
Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), 
    seuratDataSlot)`: no slot of name "data" for this object of class "Assay5"
Backtrace:
    ▆
 1. └─singleCellTK::runSeuratNormalizeData(sce) at test-computeHeatmap.R:8:3
 2.   └─singleCellTK:::.updateAssaySCE(...)
 3.     └─methods::slot(...)
── Error ('test-dimensionReduction.R:8:1'): (code run outside of `test_that()`) ──
Error in `(function (cl, name, valueClass) 
{
    ClassDef <- getClass(cl)
    slotClass <- ClassDef@slots[[name]]
    if (is.null(slotClass)) 
        stop(gettextf("%s is not a slot in class %s", sQuote(name), 
            dQuote(cl)), domain = NA)
    if (.identC(slotClass, valueClass)) 
        return(TRUE)
    ok <- possibleExtends(valueClass, slotClass, ClassDef2 = getClassDef(slotClass, 
        where = .classEnv(ClassDef)))
    if (isFALSE(ok)) 
        stop(gettextf("assignment of an object of class %s is not valid for @%s in an object of class %s; is(value, \"%s\") is not TRUE", 
            dQuote(valueClass), sQuote(name), dQuote(cl), slotClass), 
            domain = NA)
    TRUE
})(structure("Assay5", package = "SeuratObject"), "counts", structure("dgCMatrix", package = "Matrix"))`: 'counts' is not a slot in class "Assay5"
Backtrace:
    ▆
 1. └─singleCellTK::runFeatureSelection(sce, useAssay = "counts") at test-dimensionReduction.R:8:1
 2.   ├─base::do.call("runSeuratFindHVG", args = params)
 3.   └─singleCellTK::runSeuratFindHVG(...)
 4.     └─singleCellTK:::.addSeuratToMetaDataSCE(inSCE, seuratObject)
 5.       └─methods (local) `<fn>`(`<chr>`, "counts", `<chr>`)
── Error ('test-featureSelection.R:5:1'): (code run outside of `test_that()`) ──
Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), 
    seuratDataSlot)`: no slot of name "data" for this object of class "Assay5"
Backtrace:
    ▆
 1. └─singleCellTK::runSeuratNormalizeData(sce) at test-featureSelection.R:5:1
 2.   └─singleCellTK:::.updateAssaySCE(...)
 3.     └─methods::slot(...)
── Error ('test-misc.R:64:3'): Testing runGSVA ─────────────────────────────────
Error in `(function (cond) 
.Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').", 
    call = GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set), 
    old = c("::", "GSVA", "gsva"), new = "gsva()", package = "GSVA"), class = c("defunctError", 
"error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 't': Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Backtrace:
    ▆
 1. ├─singleCellTK::runGSVA(...) at test-misc.R:64:3
 2. │ ├─base::t(GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set))
 3. │ ├─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set)
 4. │ └─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set)
 5. │   └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').")
 6. │     └─base::stop(...)
 7. └─base (local) `<fn>`(`<dfnctErr>`)
── Error ('test-pathway.R:36:5'): Testing GSVA ─────────────────────────────────
Error in `(function (cond) 
.Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').", 
    call = GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set), 
    old = c("::", "GSVA", "gsva"), new = "gsva()", package = "GSVA"), class = c("defunctError", 
"error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 't': Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Backtrace:
    ▆
 1. ├─singleCellTK::runGSVA(sce, geneSetCollectionName = "GeneSetCollection") at test-pathway.R:36:5
 2. │ ├─base::t(GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set))
 3. │ ├─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set)
 4. │ └─GSVA::gsva(as.matrix(expData(inSCE, useAssay)), gene.Set)
 5. │   └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').")
 6. │     └─base::stop(...)
 7. └─base (local) `<fn>`(`<dfnctErr>`)
── Error ('test-seuratFunctions.R:9:3'): Testing standard seurat workflow ──────
Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), 
    seuratDataSlot)`: no slot of name "data" for this object of class "Assay5"
Backtrace:
    ▆
 1. └─singleCellTK::runSeuratNormalizeData(sce) at test-seuratFunctions.R:9:3
 2.   └─singleCellTK:::.updateAssaySCE(...)
 3.     └─methods::slot(...)
── Error ('test-trajectory.R:7:1'): (code run outside of `test_that()`) ────────
Error in `methods::slot(Seurat::GetAssay(seuratObject, seuratAssaySlot), 
    seuratDataSlot)`: no slot of name "data" for this object of class "Assay5"
Backtrace:
    ▆
 1. └─singleCellTK::runNormalization(...) at test-trajectory.R:7:1
 2.   └─singleCellTK::runSeuratNormalizeData(...)
 3.     └─singleCellTK:::.updateAssaySCE(...)
 4.       └─methods::slot(...)

[ FAIL 7 | WARN 22 | SKIP 0 | PASS 143 ]
Error: Test failures
Execution halted