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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CDI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CDI_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/CDI.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CDI/DESCRIPTION’ ... OK
* this is package ‘CDI’ version ‘1.9.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CDI’ 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 ... NOTE
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Package accepted by Bioconductor (2023-06-30)
* 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 ... NOTE
checkRd: (-1) one_batch_matrix_label_df.Rd:18: Lost braces; missing escapes or markup?
    18 | be {2,3,..., 7}. 
       |    ^
checkRd: (-1) two_batch_matrix_label_df.Rd:20: Lost braces; missing escapes or markup?
    20 | The number of clusters are set to be {2,3,..., 10}. 
       |                                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculate_CDI.Rd: BiocParallelParam, SerialParam
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 ‘CDI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_CDI
> ### Title: Clustering Deviance Index (CDI)
> ### Aliases: calculate_CDI
> 
> ### ** Examples
> 
> ng <- 100; nc <- 100
> set.seed(1)
> 
> # count matrix
> X <- cbind(
+ 	matrix(
+ 		c(rnbinom(ng*nc/4, size = 1, mu = 0.1),
+ 			rnbinom(ng*nc/4, size = 1, mu = 0.5)),
+ 		nrow = ng,
+ 		byrow = TRUE),
+ 	matrix(
+ 		c(rnbinom(ng*nc/4, size = 1, mu = 1),
+ 			rnbinom(ng*nc/4, size = 1, mu = 0.5)),
+ 		nrow = ng,
+ 		byrow = TRUE))
> colnames(X) <- paste0('c', seq_len(nc))
> rownames(X) <- paste0('g', seq_len(ng))
> 
> # batch label
> Batches <- rep(seq_len(2), nc/2)
> 
> # cell clustering labels
> Method1_k2 <- rep(seq_len(2), c(nc/2,nc/2))
> Method1_k3 <- sample(seq_len(3), nc, replace = TRUE)
> label_df <- data.frame(
+ 	Method1_k2 = Method1_k2,
+ 	Method1_k3 = Method1_k3)
> 
> ## select feature genes (see feature_gene_selection function)
> selected_genes <- seq_len(30)
> 
> ## calculate size factor (see size_factor function)
> size_factor_vec <- rep(1, nc)
> 
> calculate_CDI(
+  X = X[selected_genes, ],
+ 	cand_lab_df = label_df,
+ 	cell_size_factor = size_factor_vec,
+ 	batch_label = Batches)
           Label_name Cluster_method  CDI_AIC  CDI_BIC neg_llk_val N_cluster
Method1_k2 Method1_k2        Method1 5236.177 5548.797    2498.089         2
Method1_k3 Method1_k3        Method1 5967.536 6436.467    2803.768         3
> 
> ## Input: SingleCellExperiment object
> library(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: Seqinfo
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

> sim_sce <- SingleCellExperiment(
+   list(count = X),
+   colData = data.frame(
+     Cell_name = colnames(X),
+ 		 batch = Batches),
+ 	 rowData = data.frame(
+ 	   Gene_name = rownames(X)))
> 
> calculate_CDI(
+  	X = sim_sce,
+  	feature_gene_index = selected_genes, 
+  	cand_lab_df = label_df,
+  	cell_size_factor = size_factor_vec,
+  	count_slot = "count",
+  	batch_slot = "batch")
           Label_name Cluster_method  CDI_AIC  CDI_BIC neg_llk_val N_cluster
Method1_k2 Method1_k2        Method1 5236.177 5548.797    2498.089         2
Method1_k3 Method1_k3        Method1 5967.536 6436.467    2803.768         3
> 
> ## Input: Seurat object
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp

Attaching package: ‘sp’

The following object is masked from ‘package:IRanges’:

    %over%


Attaching package: ‘SeuratObject’

The following object is masked from ‘package:SummarizedExperiment’:

    Assays

The following object is masked from ‘package:GenomicRanges’:

    intersect

The following object is masked from ‘package:Seqinfo’:

    intersect

The following object is masked from ‘package:IRanges’:

    intersect

The following object is masked from ‘package:S4Vectors’:

    intersect

The following object is masked from ‘package:BiocGenerics’:

    intersect

The following objects are masked from ‘package:base’:

    intersect, t


Attaching package: ‘Seurat’

The following object is masked from ‘package:SummarizedExperiment’:

    Assays

> library(SeuratObject)
> sim_seurat <- CreateSeuratObject(counts = as.data.frame(X))
Warning: Data is of class data.frame. Coercing to dgCMatrix.
> sim_seurat <- AddMetaData(sim_seurat, colnames(X), "Cell_name")
> sim_seurat <- AddMetaData(sim_seurat, Batches, "batch")
> 
> calculate_CDI(
+ 	X = sim_seurat,
+ 	feature_gene_index = selected_genes,
+ 	cand_lab_df = label_df,
+ 	cell_size_factor = size_factor_vec,
+  count_slot = "counts", 
+  batch_slot = "batch")
Error in value[[3L]](cond) : 
  count_slot is not in assays of Seurat object X.
Calls: calculate_CDI ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
    count_slot is not in assays of Seurat object X.
  ERROR in test_size_factor: Error in value[[3L]](cond) : 
    count_slot is not in assays of Seurat object X.
  
  Test files with failing tests
  
     test_functions.R 
       test_calculate_CDI 
       test_feature_selection 
       test_size_factor 
  
  
  Error in BiocGenerics:::testPackage("CDI") : 
    unit tests failed for package CDI
  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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/CDI.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CDI
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘CDI’ ...
** this is package ‘CDI’ version ‘1.9.0’
** using staged installation
** R
** data
** 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 (CDI)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> BiocGenerics:::testPackage("CDI")
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: Seqinfo
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: SeuratObject
Loading required package: sp

Attaching package: 'sp'

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

    %over%


Attaching package: 'SeuratObject'

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

    Assays

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

    intersect

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

    intersect

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

    intersect

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

    intersect

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

    intersect

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

    intersect, t


Attaching package: 'Seurat'

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

    Assays

Warning: Data is of class data.frame. Coercing to dgCMatrix.
Timing stopped at: 0.343 0.018 0.383
Error in value[[3L]](cond) : 
  count_slot is not in assays of Seurat object X.
Warning: Data is of class data.frame. Coercing to dgCMatrix.
Timing stopped at: 0.088 0.002 0.09
Error in value[[3L]](cond) : 
  count_slot is not in assays of Seurat object X.
Warning: Data is of class data.frame. Coercing to dgCMatrix.
Timing stopped at: 0.042 0.001 0.047
Error in value[[3L]](cond) : 
  count_slot is not in assays of Seurat object X.


RUNIT TEST PROTOCOL -- Mon Dec 15 18:53:24 2025 
*********************************************** 
Number of test functions: 3 
Number of errors: 3 
Number of failures: 0 

 
1 Test Suite : 
CDI RUnit Tests - 3 test functions, 3 errors, 0 failures
ERROR in test_calculate_CDI: Error in value[[3L]](cond) : 
  count_slot is not in assays of Seurat object X.
ERROR in test_feature_selection: Error in value[[3L]](cond) : 
  count_slot is not in assays of Seurat object X.
ERROR in test_size_factor: Error in value[[3L]](cond) : 
  count_slot is not in assays of Seurat object X.

Test files with failing tests

   test_functions.R 
     test_calculate_CDI 
     test_feature_selection 
     test_size_factor 


Error in BiocGenerics:::testPackage("CDI") : 
  unit tests failed for package CDI
Execution halted