##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.9.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘benchdamic’ 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 R 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 ‘benchdamic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DA_Seurat
> ### Title: DA_Seurat
> ### Aliases: DA_Seurat
> 
> ### ** Examples
> 
> set.seed(1)
> # Create a very simple phyloseq object
> counts <- matrix(rnbinom(n = 60, size = 3, prob = 0.5), nrow = 10, ncol = 6)
> metadata <- data.frame("Sample" = c("S1", "S2", "S3", "S4", "S5", "S6"),
+                        "group" = as.factor(c("A", "A", "A", "B", "B", "B")))
> ps <- phyloseq::phyloseq(phyloseq::otu_table(counts, taxa_are_rows = TRUE),
+                          phyloseq::sample_data(metadata))
>                          
> # Differential abundance
> DA_Seurat(object = ps, contrast = c("group","B","A"))
Warning: Data is of class matrix. Coercing to dgCMatrix.
Setting A the reference level for group variable.
Extracting results for group variable, B / A
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
(default method for FindMarkers) please install the presto package
--------------------------------------------
install.packages('devtools')
devtools::install_github('immunogenomics/presto')
--------------------------------------------
After installation of presto, Seurat will automatically use the more 
efficient implementation (no further action necessary).
This message will be shown once per session
$pValMat
          rawP     adjP
sp1  0.1904303 1.000000
sp2  1.0000000 1.000000
sp3  0.6625206 1.000000
sp4  0.1840386 1.000000
sp5  0.6625206 1.000000
sp6  0.3827331 1.000000
sp7  0.3827331 1.000000
sp8  1.0000000 1.000000
sp9  0.0808556 0.808556
sp10 1.0000000 1.000000

$statInfo
         p_val  avg_log2FC pct.1 pct.2 p_val_adj
sp1  0.1904303 -1.09264009 0.667 1.000  1.000000
sp2  1.0000000  0.04134924 1.000 1.000  1.000000
sp3  0.6625206 -0.66334771 1.000 0.667  1.000000
sp4  0.1840386 -1.36463577 0.333 1.000  1.000000
sp5  0.6625206  0.90884814 0.667 1.000  1.000000
sp6  0.3827331  0.71678480 1.000 1.000  1.000000
sp7  0.3827331 -0.35805875 1.000 1.000  1.000000
sp8  1.0000000  0.04608187 1.000 0.667  1.000000
sp9  0.0808556  0.89057297 1.000 0.667  0.808556
sp10 1.0000000 -0.41820485 1.000 1.000  1.000000

$name
[1] "Seurat.LogNormalize.SF10000.wilcox"

> 
> # Perform a simple Wilcoxon test using Seurat on raw data
> DA_Seurat(object = ps, contrast = c("group","B","A"), norm = "none", 
+     test = "wilcox")
Warning: Data is of class matrix. Coercing to dgCMatrix.
Setting A the reference level for group variable.
Extracting results for group variable, B / A
Warning: Layer ‘data’ is empty
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Calls: DA_Seurat ... callGeneric -> eval -> eval -> [ -> [ -> .subscript.2ary
Execution halted
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck/00check.log’
for details.