* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/digitalDLSorteR.Rcheck’
* using R Under development (unstable) (2024-10-31 r87278)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-1) 14.2.0
    GNU Fortran (Debian 14.2.0-1) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* using option ‘--run-donttest’
* checking for file ‘digitalDLSorteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘digitalDLSorteR’ version ‘1.1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/126s] NOTE
Maintainer: ‘Diego Mañanes <dmananesc@cnic.es>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Cabo (10:401)
  Deconvolution (3:8, 10:14)
  Torroja (10:381)
  deconvolution (10:72)
  scRNA (10:129, 10:361)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-10-02 as issues were not corrected
    in time.

Found the following (possibly) invalid URLs:
  URL: https://www.nature.com/articles/ncomms15081
    From: README.md
    Status: Error
    Message: Operation timed out after 60002 milliseconds with 0 bytes received
  URL: https://www.nature.com/articles/s41588-020-0636-z
    From: README.md
    Status: 503
    Message: Service Unavailable
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘digitalDLSorteR’ can be installed ... [26s/26s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking whether startup messages can be suppressed ... [7s/7s] OK
* checking use of S3 registration ... 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 ... [36s/36s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] ERROR
Running examples in ‘digitalDLSorteR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interGradientsDL
> ### Title: Calculate gradients of predicted cell types/loss function with
> ###   respect to input features for interpreting trained deconvolution
> ###   models
> ### Aliases: interGradientsDL
> 
> ### ** Examples
> 
> ## No test: 
> set.seed(123)
> sce <- SingleCellExperiment::SingleCellExperiment(
+   assays = list(
+     counts = matrix(
+       rpois(30, lambda = 5), nrow = 15, ncol = 10,
+       dimnames = list(paste0("Gene", seq(15)), paste0("RHC", seq(10)))
+     )
+   ),
+   colData = data.frame(
+     Cell_ID = paste0("RHC", seq(10)),
+     Cell_Type = sample(x = paste0("CellType", seq(2)), size = 10,
+                        replace = TRUE)
+   ),
+   rowData = data.frame(
+     Gene_ID = paste0("Gene", seq(15))
+   )
+ )
> DDLS <- createDDLSobject(
+   sc.data = sce,
+   sc.cell.ID.column = "Cell_ID",
+   sc.gene.ID.column = "Gene_ID",
+   sc.filt.genes.cluster = FALSE
+ )
=== Bulk RNA-seq data not provided
=== Processing single-cell data
      - Filtering features:
         - Selected features: 15
         - Discarded features: 0

=== No mitochondrial genes were found by using ^mt- as regrex

=== Final number of dimensions for further analyses: 15
> prop.design <- data.frame(
+   Cell_Type = paste0("CellType", seq(2)),
+   from = c(1, 30),
+   to = c(15, 70)
+ )
> DDLS <- generateBulkCellMatrix(
+   object = DDLS,
+   cell.ID.column = "Cell_ID",
+   cell.type.column = "Cell_Type",
+   prob.design = prop.design, 
+   num.bulk.samples = 50,
+   verbose = TRUE
+ )

=== The number of bulk RNA-Seq samples that will be generated is equal to 50

=== Training set cells by type:
    - CellType1: 4
    - CellType2: 3

=== Test set cells by type:
    - CellType1: 2
    - CellType2: 1

=== Probability matrix for training data:
    - Bulk RNA-Seq samples: 38
    - Cell types: 2

=== Probability matrix for test data:
    - Bulk RNA-Seq samples: 12
    - Cell types: 2

DONE
> DDLS <- simBulkProfiles(DDLS)
=== Setting parallel environment to 1 thread(s)

=== Generating train bulk samples:

=== Generating test bulk samples:

DONE
> DDLS <- trainDDLSModel(
+   object = DDLS,
+   batch.size = 12,
+   num.epochs = 5
+ )
Error: There is no a Python interpreter with all the digitalDLSorteR 
        dependencies covered available. Please, look at 
        https://diegommcc.github.io/digitalDLSorteR/articles/kerasIssues.html 
        or see ?installPythonDepend
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [30s/30s] OK
  Running ‘testthat.R’ [29s/30s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [4s/4s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE