* using log directory 'd:/RCompile/CRANincoming/R-devel/rCISSVAE.Rcheck'
* using R Under development (unstable) (2025-12-16 r89184 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'rCISSVAE/DESCRIPTION' ... OK
* this is package 'rCISSVAE' version '0.0.2.0000'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Danielle Vaithilingam <vaithid1@mskcc.org>'

New submission

Version contains leading zeroes (0.0.2.0000)

Possibly misspelled words in DESCRIPTION:
  Autoencoder (2:57, 14:78)
  CISS (3:10)
  Charvadeh (14:179)
  Khadem (14:172)
  MCAR (14:325)
  MNAR (14:384, 14:431)
  VAE (3:15)
  Variational (2:45, 14:66)
  al (14:192)
  et (14:189)
* 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 'rCISSVAE' can be installed ... OK
* checking installed package size ... 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 ... 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 loading without being on the library search path ... 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 ... OK
* checking Rd files ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [66s] ERROR
Running examples in 'rCISSVAE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cluster_on_missing_prop
> ### Title: Cluster Samples Based on Missingness Proportions
> ### Aliases: cluster_on_missing_prop
> 
> ### ** Examples
> 
> set.seed(123)
> dat <- data.frame(
+   sample_id = paste0("s", 1:12),
+   # Two features measured at 3 timepoints each → proportions by feature per sample
+   A_1 = c(NA, rnorm(11)), A_2 = c(NA, rnorm(11)), A_3 = rnorm(12),
+   B_1 = rnorm(12),        B_2 = c(rnorm(10), NA, NA), B_3 = rnorm(12)
+ )
> pm <- create_missingness_prop_matrix(dat, index_col = "sample_id",
+                                      repeat_feature_names = c("A","B"))
> res <- cluster_on_missing_prop(pm, n_clusters = 2, metric = "cosine", scale_features = TRUE)
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'ciss_vae'
Run `reticulate::py_last_error()` for details.
Calls: cluster_on_missing_prop -> <Anonymous> -> py_module_import
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [93s] OK
  Running 'testthat.R' [93s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [61s] OK
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE