• using R version 4.5.2 (2025-10-31)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘PRECAST/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PRECAST’ version ‘1.7’
• 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 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 ‘PRECAST’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
• 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 ... [19s/22s] OK
• checking whether the package can be loaded with stated dependencies ... [18s/21s] OK
• checking whether the package can be unloaded cleanly ... [19s/24s] OK
• checking whether the namespace can be loaded with stated dependencies ... [17s/19s] OK
• checking whether the namespace can be unloaded cleanly ... [18s/25s] OK
• checking loading without being on the library search path ... [18s/22s] OK
• checking whether startup messages can be suppressed ... [18s/24s] 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 ... [83s/101s] OK
• checking Rd files ... [0s/1s] 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 ... [20s/26s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [19s/21s] ERROR Running examples in ‘PRECAST-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CreatePRECASTObject > ### Title: Create the PRECAST object with preprocessing step. > ### Aliases: CreatePRECASTObject > > ### ** Examples > > data(PRECASTObj) > library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: ‘SeuratObject’ The following objects are masked from ‘package:base’:     intersect, t > seuList <- PRECASTObj@seulist > ## Check the input of seuList for create PRECAST object. > ## Check the default assay for each data batch > lapply(seuList, DefaultAssay) [[1]] [1] "RNA" [[2]] [1] "RNA" > ## Check the spatial coordinates in the meta data named "row" and "col". > head(seuList[[1]]@meta.data)         orig.ident nCount_RNA nFeature_RNA row col true_cluster cell1_1 cell1 10004 55 1 1 2 cell1_2 cell1 12614 54 2 1 2 cell1_3 cell1 18233 57 3 1 2 cell1_4 cell1 1726 50 4 1 7 cell1_5 cell1 3451 53 5 1 7 cell1_6 cell1 134457 60 6 1 6 > ## Then create PRECAST object using this seuList. > ## For convenience, we show the user-specified genes' list for creating PRECAST object. > ## Users can use SVGs from SPARK-X or HVGs. > PRECASTObj2 <- CreatePRECASTObject(seuList, + customGenelist= row.names(seuList[[1]]), verbose=FALSE) Error in FUN(X[[i]], ...) :   filter_gene: Seuat object must provide slots count or data in assay! Calls: CreatePRECASTObject -> <Anonymous> -> lapply -> FUN Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [29s/41s] OK
• checking PDF version of manual ... [7s/12s] OK
• checking HTML version of manual ... [1s/5s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR