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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:padma.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings padma_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/padma.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘padma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘padma’ version ‘1.14.0’
* 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 ‘padma’ 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 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 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) padma.Rd:94-95: Lost braces
    94 | {pathway name, full MFA results, number of genes, and names of imputed 
       | ^
checkRd: (-1) padmaRun.Rd:63-64: Lost braces
    63 | {pathway name, full MFA results, number of genes, and names of imputed 
       | ^
* 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 ‘padma-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: factorMap
> ### Title: Plot an MFA factor map for individuals or partial factor map
> ###   based on padma analysis
> ### Aliases: factorMap
> 
> ### ** Examples
> 
> 
> LUAD_subset <- padma::LUAD_subset
> ## Create MultiAssayExperiment object with LUAD data
> omics_data <- 
+   list(rnaseq = as.matrix(LUAD_subset$rnaseq),
+        methyl = as.matrix(LUAD_subset$methyl),
+        mirna = as.matrix(LUAD_subset$mirna),
+        cna = as.matrix(LUAD_subset$cna))
> pheno_data <- 
+   data.frame(LUAD_subset$clinical, 
+              row.names = LUAD_subset$clinical$bcr_patient_barcode)
> mae <-
+   suppressMessages(
+     MultiAssayExperiment::MultiAssayExperiment(
+       experiments = omics_data, colData = pheno_data))
> 
> ## Run padma
> run_padma <- 
+   padma(mae, gene_map = padma::mirtarbase,
+         pathway_name = "c2_cp_BIOCARTA_D4GDI_PATHWAY", verbose = FALSE)
Error in .longFormatANY(obj, i = idx) : 
  Package 'reshape2' is required for 'longFormat()' conversion
Calls: padma ... mapply -> <Anonymous> -> data.frame -> .longFormatANY
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5.       └─MultiAssayExperiment::wideFormat(base_data, check.names = FALSE)
    6.         └─MultiAssayExperiment:::.longFormatElist(...)
    7.           └─BiocGenerics::mapply(...)
    8.             ├─BiocGenerics (local) standardGeneric("mapply")
    9.             │ ├─BiocGenerics::eval(mc, env)
   10.             │ └─base::eval(mc, env)
   11.             │   └─base::eval(mc, env)
   12.             └─base::mapply(FUN = FUN, ..., SIMPLIFY = SIMPLIFY)
   13.               └─MultiAssayExperiment (local) `<fn>`(obj = dots[[1L]][[1L]], obname = dots[[2L]][[1L]], idx = dots[[3L]][[1L]])
   14.                 ├─base::data.frame(...)
   15.                 └─MultiAssayExperiment:::.longFormatANY(obj, i = idx)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/padma.Rcheck/00check.log’
for details.