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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:padma.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings padma_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/padma.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘padma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘padma’ version ‘1.15.0’
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘padma.Rmd’ using rmarkdown

Quitting from lines 357-360 [runpadma] (padma.Rmd)
Error: processing vignette 'padma.Rmd' failed with diagnostics:
Package 'reshape2' is required for 'longFormat()' conversion
--- failed re-building ‘padma.Rmd’

SUMMARY: processing the following file failed:
  ‘padma.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/padma.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL padma
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘padma’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (padma)

R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("padma")
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("padma")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_padma.R:14:1'): (code run outside of `test_that()`) ────────────
Error in `.longFormatANY(obj, i = idx)`: Package 'reshape2' is required for 'longFormat()' conversion
Backtrace:
     ▆
  1. ├─padma::padma(...) at test_padma.R:14:1
  2. └─padma::padma(...)
  3.   └─padma (local) .local(object, ...)
  4.     └─padma::padmaRun(...)
  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)
── Error ('test_padma_plots.R:14:1'): (code run outside of `test_that()`) ──────
Error in `.longFormatANY(obj, i = idx)`: Package 'reshape2' is required for 'longFormat()' conversion
Backtrace:
     ▆
  1. ├─padma::padma(...) at test_padma_plots.R:14:1
  2. └─padma::padma(...)
  3.   └─padma (local) .local(object, ...)
  4.     └─padma::padmaRun(...)
  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