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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Pirat.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Pirat_1.0.1.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Pirat.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Pirat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pirat’ version ‘1.0.1’
* 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 ‘Pirat’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Pirat.Rcheck/00install.out’ for details.
* 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 ... NOTE
plot_pep_correlations: no visible binding for global variable ‘group’
Undefined global functions or variables:
  group
* checking Rd files ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Pirat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: impute_from_blocks
> ### Title: Impute abundance table from PGs results
> ### Aliases: impute_from_blocks
> 
> ### ** Examples
> 
> Py_impute_block_llk_reset <- function(data.pep.rna.mis, psi) { 
+ proc <- basilisk::basiliskStart(envPirat)
+ 
+ func <- basilisk::basiliskRun(proc, 
+     fun = function(arg1, arg2) {
+         
+         imputed_pgs <- Pirat::impute_block_llk_reset(arg1, arg2)
+         imputed_pgs 
+     }, arg1 = data.pep.rna.mis, arg2 = psi)
+ 
+ basilisk::basiliskStop(proc)
+ func
+ }
> 
> 
> data(subbouyssie)
> obj <- subbouyssie
> # Keep only fully observed peptides
> obs2NApep <- obj$peptides_ab[ ,colSums(is.na(obj$peptides_ab)) <= 0] 
> res_hyperparam <- estimate_psi_df(obs2NApep)
> psi <- res_hyperparam$psi
> imputed_pgs <- Py_impute_block_llk_reset(obj, psi)
Error in Pirat::impute_block_llk_reset(arg1, arg2) : 
  ermsg == "success" is not TRUE
Calls: Py_impute_block_llk_reset -> <Anonymous> -> fun -> <Anonymous> -> stopifnot
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_pirat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Pirat.Rcheck/00check.log’
for details.