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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ProteoDisco_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ProteoDisco.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ProteoDisco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProteoDisco’ version ‘1.5.0’
* 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 ‘ProteoDisco’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
See ‘/home/biocbuild/bbs-3.17-bioc/meat/ProteoDisco.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 R 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘ProteoDisco’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... 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 cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'show' and siglist 'ProteoDiscography'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
  Error loading dataset 'ProteoDiscographyExample.hg19':
   Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed
  
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ProteoDisco-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateJunctionModels
> ### Title: Generate putative transcript-models derived from
> ###   splice-junctions.
> ### Aliases: generateJunctionModels
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
>  ProteoDiscography.hg19 <- ProteoDisco::generateProteoDiscography(
+    TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene,
+    genomeSeqs = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
+  )
ProteoDisco - Generating the annotation database (ProteoDiscography)
> 
>  # Import splice-junctions (even spanning different chromosomes) based on our format.
>  testSJ <- readr::read_tsv(system.file('extdata', 'validationSetSJ_hg19.txt', package = 'ProteoDisco'))
Rows: 9 Columns: 7
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (7): junctionA, junctionB, sample, expectedSeq.confirmedWithBLASTP, junc...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
> 
>  # Add custom SJ to ProteoDiscography.
>  ProteoDiscography.hg19 <- ProteoDisco::importSpliceJunctions(
+    ProteoDiscography = ProteoDiscography.hg19,
+    inputSpliceJunctions = testSJ
+  )
ProteoDisco - Importing splice-junctions to the ProteoDiscography.
> 
>  # Generate junction-models from non-canonical splice-junctions.
>  ProteoDiscography.hg19 <- ProteoDisco::generateJunctionModels(
+    ProteoDiscography = ProteoDiscography.hg19,
+    # Max. distance from a known exon-boundary before introducing a novel exon.
+    # If an adjacent exon is found within this distance, it will shorten or elongate that exon towards the SJ.
+    maxDistance = 150,
+    # Should we skip known exon-exon junctions (in which both the acceptor and donor are located on known adjacent exons within the same transcript)
+    skipCanonical = TRUE,
+    # Perform on multiple threads (optional)
+    threads = 1
+  )
ProteoDisco - Generating splice-junctions models based on 9 unique (sample-specific or aggregated) splice-junctions.

  |                                                                            
  |                                                                      |   0%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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname


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Killed
* 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:
  7: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco' 
  8: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco' 
  9: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco' 
  > 
  > testthat::test_check("ProteoDisco")
  ProteoDisco - Importing manual transcript sequences to the ProteoDiscography.
  ProteoDisco - Importing splice-junctions to the ProteoDiscography.
  ProteoDisco - Generating splice-junctions models based on 9 unique (sample-specific or aggregated) splice-junctions.
  
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  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Overview_ProteoDisco.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview_ProteoDisco.Rmd’ using rmarkdown
Killed

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

Status: 3 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ProteoDisco.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ProteoDisco
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ProteoDisco’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
** testing if installed package keeps a record of temporary installation path
* DONE (ProteoDisco)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(ProteoDisco)
Warning messages:
1: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco' 
2: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco' 
3: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'ProteoDisco' 
4: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco' 
5: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco' 
6: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco' 
7: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco' 
8: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco' 
9: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco' 
> 
> testthat::test_check("ProteoDisco")
ProteoDisco - Importing manual transcript sequences to the ProteoDiscography.
ProteoDisco - Importing splice-junctions to the ProteoDiscography.
ProteoDisco - Generating splice-junctions models based on 9 unique (sample-specific or aggregated) splice-junctions.

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