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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scafari.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scafari_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scafari.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scafari/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scafari’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘scafari’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scafari-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotateVariants
> ### Title: Function: annotateVariants This function takes a
> ###   SingleCellExperiment object as input and performs variant annotation.
> ### Aliases: annotateVariants
> 
> ### ** Examples
> 
> # Assume `sce` is a SingleCellExperiment object with variants in altExp()
> sce_filtered <- readRDS(system.file("extdata", "sce_filtered_demo.rds",
+     package = "scafari"
+ ))
> sce <- annotateVariants(sce_filtered, shiny = FALSE)
Error in check_MBAPI() : URL not available. Status code:502
Calls: annotateVariants -> check_MBAPI
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
annotateAmplicons 61.869  1.526  69.611
* 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:
  Saving _problems/test-testing-513.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-testing.R:513:5'): Variant annotation works ────────────────────
  Error in `check_MBAPI()`: URL not available. Status code:502
  Backtrace:
      ▆
   1. └─scafari::annotateVariants(sce_filtered) at test-testing.R:513:5
   2.   └─scafari:::check_MBAPI()
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
  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 ‘scafari_vignette.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scafari.Rcheck/vign_test/scafari/vignettes/scafari_vignette_files/figure-html/loglopplot-1.png" but not available.
trying URL 'http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownCanonical.txt.gz'
Content type 'application/x-gzip' length 1793077 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scafari.Rcheck/vign_test/scafari/vignettes/scafari_vignette_files/figure-html/plot_amp_dist-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scafari.Rcheck/vign_test/scafari/vignettes/scafari_vignette_files/figure-html/plot_norm_rc-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scafari.Rcheck/vign_test/scafari/vignettes/scafari_vignette_files/figure-html/plot_panel_uniformity-1.png" but not available.

Quitting from scafari_vignette.Rmd:232-251 [annotate_variants]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `check_MBAPI()`:
! URL not available. Status code:502
---
Backtrace:
    ▆
 1. └─scafari::annotateVariants(sce = sce_filtered)
 2.   └─scafari:::check_MBAPI()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scafari_vignette.Rmd' failed with diagnostics:
URL not available. Status code:502
--- failed re-building ‘scafari_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scafari.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scafari
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scafari’ ...
** this is package ‘scafari’ version ‘1.0.0’
** using staged installation
** R
** 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 (scafari)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(scafari)

> 
> test_check("scafari")
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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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

start variant filtering...

start variant filtering...

start variant filtering...

start variant filtering...

start variant filtering...

start variant filtering...

Saving _problems/test-testing-513.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-testing.R:513:5'): Variant annotation works ────────────────────
Error in `check_MBAPI()`: URL not available. Status code:502
Backtrace:
    ▆
 1. └─scafari::annotateVariants(sce_filtered) at test-testing.R:513:5
 2.   └─scafari:::check_MBAPI()

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
Error:
! Test failures.
Execution halted