##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:partCNV.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings partCNV_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/partCNV.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘partCNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘partCNV’ version ‘1.2.0’
* 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 ‘partCNV’ 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 ... NOTE
GetCytoLocation: no visible global function definition for ‘data’
GetExprCountCyto: no visible global function definition for ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘partCNV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetCytoLocation
> ### Title: Get exact location of the interested cytogenetics feature
> ### Aliases: GetCytoLocation
> 
> ### ** Examples
> 
> ### example 1
> GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)")
downloading 1 resources
retrieving 1 resource
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/59916’
  local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/file32f9db79c3c06f’
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC62
  file: ‘https://annotationhub.bioconductor.org/fetch/59916’
  reason: download failed
Warning: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/59916’
  cache resource: ‘AH53178 : 59916’
  reason: download failed; see warnings()
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: 1 resources failed to download
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:
       ▆
    1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-partCNVH.R:3:3
    2.   ├─base::data.frame(AnnotationHub()[["AH53178"]])
    3.   ├─AnnotationHub()[["AH53178"]]
    4.   └─AnnotationHub()[["AH53178"]]
    5.     └─AnnotationHub (local) .local(x, i, j = j, ...)
    6.       └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
    7.         └─base::tryCatch(...)
    8.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.               └─value[[3L]](cond)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1 ]
  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 ‘partCNV_vignette.Rmd’ using rmarkdown

Quitting from lines 83-84 [s1] (partCNV_vignette.Rmd)
Error: processing vignette 'partCNV_vignette.Rmd' failed with diagnostics:
failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
--- failed re-building ‘partCNV_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/partCNV.Rcheck/00check.log’
for details.