##############################################################################
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###
### 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
###
##############################################################################
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* 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.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL partCNV
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘partCNV’ ...
** using staged installation
** R
** data
** 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 (partCNV)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> # 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(partCNV)
> 
> test_check("partCNV")
downloading 1 resources
retrieving 1 resource
loading from cache
loading from cache
loading from cache
loading from cache
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-GetCytoLocation.R:2:3'): GetCytoLocation ───────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-GetCytoLocation.R:2:3
  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)
── Error ('test-GetExprCountCyto.R:3:3'): GetExprCountCyto ─────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-GetExprCountCyto.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)
── Error ('test-partCNV.R:3:3'): partCNV ───────────────────────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  1. └─partCNV::GetCytoLocation(cyto_feature = "chr20(q11.1-q13.1)") at test-partCNV.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)
── Error ('test-partCNVH.R:3:3'): partCNVH ─────────────────────────────────────
Error: failed to load resource
  name: AH53178
  title: UCSC cytoBand track for hg38
  reason: unknown input format
Backtrace:
     ▆
  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