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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:brainflowprobes.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings brainflowprobes_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/brainflowprobes.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 ‘brainflowprobes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘brainflowprobes’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘brainflowprobes’ 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘brainflowprobes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: brainflowprobes_cov
> ### Title: Extract coverage data for a set of regions
> ### Aliases: brainflowprobes_cov
> 
> ### ** Examples
> 
> 
> ## This function loads data from BigWig files using the rtracklayer package.
> ## This functionality is not supported on Windows OS machines!
> if (.Platform$OS.type != "windows") {
+     ## How long this takes to run will depend on your internet connection.
+     example_cov <- brainflowprobes_cov("chr20:10286777-10288069:+",
+         PD = lapply(brainflowprobes::pd, head, n = 2)
+     )
+ 
+     ## Output examination:
+     # A list with one element per element in brainflowprobes::pd
+     stopifnot(is.list(example_cov))
+     stopifnot(identical(
+         names(example_cov),
+         names(brainflowprobes::pd)
+     ))
+ 
+     # For each dataset, brainflowprobes_cov() returns a list of region
+     # coverage data.frames. In this example, there was a single input region.
+     stopifnot(all(
+         sapply(example_cov, length) ==
+             length(
+                 GenomicRanges::GRanges("chr20:10286777-10288069:+")
+             )
+     ))
+ 
+     # Then each data.frame itself has 1 row per genome base-pair in the region
+     stopifnot(
+         all(
+             sapply(example_cov, function(x) {
+                 nrow(x[[1]])
+             }) ==
+                 GenomicRanges::width(
+                     GenomicRanges::GRanges("chr20:10286777-10288069:+")
+                 )
+         )
+     )
+ 
+     # and one column per sample in the dataset unless you subsetted the data
+     # like we did earlier when creating "example_cov".
+     stopifnot(identical(
+         sapply(four_panels_example_cov, function(x) {
+             ncol(x[[1]])
+         }),
+         sapply(pd, nrow)
+     ))
+ }
2024-12-19 20:58:01.341862 getRegionCoverage : attempting to load coverage data from 'files'.
2024-12-19 20:58:01.370726 fullCoverage: processing chromosome chr20
2024-12-19 20:58:01.409444 loadCoverage: finding chromosome lengths
Warning in seqinfo(x) :
  Couldn't open http://brain-flow-rna.s3.us-east-2.amazonaws.com/Sep/Br1113C1_polyA.bw
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'seqlengths': UCSC library operation failed
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/brainflowprobes.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL brainflowprobes
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘brainflowprobes’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
Warning in fun(libname, pkgname) :
  Package 'brainflowprobes' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'brainflowprobes' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (brainflowprobes)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> library(testthat)
> library(brainflowprobes)
Warning message:
In fun(libname, pkgname) :
  Package 'brainflowprobes' is deprecated and will be removed from
  Bioconductor version 3.21
> 
> test_check("brainflowprobes")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 27.995   1.467  30.016