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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:snapcount.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings snapcount_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/snapcount.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘snapcount/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘snapcount’ version ‘1.21.0’
* 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 ‘snapcount’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘snapcount-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: junction_intersection
> ### Title: Get the intersection of junctions from 2 or more compilations
> ###   which are on the same reference
> ### Aliases: junction_intersection
> 
> ### ** Examples
> 
> # Using query builder wrappers
> sb1 <- QueryBuilder(compilation = "gtex", regions = "chr1:1879786-1879786")
> sb1 <- set_coordinate_modifier(sb1, Coordinates$EndIsExactOrWithin)
> sb1 <- set_row_filters(sb1, strand == "-")
> 
> sb2 <- QueryBuilder(compilation = "tcga", regions = "chr1:1879786-1879786")
> sb2 <- set_coordinate_modifier(sb2, Coordinates$EndIsExactOrWithin)
> sb2 <- set_row_filters(sb2, strand == "-")
> 
> junction_intersection(sb1, sb2)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Transferred a partial file [snaptron.cs.jhu.edu]:
transfer closed with outstanding read data remaining
Calls: junction_intersection ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
Compilation 3.346  0.182  13.127
* 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:
    2. │ └─base::lapply(...)
    3. │   └─snapcount (local) FUN(X[[i]], ...)
    4. │     └─snapcount:::tissue_specificity_per_group(g[[1]], g[[2]], name)
    5. │       └─snapcount:::get_compilation_metadata(group1[[1]]$compilation())
    6. │         └─snapcount:::submit_query(uri)
    7. │           └─httr::GET(uri)
    8. │             └─httr:::request_perform(req, hu$handle$handle)
    9. │               ├─httr:::request_fetch(req$output, req$url, handle)
   10. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   11. │                 └─curl::curl_fetch_memory(url, handle = handle)
   12. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/snapcount.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL snapcount
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘snapcount’ ...
** this is package ‘snapcount’ version ‘1.21.0’
** 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 (snapcount)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
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.

> library(testthat)
> library(snapcount)
> 
> test_check("snapcount")
Read 2 items
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-higher-level-functions.R:141:5'): tissue specificity ───────────
<curl_error_partial_file/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Transferred a partial file [snaptron.cs.jhu.edu]:
transfer closed with outstanding read data remaining
Backtrace:
     ▆
  1. ├─snapcount::tissue_specificity(list(sb1, sb2)) at test-higher-level-functions.R:141:5
  2. │ └─base::lapply(...)
  3. │   └─snapcount (local) FUN(X[[i]], ...)
  4. │     └─snapcount:::tissue_specificity_per_group(g[[1]], g[[2]], name)
  5. │       └─snapcount:::get_compilation_metadata(group1[[1]]$compilation())
  6. │         └─snapcount:::submit_query(uri)
  7. │           └─httr::GET(uri)
  8. │             └─httr:::request_perform(req, hu$handle$handle)
  9. │               ├─httr:::request_fetch(req$output, req$url, handle)
 10. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 11. │                 └─curl::curl_fetch_memory(url, handle = handle)
 12. └─curl:::raise_libcurl_error(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 79 ]
Error: Test failures
Execution halted