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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:snapcount.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings snapcount_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/snapcount.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snapcount/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘snapcount’ version ‘1.23.0’
* 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 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: Compilation
> ### Title: Enum for Snaptron compilations
> ### Aliases: Compilation
> ### Keywords: datasets
> 
> ### ** Examples
> 
> qb <- QueryBuilder(compilation = Compilation$gtex, regions = "KCNIP4")
> query_jx(qb)
Error: API did not return tsv
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. └─sb$from_url("http://snaptron.cs.jhu.edu/gtex/snaptron?regions=CD99&rfilter=samples_count<:10&sfilter=SMTS:Brain&sids=50099,50102") at test-query-builder.R:69:5
  ── Error ('test-query-builder.R:83:5'): test building from url with coordinate modifiers ──
  Error: http: is not a valid URLsnaptron.cs.jhu.edu: is not a valid URLNULL: is not a valid URLgtex/snaptron: is not a valid URLlist(regions = "CD99", either = "1"): is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URL
  Backtrace:
      ▆
   1. └─sb$from_url(paste(url, "either=1", sep = "&")) at test-query-builder.R:83:5
  ── Failure ('test-query-functions.R:81:5'): invalid sample filter name ─────────
  Expected `query_jx(sb)` to throw a error.
  ── Failure ('test-query-functions.R:91:5'): invalid sample filter value ────────
  Expected `query_jx(sb)` to throw a error.
  
  [ FAIL 11 | WARN 0 | SKIP 0 | PASS 50 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/snapcount.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL snapcount
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘snapcount’ ...
** this is package ‘snapcount’ version ‘1.23.0’
** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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")
Saving _problems/test-assertions-26.R
Saving _problems/test-higher-level-functions-10.R
Saving _problems/test-higher-level-functions-55.R
Saving _problems/test-higher-level-functions-80.R
Saving _problems/test-higher-level-functions-111.R
Saving _problems/test-higher-level-functions-141.R
Saving _problems/test-query-builder-wrappers-75.R
Saving _problems/test-query-builder-69.R
Saving _problems/test-query-builder-83.R
Saving _problems/test-query-functions-83.R
Saving _problems/test-query-functions-93.R
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 50 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-assertions.R:25:5'): Invalid sample filters ──────────────────
`query_gene(sb)` threw an error with unexpected message.
Expected match: "(is not a valid sample filter)|(Invalid sample filter)"
Actual message: "API did not return tsv"
Backtrace:
     ▆
  1. ├─testthat::expect_error(query_gene(sb), "(is not a valid sample filter)|(Invalid sample filter)") at test-assertions.R:25:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─snapcount::query_gene(sb)
  7.   └─base::lapply(...)
  8.     └─snapcount (local) FUN(X[[i]], ...)
  9.       └─snapcount:::run_query(...)
 10.         └─snapcount:::submit_query(uri)
── Error ('test-higher-level-functions.R:10:5'): junction union ────────────────
<assertError/simpleError/error/condition>
Error: encode1159: is not a valid compilation
Backtrace:
    ▆
 1. └─sb1$compilation("encode1159") at test-higher-level-functions.R:10:5
 2.   └─assertthat::assert_that(...)
── Error ('test-higher-level-functions.R:55:5'): shared sample count ───────────
Error: API did not return tsv
Backtrace:
     ▆
  1. ├─snapcount::shared_sample_counts(group1, group2, group3) at test-higher-level-functions.R:55:5
  2. │ ├─... %>% unlist()
  3. │ └─base::lapply(...)
  4. │   └─snapcount (local) FUN(X[[i]], ...)
  5. │     └─snapcount:::shared_sample_count(g[[1]], g[[2]])
  6. │       └─snapcount:::run_queries(group1, group2)
  7. │         └─base::lapply(list(...), count_samples, summarize = summarize)
  8. │           └─snapcount (local) FUN(X[[i]], ...)
  9. │             └─base::lapply(...)
 10. │               └─snapcount (local) FUN(X[[i]], ...)
 11. │                 └─sb$query_jx(return_rse = FALSE)
 12. │                   └─private$call("query_jx", list(sb = self, return_rse = return_rse))
 13. │                     ├─base::do.call(fn, args)
 14. │                     └─snapcount (local) `<fn>`(sb = `<SnptrnQB>`, return_rse = FALSE)
 15. │                       └─base::lapply(...)
 16. │                         └─snapcount (local) FUN(X[[i]], ...)
 17. │                           └─snapcount:::run_query(...)
 18. │                             └─snapcount:::submit_query(uri)
 19. └─base::unlist(.)
── Error ('test-higher-level-functions.R:80:5'): junction inclusion ratio ──────
Error: API did not return tsv
Backtrace:
     ▆
  1. └─snapcount::junction_inclusion_ratio(list(sb1), list(sb2)) at test-higher-level-functions.R:80:5
  2.   └─snapcount:::run_queries(group1, group2)
  3.     └─base::lapply(list(...), count_samples, summarize = summarize)
  4.       └─snapcount (local) FUN(X[[i]], ...)
  5.         └─base::lapply(...)
  6.           └─snapcount (local) FUN(X[[i]], ...)
  7.             └─sb$query_jx(return_rse = FALSE)
  8.               └─private$call("query_jx", list(sb = self, return_rse = return_rse))
  9.                 ├─base::do.call(fn, args)
 10.                 └─snapcount (local) `<fn>`(sb = `<SnptrnQB>`, return_rse = FALSE)
 11.                   └─base::lapply(...)
 12.                     └─snapcount (local) FUN(X[[i]], ...)
 13.                       └─snapcount:::run_query(...)
 14.                         └─snapcount:::submit_query(uri)
── Error ('test-higher-level-functions.R:111:5'): percent spliced in ───────────
Error: API did not return tsv
Backtrace:
     ▆
  1. └─snapcount::percent_spliced_in(...) at test-higher-level-functions.R:111:5
  2.   └─snapcount:::run_queries(inclusion_group1, inclusion_group2, exclusion_group)
  3.     └─base::lapply(list(...), count_samples, summarize = summarize)
  4.       └─snapcount (local) FUN(X[[i]], ...)
  5.         └─base::lapply(...)
  6.           └─snapcount (local) FUN(X[[i]], ...)
  7.             └─sb$query_jx(return_rse = FALSE)
  8.               └─private$call("query_jx", list(sb = self, return_rse = return_rse))
  9.                 ├─base::do.call(fn, args)
 10.                 └─snapcount (local) `<fn>`(sb = `<SnptrnQB>`, return_rse = FALSE)
 11.                   └─base::lapply(...)
 12.                     └─snapcount (local) FUN(X[[i]], ...)
 13.                       └─snapcount:::run_query(...)
 14.                         └─snapcount:::submit_query(uri)
── Error ('test-higher-level-functions.R:141:5'): tissue specificity ───────────
Error: API did not return tsv
Backtrace:
     ▆
  1. └─snapcount::tissue_specificity(list(sb1, sb2)) at test-higher-level-functions.R:141:5
  2.   └─base::lapply(...)
  3.     └─snapcount (local) FUN(X[[i]], ...)
  4.       └─snapcount:::tissue_specificity_per_group(g[[1]], g[[2]], name)
  5.         └─snapcount:::run_queries(group1, group2, summarize = FALSE)
  6.           └─base::lapply(list(...), count_samples, summarize = summarize)
  7.             └─snapcount (local) FUN(X[[i]], ...)
  8.               └─base::lapply(...)
  9.                 └─snapcount (local) FUN(X[[i]], ...)
 10.                   └─sb$query_jx(return_rse = FALSE)
 11.                     └─private$call("query_jx", list(sb = self, return_rse = return_rse))
 12.                       ├─base::do.call(fn, args)
 13.                       └─snapcount (local) `<fn>`(sb = `<SnptrnQB>`, return_rse = FALSE)
 14.                         └─base::lapply(...)
 15.                           └─snapcount (local) FUN(X[[i]], ...)
 16.                             └─snapcount:::run_query(...)
 17.                               └─snapcount:::submit_query(uri)
── Error ('test-query-builder-wrappers.R:75:5'): query builder from url ────────
Error: http: is not a valid URLsnaptron.cs.jhu.edu: is not a valid URLNULL: is not a valid URLgtex/snaptron: is not a valid URLlist(regions = "CD99"): is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URL
Backtrace:
    ▆
 1. └─snapcount::from_url("http://snaptron.cs.jhu.edu/gtex/snaptron?regions=CD99") at test-query-builder-wrappers.R:75:5
 2.   └─SnaptronQueryBuilder$new()$from_url(url)
── Error ('test-query-builder.R:69:5'): test building from url ─────────────────
Error: http: is not a valid URLsnaptron.cs.jhu.edu: is not a valid URLNULL: is not a valid URLgtex/snaptron: is not a valid URLlist(regions = "CD99", rfilter = "samples_count<:10", sfilter = "SMTS:Brain", sids = "50099,50102"): is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URL
Backtrace:
    ▆
 1. └─sb$from_url("http://snaptron.cs.jhu.edu/gtex/snaptron?regions=CD99&rfilter=samples_count<:10&sfilter=SMTS:Brain&sids=50099,50102") at test-query-builder.R:69:5
── Error ('test-query-builder.R:83:5'): test building from url with coordinate modifiers ──
Error: http: is not a valid URLsnaptron.cs.jhu.edu: is not a valid URLNULL: is not a valid URLgtex/snaptron: is not a valid URLlist(regions = "CD99", either = "1"): is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URLNULL: is not a valid URL
Backtrace:
    ▆
 1. └─sb$from_url(paste(url, "either=1", sep = "&")) at test-query-builder.R:83:5
── Failure ('test-query-functions.R:81:5'): invalid sample filter name ─────────
Expected `query_jx(sb)` to throw a error.
── Failure ('test-query-functions.R:91:5'): invalid sample filter value ────────
Expected `query_jx(sb)` to throw a error.

[ FAIL 11 | WARN 0 | SKIP 0 | PASS 50 ]
Error:
! Test failures.
Execution halted