* using log directory ‘/Users/ripley/R/packages/tests-devel/craftgrn.Rcheck’
* using R Under development (unstable) (2026-06-18 r90173)
* using platform: aarch64-apple-darwin25.5.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.1.1.101)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.5.1
* using session charset: UTF-8
* current time: 2026-06-19 06:26:56 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘craftgrn/DESCRIPTION’ ... OK
* this is package ‘craftgrn’ version ‘0.1.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘EnsDb.Mmusculus.v79’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘craftgrn’ can be installed ... [15s/15s] OK
* used C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.1.1.101)’
* used SDK: ‘MacOSX26.5.sdk’
* 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 use of S3 registration ... 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 ... [18s/18s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’ [24s/24s]
 [24s/25s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # 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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(craftgrn)
  > 
  > test_check("craftgrn")
  Saving _problems/test-config-34.R
  Saving _problems/test-config-38.R
  Saving _problems/test-config-42.R
  [2026-06-19 07:28:01] WarpLDA: dtm dims = 8 x 12, nnzero = 96, tokens = 896; completed K = 0/1; workers = 1; threads/model = 2
  [2026-06-19 07:28:01] WarpLDA sampler = warp_omp.
  [2026-06-19 07:28:01] WarpLDA: fitting K=2, iterations=2, alpha=0.5, beta=0.1, seed=10
  [2026-06-19 07:28:08] topic_links gene_prob: peak_and_gene_prob pass 2/4 rows (gene_prob = max).
  [2026-06-19 07:28:09] topic_links gammafit: gene_only pass 2/2 rows.
  [2026-06-19 07:28:09] topic_links gammafit: gene_only pass 1/2 rows.
  [2026-06-19 07:28:09] topic_links gammafit: peak_and_gene pass 1/4 rows.
  [2026-06-19 07:28:09] topic_links gammafit: peak_and_gene pass 4/8 rows.
  [2026-06-19 07:28:09] topic_links gammafit: peak_and_gene pass 4/8 rows.
  [ FAIL 3 | WARN 0 | SKIP 44 | PASS 959 ]
  
  ══ Skipped tests (44) ══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-app-contract.R:59:5'
  • dev benchmark script is not included in built package (34):
    'test-benchmark-pathway-activity.R:10:3',
    'test-benchmark-pathway-activity.R:42:3',
    'test-benchmark-pathway-activity.R:80:3',
    'test-benchmark-pathway-activity.R:105:3',
    'test-benchmark-pathway-activity.R:112:3',
    'test-benchmark-pathway-activity.R:165:3',
    'test-benchmark-pathway-activity.R:198:3',
    'test-benchmark-pathway-activity.R:253:3',
    'test-benchmark-pathway-activity.R:310:3', 'test-topic-distance.R:10:3',
    'test-topic-projects.R:17:3', 'test-topic-reports.R:17:3',
    'test-topic-reports.R:48:3', 'test-topic-reports.R:68:3',
    'test-topic-reports.R:80:3', 'test-topic-reports.R:96:3',
    'test-topic-reports.R:112:3', 'test-topic-reports.R:128:3',
    'test-topic-reports.R:140:3', 'test-topic-reports.R:168:3',
    'test-topic-reports.R:187:3', 'test-topic-reports.R:215:3',
    'test-topic-reports.R:243:3', 'test-topic-reports.R:266:3',
    'test-topic-reports.R:292:3', 'test-topic-reports.R:320:3',
    'test-topic-reports.R:373:3', 'test-topic-reports.R:393:3',
    'test-topic-reports.R:406:3', 'test-topic-reports.R:448:3',
    'test-topic-reports.R:465:3', 'test-topic-reports.R:480:3',
    'test-topic-theta-review.R:10:3', 'test-topic-theta-review.R:72:3'
  • file.exists(path) is not TRUE (4): 'test-config-pkgdown.R:13:3',
    'test-config-pkgdown.R:24:3', 'test-config-pkgdown.R:37:3',
    'test-config-pkgdown.R:82:3'
  • length(hit) > 0L is not TRUE (3): 'test-config-readme-public-api.R:18:3',
    'test-config-readme-public-api.R:28:3',
    'test-config-readme-public-api.R:47:3'
  • {EnsDb.Mmusculus.v79} is not installed (1): 'test-module2-gene-tss.R:12:3'
  • {enrichly} is not installed (1): 'test-module3-reports-api.R:64:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-config.R:31:3'): load_config resolves relative paths against the config directory ──
  Expected `get("sample_metadata", envir = env)` to equal `normalizePath(...)`.
  Differences:
  actual vs expected
  - "/private/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/Rtmpw5ujyx/working_dir/RtmpHOt7Zi/craftgrn-project-91fe81926f6/data/sample_metadata_strict.csv"
  + "/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmpw5ujyx/working_dir/RtmpHOt7Zi/craftgrn-project-91fe81926f6/data/sample_metadata_strict.csv"
  
  ── Failure ('test-config.R:35:3'): load_config resolves relative paths against the config directory ──
  Expected `get("atac_master", envir = env)` to equal `normalizePath(...)`.
  Differences:
  actual vs expected
  - "/private/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/Rtmpw5ujyx/working_dir/RtmpHOt7Zi/craftgrn-project-91fe81926f6/data/atac_master.csv"
  + "/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmpw5ujyx/working_dir/RtmpHOt7Zi/craftgrn-project-91fe81926f6/data/atac_master.csv"
  
  ── Failure ('test-config.R:39:3'): load_config resolves relative paths against the config directory ──
  Expected `get("rna_mapped", envir = env)` to equal `normalizePath(...)`.
  Differences:
  actual vs expected
  - "/private/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/Rtmpw5ujyx/working_dir/RtmpHOt7Zi/craftgrn-project-91fe81926f6/data/rna_strict.csv"
  + "/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmpw5ujyx/working_dir/RtmpHOt7Zi/craftgrn-project-91fe81926f6/data/rna_strict.csv"
  
  
  [ FAIL 3 | WARN 0 | SKIP 44 | PASS 959 ]
  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
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/craftgrn.Rcheck/00check.log’
for details.

       86.51 real        73.13 user        10.00 sys