Last updated on 2026-11-09 06:54:14 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.7 | 51.78 | 243.27 | 295.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.7 | 36.33 | 173.42 | 209.75 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.7 | 36.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.7 | 39.00 | 154.15 | 193.15 | OK | |
| r-devel-windows-x86_64 | 0.1.7 | 58.00 | 311.00 | 369.00 | OK | |
| r-patched-linux-x86_64 | 0.1.7 | OK | ||||
| r-release-linux-x86_64 | 0.1.7 | 53.83 | 222.11 | 275.94 | OK | |
| r-release-macos-arm64 | 0.1.7 | 13.00 | 49.00 | 62.00 | OK | |
| r-release-macos-x86_64 | 0.1.7 | 36.00 | 195.00 | 231.00 | OK | |
| r-release-windows-x86_64 | 0.1.7 | 65.00 | 242.00 | 307.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.7 | 10.00 | 55.00 | 65.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.7 | 35.00 | 195.00 | 230.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.7 | 75.00 | 301.00 | 376.00 | OK |
Version: 0.1.7
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [66s/87s]
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-module1-footprints-83.R
Saving _problems/test-module1-footprints-132.R
Saving _problems/test-module1-footprints-184.R
[2026-11-08 16:42:25] WarpLDA: dtm dims = 8 x 12, nnzero = 96, tokens = 896; completed K = 0/1; workers = 1; threads/model = 2
[2026-11-08 16:42:25] WarpLDA sampler = warp_omp.
[2026-11-08 16:42:25] WarpLDA memory available now: 207.84 GB.
[2026-11-08 16:42:25] WarpLDA: fitting K=2, iterations=2, alpha=0.5, beta=0.1, seed=10
[2026-11-08 16:42:50] topic_links gene_prob: peak_and_gene_prob pass 2/4 rows (gene_prob = max).
[2026-11-08 16:42:52] train_topic_models using 1 data.table thread(s).
[2026-11-08 16:42:52] Loading 1 delta-link file(s) from /home/hornik/tmp/scratch/RtmpIMKhUW/file26865a77230f3e/filtered.
[2026-11-08 16:42:52] Loaded 6 delta-link row(s).
[2026-11-08 16:42:52] Preparing topic input for count_input_test: doc_design=comparison, doc_mode=tf, fp_term_mode=unique, backend=warplda.
[2026-11-08 16:42:52] count_input_test: filtering 6 edge row(s).
[2026-11-08 16:42:52] count_input_test: retained 6 edge row(s) after topic filters in 0 sec.
[2026-11-08 16:42:52] count_input_test: building comparison-level TF documents.
[2026-11-08 16:42:52] count_input_test: built 6 comparison-level document edge row(s) in 0 sec.
[2026-11-08 16:42:52] count_input_test: building comparison-level doc_term.
[2026-11-08 16:42:52] count_input_test: comparison-level doc_term build finished in 0 sec.
[2026-11-08 16:42:52] count_input_test: doc_term has 12 row(s), 2 document(s), and 12 term(s).
[2026-11-08 16:42:52] count_input_test: writing WarpLDA input caches in /home/hornik/tmp/scratch/RtmpIMKhUW/file26865a77230f3e/models.
[2026-11-08 16:42:52] count_input_test: WarpLDA input cache writing finished in 0 sec.
[2026-11-08 16:42:52] count_input_test: building sparse DTM for WarpLDA.
[2026-11-08 16:42:52] count_input_test: WarpLDA sparse DTM cache finished in 0 sec.
[2026-11-08 16:42:52] count_input_test: starting WarpLDA model fits.
[2026-11-08 16:42:52] WarpLDA: dtm dims = 2 x 12, nnzero = 12, tokens = 451; completed K = 0/1; workers = 1; threads/model = 1
[2026-11-08 16:42:52] WarpLDA sampler = warp_omp.
[2026-11-08 16:42:52] WarpLDA memory estimate: peak per model <= 19.44 KB at max K=2; concurrent peak <= 19.44 KB.
[2026-11-08 16:42:52] WarpLDA memory available now: 208.18 GB.
[2026-11-08 16:42:52] WarpLDA: fitting K=2, iterations=1, alpha=25, beta=1/K, seed=123
[2026-11-08 16:42:54] count_input_test: finished WarpLDA model fits in 1.7 sec.
[2026-11-08 16:42:56] count_input_test: finished train_topic_models analysis stage in 3.5 sec.
[2026-11-08 16:42:57] topic_links gammafit: gene_only pass 2/2 rows.
[2026-11-08 16:42:57] topic_links gammafit: gene_only pass 1/2 rows.
[2026-11-08 16:42:57] topic_links gammafit: peak_and_gene pass 1/4 rows.
[2026-11-08 16:42:57] topic_links gammafit: peak_and_gene pass 4/8 rows.
[2026-11-08 16:42:57] topic_links gammafit: peak_and_gene pass 4/8 rows.
[ FAIL 3 | WARN 5 | SKIP 43 | PASS 982 ]
══ Skipped tests (43) ══════════════════════════════════════════════════════════
• 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'
• {enrichly} is not installed (1): 'test-module3-reports-api.R:64:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-module1-footprints.R:80:3'): aligned footprint cache loader reads Parquet cache when available ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─arrow::write_parquet(...) at test-module1-footprints.R:80:3
2. ├─ParquetFileWriter$create(...)
3. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
4. └─ParquetWriterProperties$create(...)
5. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-module1-footprints.R:129:3'): aligned footprint cache loader defaults to CSV when both formats exist ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─arrow::write_parquet(...) at test-module1-footprints.R:129:3
2. ├─ParquetFileWriter$create(...)
3. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
4. └─ParquetWriterProperties$create(...)
5. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-module1-footprints.R:169:3'): footprint alignment can write Parquet cache ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─craftgrn:::align_footprints(...) at test-module1-footprints.R:169:3
2. └─craftgrn:::.aligned_fp_write_table(...)
3. └─craftgrn:::.write_parquet_table(x, path)
4. └─arrow::write_parquet(x, path, compression = codec)
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
[ FAIL 3 | WARN 5 | SKIP 43 | PASS 982 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc