Last updated on 2025-05-23 04:51:18 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.2.0 | 135.37 | 582.64 | 718.01 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.2.0 | 96.49 | 398.14 | 494.63 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.2.0 | 967.03 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.2.0 | 1151.99 | OK | |||
| r-devel-windows-x86_64 | 2.2.0 | 153.00 | 602.00 | 755.00 | OK | |
| r-patched-linux-x86_64 | 2.2.0 | 135.69 | 540.91 | 676.60 | OK | |
| r-release-linux-x86_64 | 2.2.0 | 133.79 | 537.97 | 671.76 | OK | |
| r-release-macos-arm64 | 2.2.0 | 187.00 | OK | |||
| r-release-macos-x86_64 | 2.2.0 | 390.00 | OK | |||
| r-release-windows-x86_64 | 2.2.0 | 145.00 | 588.00 | 733.00 | OK | |
| r-oldrel-macos-arm64 | 2.2.0 | 219.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.2.0 | 433.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.2.0 | 177.00 | 797.00 | 974.00 | OK |
Version: 2.2.0
Check: examples
Result: ERROR
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:
> ### Name: createH5LigerDataset
> ### Title: Create on-disk ligerDataset Object
> ### Aliases: createH5LigerDataset
>
> ### ** Examples
>
> h5Path <- system.file("extdata/ctrl.h5", package = "rliger")
> tempPath <- tempfile(fileext = ".h5")
> file.copy(from = h5Path, to = tempPath)
[1] TRUE
> ld <- createH5LigerDataset(tempPath)
Warning: Building liger object with specifying paths to HDF5 files was deprecated in
rliger 2.2.0.
ℹ Please use `read10XH5()` instead.
ℹ It is now possible to load HDF5 backed data into memory with read10XH5() by
default, or featuring the on-disk scalability with read10XH5(inMemory =
FALSE)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/data/gannet/ripley/R/test-clang/hdf5r/libs/hdf5r.so':
libhdf5_hl.so.200: cannot open shared object file: No such file or directory
Calls: createH5LigerDataset -> loadNamespace -> library.dynam -> dyn.load
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [95s/140s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
We recommand you backup your old analysis before overwriting any existing result.
`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
>
> test_check("rliger")
Working ctrl H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/ctrltest_13800f875ac15.h5
Working stim H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/stimtest_13800f1170db69.h5
Working ctrl H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/ctrltest_13800f444d3f48.h5
Working stim H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/stimtest_13800f325e8bf1.h5
Working ctrl H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/ctrltest_13800f220f381c.h5
Working stim H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/stimtest_13800f62305c54.h5
Working ctrl H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/ctrltest_13800f4d33169a.h5
Working stim H5 file path: /tmp/RtmptdwpMw/working_dir/RtmpUSNcEc/stimtest_13800f7996fece.h5
[ FAIL 3 | WARN 0 | SKIP 28 | PASS 1048 ]
══ Skipped tests (28) ══════════════════════════════════════════════════════════
• On CRAN (5): 'test_downstream.R:283:5', 'test_downstream.R:308:5',
'test_factorization.R:299:5', 'test_object.R:390:5', 'test_object.R:443:5'
• Skipping (6): 'test_object.R:68:5', 'test_object.R:321:5',
'test_preprocessing.R:41:13', 'test_preprocessing.R:153:13',
'test_preprocessing.R:218:13', 'test_preprocessing.R:285:13'
• {RcppPlanc} cannot be loaded (16): 'test_downstream.R:49:5',
'test_downstream.R:129:5', 'test_downstream.R:171:5',
'test_downstream.R:227:5', 'test_factorization.R:38:5',
'test_factorization.R:75:5', 'test_factorization.R:103:5',
'test_factorization.R:137:5', 'test_factorization.R:181:5',
'test_factorization.R:217:5', 'test_factorization.R:231:5',
'test_factorization.R:250:5', 'test_object.R:114:5', 'test_object.R:216:5',
'test_subset.R:42:5', 'test_subset.R:57:5'
• {fields} is not installed (1): 'test_preprocessing.R:94:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_object.R:519:5'): H5AD ───────────────────────────────────────
Expected `writeH5AD(ctrlRaw, tempfilename1, overwrite = FALSE)` to run without any errors.
ℹ Actually got a <simpleError> with text:
unable to load shared object '/data/gannet/ripley/R/test-clang/hdf5r/libs/hdf5r.so':
libhdf5_hl.so.200: cannot open shared object file: No such file or directory
── Failure ('test_object.R:522:5'): H5AD ───────────────────────────────────────
`writeH5AD(ctrlRaw, tempfilename1, overwrite = FALSE)` threw an error with unexpected message.
Expected match: "file exists"
Actual message: "unable to load shared object '/data/gannet/ripley/R/test-clang/hdf5r/libs/hdf5r.so':\n libhdf5_hl.so.200: cannot open shared object file: No such file or directory"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_object.R:522:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─rliger::writeH5AD(ctrlRaw, tempfilename1, overwrite = FALSE)
7. ├─rliger:::writeH5AD.dgCMatrix(ctrlRaw, tempfilename1, overwrite = FALSE)
8. └─base::loadNamespace(x)
9. └─base::library.dynam(lib, package, package.lib)
10. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test_object.R:527:5'): H5AD ─────────────────────────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/data/gannet/ripley/R/test-clang/hdf5r/libs/hdf5r.so':
libhdf5_hl.so.200: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─rliger::readH5AD(tempfilename1, layer = "X", inMemory = TRUE) at test_object.R:527:5
2. │ └─rliger::readH5ADMem(filename, layer, obs)
3. └─base::loadNamespace(x)
4. └─base::library.dynam(lib, package, package.lib)
5. └─base::dyn.load(file, DLLpath = DLLpath, ...)
[ FAIL 3 | WARN 0 | SKIP 28 | PASS 1048 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.2.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘reactome.db’
Flavor: r-oldrel-macos-arm64
Version: 2.2.0
Check: installed package size
Result: NOTE
installed size is 11.1Mb
sub-directories of 1Mb or more:
R 2.1Mb
libs 6.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64