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