Last updated on 2026-04-05 07:51:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.3 | 128.98 | 152.85 | 281.83 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.1.3 | 99.08 | 104.47 | 203.55 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.3 | 183.00 | 550.59 | 733.59 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.3 | 294.00 | 564.30 | 858.30 | OK | |
| r-devel-macos-arm64 | 1.1.3 | 32.00 | 115.00 | 147.00 | OK | |
| r-devel-windows-x86_64 | 1.1.3 | 148.00 | 216.00 | 364.00 | NOTE | |
| r-patched-linux-x86_64 | 1.1.3 | 123.06 | 138.46 | 261.52 | NOTE | |
| r-release-linux-x86_64 | 1.1.3 | 119.05 | 135.07 | 254.12 | OK | |
| r-release-macos-arm64 | 1.1.3 | OK | ||||
| r-release-macos-x86_64 | 1.1.3 | 77.00 | 170.00 | 247.00 | OK | |
| r-release-windows-x86_64 | 1.1.3 | 140.00 | 192.00 | 332.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.3 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.1.3 | 76.00 | 143.00 | 219.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.1.3 | 162.00 | 243.00 | 405.00 | OK |
Version: 1.1.3
Check: compiled code
Result: NOTE
File ‘phyr/libs/phyr.so’:
Found non-API call to R: ‘R_UnboundValue’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(phyr)
>
> test_check("phyr")
Dropping tips from the phylogeny that are not in the community data
1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
1 2 3 4 5 6 7 8 9 10 11 12 13 14 Dropping tips from the phylogeny that are not in the community data
1 2 3 4 5 6 7 8 9 10 11 12 13 14 'as(<matrix>, "dgTMatrix")' is deprecated.
Use 'as(as(as(., "dMatrix"), "generalMatrix"), "TsparseMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
Saving _problems/test-pglmm_compare-15.R
[ FAIL 1 | WARN 1 | SKIP 3 | PASS 29 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-cor_phylo.R:5:3', 'test-pglmm.R:4:3',
'test_pglmm_utils.R:4:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-pglmm_compare.R:15:3'): ignore these tests when on CRAN since they are time consuming ──
Expected `pglmm_compare(Y ~ X1, family = "binomial", phy = phy, data = sim.dat)` not to throw any errors.
Actually got a <Rcpp::exception> with message:
Estimation of B failed. Check for lack of variation in Y. You could try with a smaller s2.init, but this might not help.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-pglmm_compare.R:15:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─phyr::pglmm_compare(Y ~ X1, family = "binomial", phy = phy, data = sim.dat)
8. └─phyr::pglmm(...)
9. └─phyr:::communityPGLMM.glmm(...)
10. └─phyr:::pglmm_internal_cpp(...)
[ FAIL 1 | WARN 1 | SKIP 3 | PASS 29 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: compiled code
Result: NOTE
File 'phyr/libs/x64/phyr.dll':
Found non-API call to R: 'R_UnboundValue'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Flavor: r-devel-windows-x86_64
Version: 1.1.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘INLA’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.1.3
Check: installed package size
Result: NOTE
installed size is 12.8Mb
sub-directories of 1Mb or more:
doc 2.0Mb
libs 10.2Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64