Last updated on 2025-02-11 19:49:22 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| deltaccd | 13 | ||
| limorhyde | 3 | 10 | |
| limorhyde2 | 1 | 12 | |
| phers | 13 | ||
| pmparser | 13 | ||
| seeker | 8 | 5 | |
| simphony | 13 | ||
| spectr | 13 | ||
| tipa | 13 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
Version: 1.0.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-arm64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-30 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘limorhyde2-Ex.R’ failed
The error most likely occurred in:
> ### Name: getDiffRhythmStats
> ### Title: Compute differential rhythm statistics from fitted models
> ### Aliases: getDiffRhythmStats
>
> ### ** Examples
>
> library('data.table')
>
> # rhythmicity in one condition
> y = GSE54650$y
> metadata = GSE54650$metadata
>
> fit = getModelFit(y, metadata)
> fit = getPosteriorFit(fit)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/data/gannet/ripley/R/test-dev/mashr/libs/mashr.so':
libgsl.so.25: cannot open shared object file: No such file or directory
Calls: getPosteriorFit ... getMash -> loadNamespace -> library.dynam -> dyn.load
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(limorhyde2)
>
> test_check('limorhyde2')
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_exported.R:58:3'): getPosteriorFit ─────────────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/data/gannet/ripley/R/test-dev/mashr/libs/mashr.so':
libgsl.so.25: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─limorhyde2::getPosteriorFit(fit) at test_exported.R:58:3
2. │ └─limorhyde2:::getMash(...)
3. └─base::loadNamespace(x)
4. └─base::library.dynam(lib, package, package.lib)
5. └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test_exported.R:79:3'): getPosteriorSamples ─────────────────────────
Error in `{
mpr = mashr::mash_compute_posterior_matrices(mf, md, algorithm.version = "R",
posterior_samples = nPostSamps)
mpi = mpr$PosteriorSamples
}`: task 1 failed - "unable to load shared object '/data/gannet/ripley/R/test-dev/mashr/libs/mashr.so':
libgsl.so.25: cannot open shared object file: No such file or directory"
Backtrace:
▆
1. └─limorhyde2::getPosteriorSamples(fitObs, nPosteriorSamples = 10) at test_exported.R:79:3
2. └─foreach(mf = fit$mashFits, md = fit$mashData) %do% ...
3. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 62 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘differential-rhythmicity.Rmd’ using rmarkdown
Quitting from lines 52-54 [fit] (differential-rhythmicity.Rmd)
Error: processing vignette 'differential-rhythmicity.Rmd' failed with diagnostics:
unable to load shared object '/data/gannet/ripley/R/test-dev/mashr/libs/mashr.so':
libgsl.so.25: cannot open shared object file: No such file or directory
--- failed re-building ‘differential-rhythmicity.Rmd’
--- re-building ‘rhythmicity.Rmd’ using rmarkdown
Quitting from lines 60-61 [posterior_fit] (rhythmicity.Rmd)
Error: processing vignette 'rhythmicity.Rmd' failed with diagnostics:
unable to load shared object '/data/gannet/ripley/R/test-dev/mashr/libs/mashr.so':
libgsl.so.25: cannot open shared object file: No such file or directory
--- failed re-building ‘rhythmicity.Rmd’
--- re-building ‘rnaseq.Rmd’ using rmarkdown
--- finished re-building ‘rnaseq.Rmd’
--- re-building ‘uncertainty.Rmd’ using rmarkdown
Quitting from lines 55-57 [fit] (uncertainty.Rmd)
Error: processing vignette 'uncertainty.Rmd' failed with diagnostics:
unable to load shared object '/data/gannet/ripley/R/test-dev/mashr/libs/mashr.so':
libgsl.so.25: cannot open shared object file: No such file or directory
--- failed re-building ‘uncertainty.Rmd’
SUMMARY: processing the following files failed:
‘differential-rhythmicity.Rmd’ ‘rhythmicity.Rmd’ ‘uncertainty.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 8, OK: 5
Version: 1.1.6
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘fetch.R’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 1.1.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavor: r-release-macos-arm64
Version: 1.1.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ArrayExpress’
Flavor: r-oldrel-macos-arm64
Version: 1.1.6
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.1.6
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ArrayExpress', 'org.Mm.eg.db'
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13