Last updated on 2025-09-26 08:50:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.3 | 23.98 | 330.74 | 354.72 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.3 | 15.80 | 144.09 | 159.89 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.3 | 552.83 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.3 | 558.45 | OK | |||
| r-devel-windows-x86_64 | 0.1.3 | 25.00 | 293.00 | 318.00 | OK | |
| r-patched-linux-x86_64 | 0.1.3 | 22.47 | 315.13 | 337.60 | OK | |
| r-release-linux-x86_64 | 0.1.3 | 20.10 | 313.33 | 333.43 | OK | |
| r-release-macos-arm64 | 0.1.3 | 142.00 | OK | |||
| r-release-macos-x86_64 | 0.1.3 | 290.00 | OK | |||
| r-release-windows-x86_64 | 0.1.3 | 24.00 | 294.00 | 318.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.3 | 102.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.3 | 13.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.1.3 | 34.00 | 384.00 | 418.00 | OK |
Version: 0.1.3
Check: examples
Result: ERROR
Running examples in ‘longreadvqs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AAcompare
> ### Title: Comparing viral quasispecies diversity metrics at amino acid
> ### level
> ### Aliases: AAcompare
>
> ### ** Examples
>
> ## Locate input FASTA files-----------------------------------------------------------------------
> sample1filepath <- system.file("extdata", "s1.fasta", package = "longreadvqs")
> sample2filepath <- system.file("extdata", "s2.fasta", package = "longreadvqs")
>
> ## Prepare data for viral quasispecies comparison between two samples-----------------------------
> set.seed(123)
> sample1 <- vqsassess(sample1filepath, pct = 5, samsize = 50, label = "sample1")
Error in (function (cond) :
error in evaluating the argument 'pattern' in selecting a method for function 'nmismatch': pairwiseAlignment() has moved from Biostrings to the pwalign package, and is
formally defunct in Biostrings >= 2.77.1. Please call
pwalign::pairwiseAlignment() to get rid of this error.
Calls: vqsassess ... pairwiseAlignment -> .call_fun_in_pwalign -> .Defunct
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘longreadvqs-vignette.Rmd’ using rmarkdown
Quitting from longreadvqs-vignette.Rmd:44-47 [cmd0]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'pattern' in selecting a method for function 'nmismatch': pairwiseAlignment() has moved from Biostrings to the pwalign package, and is
formally defunct in Biostrings >= 2.77.1. Please call
pwalign::pairwiseAlignment() to get rid of this error.
---
Backtrace:
▆
1. ├─longreadvqs::vqssub(sample1, pct = 10, label = "sample1")
2. │ ├─Biostrings::nmismatch(pairwiseAlignment(hapre$seqs, hapre$seqs[1]))
3. │ └─Biostrings::pairwiseAlignment(hapre$seqs, hapre$seqs[1])
4. │ └─Biostrings:::.call_fun_in_pwalign("pairwiseAlignment", ...)
5. │ └─base::.Defunct(msg = wmsg(msg))
6. │ └─base::stop(...)
7. └─base (local) `<fn>`(`<dfnctErr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'longreadvqs-vignette.Rmd' failed with diagnostics:
error in evaluating the argument 'pattern' in selecting a method for function 'nmismatch': pairwiseAlignment() has moved from Biostrings to the pwalign package, and is
formally defunct in Biostrings >= 2.77.1. Please call
pwalign::pairwiseAlignment() to get rid of this error.
--- failed re-building ‘longreadvqs-vignette.Rmd’
SUMMARY: processing the following file failed:
‘longreadvqs-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.3
Check: package dependencies
Result: ERROR
Package required but not available: ‘QSutils’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64