pairwiseAlignment() moved to pwalign warning in Biostrings >= 2.72.0

[ecrespoSSF]

I was having issues with pairwise alignments using the crossSetSim() and parSeqSim() examples listed in the vignette https://cran.r-project.org/web/packages/protr/vignettes/protr.html#Similarity_calculation_by_sequence_alignment

It wasn't until I tried twoSeqSim() that I received this error:
<simpleError in .load_package_gracefully("pwalign", "starting with BioC 3.19, ", "calling ", fun, "()"): Could not load package pwalign. Is it installed?

Note that starting with BioC 3.19, calling pairwiseAlignment() requires the pwalign package.
Please install it with:

BiocManager::install("pwalign")>

Installing pwalign has fixed the issue using R version 4.4.1 (2024-06-14) -- "Race for Your Life" on this Platform: x86_64-apple-darwin20

[ecrespoSSF]

This twoSeqSim() function is still a problem
In .call_fun_in_pwalign("pairwiseAlignment", ...) :
pairwiseAlignment() has moved to the pwalign package. Please call pwalign::pairwiseAlignment() to
get rid of this warning.

[nanxstats]

Thanks for reporting. It seems the pairwise sequence alignment stuff has been moved from Biostrings to pwalign (Bioconductor/Contributions#3361). I will make a CRAN update soon to fix this issue.

[nanxstats]

protr 1.7.3 is now on CRAN. You can use install.packages("protr") to try the new version. Use type = "source" if the binary is not built by CRAN yet.

In brief, the new behavior is:

• If Biostrings is not installed, there should be an error saying Biostrings is required and should be installed from Bioconductor.
• If you have Bioconductor >= 3.19 and Biostrings >= 2.72.0 without pwalign installed, there should be an explicit error in the results saying pwalign is required and should be installed from Bioconductor.
• If a lower version of Biostrings is installed (possibily due to using a lower version of R and Bioconductor), then things should work as before.