Enter the body of text here I am running the AA alignment with msa package, previously it works OK. Just suddenly got this matrix problem.

Code should be placed in three backticks as shown below

test<-AAStringSet(c("MMNR","MVNR")) msa(test)

include your problematic code here with any corresponding output

use default substitution matrix CLUSTAL 2.1

Call: msa(test)

MsaAAMultipleAlignment with 2 rows and 963 columns Error in .local(x, ...) : consensus matrix 'x' is not in proper format

please also include the results of running the following in an R session

sessionInfo( )

R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_Singapore.utf8 LC_CTYPE=English_Singapore.utf8
[3] LC_MONETARY=English_Singapore.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Singapore.utf8

time zone: Asia/Singapore tzcode source: internal

attached base packages: character(0)

other attached packages: [1] msa_1.33.0

loaded via a namespace (and not attached): [1] GenomeInfoDb_1.37.2 methods_4.3.1 zlibbioc_1.47.0
[4] GenomeInfoDbData_1.2.10 XVector_0.41.1 BiocGenerics_0.47.0
[7] RCurl_1.98-1.12 Biostrings_2.69.2 stats4_4.3.1
[10] utils_4.3.1 bitops_1.0-7 IRanges_2.35.2
[13] graphics_4.3.1 grDevices_4.3.1 stats_4.3.1
[16] compiler_4.3.1 base_4.3.1 rstudioapi_0.15.0
[19] tools_4.3.1 Rcpp_1.0.11 BiocManager_1.30.21
[22] S4Vectors_0.39.1 crayon_1.5.2 rBLAST_0.99.2
[25] datasets_4.3.1