Unhelpful error message when calling RealValET_conservativity

[richelbilderbeek]

Hi @stolarczyk,

BALCONY seems just what I need for my research! Sadly, I quickly get an unhelpful error message. I hope that, due to this bugreport, that in the future BALCONY will help its users more.

Describe the bug

When I run RealValET_conservativity on the supplied alignment, everything is just fine, i.e. this code works without errors:

library(BALCONY)
data("small_alignment")
alignment = small_alignment
weights = get_seq_weights(alignment)
weights = RealValET_conservativity(alignment)

When I use a different alignment, however, I get an unhelpful error message.

Output of the sessionInfo()

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BALCONY_0.2.10

loaded via a namespace (and not attached):
 [1] progress_1.2.2          tidyselect_1.1.0        xfun_0.18              
 [4] purrr_0.3.4             testthat_2.3.2          colorspace_1.4-1       
 [7] vctrs_0.3.4             generics_0.0.2          miniUI_0.1.1.1         
[10] htmltools_0.5.0.9001    stats4_3.6.3            rlang_0.4.8            
[13] manipulateWidget_0.10.1 later_1.1.0.1           pillar_1.4.6           
[16] glue_1.4.2              BiocGenerics_0.32.0     lifecycle_0.2.0        
[19] Rpdb_2.3                zlibbioc_1.32.0         Biostrings_2.54.0      
[22] munsell_0.5.0           htmlwidgets_1.5.2       knitr_1.30             
[25] IRanges_2.20.2          fastmap_1.0.1           httpuv_1.5.4           
[28] crosstalk_1.1.0.1       parallel_3.6.3          Rcpp_1.0.5             
[31] xtable_1.8-4            readr_1.4.0             promises_1.1.1         
[34] scales_1.1.1            S4Vectors_0.24.4        webshot_0.5.2          
[37] jsonlite_1.7.1          XVector_0.26.0          mime_0.9               
[40] hms_0.5.3               digest_0.6.27           dplyr_1.0.2            
[43] shiny_1.5.0             ade4_1.7-15             tools_3.6.3            
[46] magrittr_1.5            rgl_0.100.54            tibble_3.0.4           
[49] crayon_1.3.4            seqinr_4.2-4            pkgconfig_2.0.3        
[52] ellipsis_0.3.1          MASS_7.3-51.5           prettyunits_1.1.1      
[55] rstudioapi_0.11         R6_2.4.1                compiler_3.6.3   

To Reproduce

• Download and unzip the multiple sequence alignment from here: bug.zip

Then run this code:

library(BALCONY)
fasta_filename <- "bug.msa"
testthat::expect_true(file.exists(fasta_filename))
alignment <- seqinr::read.alignment(file = fasta_filename, format = "fasta")
et <- BALCONY::RealValET_conservativity(alignment = alignment)

This gives the unhelpful error:

Error in stats::hclust(dist, method = "average") : 
  NA/NaN/Inf in foreign function call (arg 10)

Expected behavior

A helpful error message.

Desktop (please complete the following information):

• OS: Linux Ubuntu 20.04 Focal Fossa

Additional context

None.