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rmelting's Issues

rmelting frequently crashes the R session on MacBook Pro with M2 chip

Running rmelting regularly makes my R session abort (the "R Session Aborted" with a cartoon of a bomb).

Maybe it's something to do with Java? I had to install Java on my laptop to make rmelting work (sometimes).

I installed from
https://www.java.com/en/download/
And made sure to use "ARM64 version of the JRE".

I tried using the Intel version, but then loading rmelting (library(rmelting)) throws an error.

Sometimes it can go through a given calculation without throwing an error, sometimes (most often) not. It seems completely random. Unfortunately, that makes it almost impossible for me to do Tm calculations in a loop as it is almost guaranteed it will crash.

Otherwise, thanks for a very useful package!

Edit: weirdly, it seems that rmelting does not like to be rushed... If I add Sys.sleep(1) at each iteration of my loop, it seems more likely to finish successfully...

Problems with consecutive locked nucleic acids at the end of the sequence?

Why is there a IndexOutOfBoundsException if the sequence contains consecutive locked nucleic acids at the end?

Please see the examples below:
Consecutive locked nucleic acids effect - owc11 (DNA/DNA) / example from vignette

melting(sequence = "GALCLC", nucleic.acid.conc = 0.0001, hybridisation.type = "dnadna", Na.conc = 1, method.consecutive.locked = "owc11")
[1] 12.94323

add an locked nucleic acid at the end

melting(sequence = "GALCLCL", nucleic.acid.conc = 0.0001, hybridisation.type = "dnadna", Na.conc = 1, method.consecutive.locked = "owc11")
[1] NA
ERROR: java.lang.IndexOutOfBoundsException: Index: 4, Size: 4

delete locked nucleic acids in the middle

melting(sequence = "GALCCL", nucleic.acid.conc = 0.0001, hybridisation.type = "dnadna", Na.conc = 1, method.consecutive.locked = "owc11")
[1] 9.302131

locked nucleic acids -- the last two positions

melting(sequence = "GACLCL", nucleic.acid.conc = 0.0001, hybridisation.type = "dnadna", Na.conc = 1, method.consecutive.locked = "owc11")
[1] NA
ERROR: java.lang.IndexOutOfBoundsException: Index: 4, Size: 4

locked nucleic acids -- only the last position

melting(sequence = "GACCL", nucleic.acid.conc = 0.0001, hybridisation.type = "dnadna", Na.conc = 1, method.consecutive.locked = "owc11")
[1] 4.459016

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