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View Code? Open in Web Editor NEWR Interface to MELTING 5
Home Page: https://aravind-j.github.io/rmelting/
R Interface to MELTING 5
Home Page: https://aravind-j.github.io/rmelting/
When re-running my R code using the rmelting package, I encountered an error
Error in ._jobjRef_dollar(x[["jobj"]], name) :
no field, method or inner class called 'use_cli_format'
I did not change my code. The last time I ran (about 1 month ago), there was no error. Today I rerun the code, this error occurred.
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...
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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