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20 hours ago •
CDK-R
CDK-R
`get.formula` fails if elements has length one
generate.formula gets an error if the specified element list has only one element specified. Inserting a dummy element with max count of zero circumvents the issue. Of course, I don't know if the actual root cause has anything to to with list length.
generate.formula(120, window = 0.0036, list(c("C", "0", "12")))
# Error in .jcall(mfTool, "Lorg/openscience/cdk/interfaces/IMolecularFormulaSet;", :
# java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
generate.formula(120, window = 0.0036, list(c("C", "0", "12"), c("H", "0", "0")))
# [[1]] cdkFormula: C10 , mass = 120 , charge = 0
generate.formula(120, window = 0.0036, list(c("H", "0", "200")))
# Error in .jcall(mfTool, "Lorg/openscience/cdk/interfaces/IMolecularFormulaSet;", :
# java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
list(c("C", "0", "12")) is in fact a list of length one, so the issue isn't that it got converted to a list of length 3:
list(c("C", "0", "12"))
# [[1]]
# [1] "C" "0" "12"
(I am aware that the doc specifies c("C", 0, 50) but of course 0 and 50 get converted to character anyway.)
System (please complete the following information):
> session_info()
- Session info -------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 4.1.2 (2021-11-01)
os Windows 10 x64 (build 19042)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz Europe/Berlin
date 2022-03-17
rstudio 2021.09.0+351 Ghost Orchid (desktop)
pandoc 2.14.0.3 @ C:/Program Files/RStudio/bin/pandoc/ (via rmarkdown)
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