Some SMILEs crash the entire R

[lz100]

Some SMILEs break extractDrugLongestAliphaticChain

library(rcdk)
library(Rcpi)
library(magrittr)
"[H]OC1=C2OC(=O)C34C5=C6C7([H])C8=C(C([H])([H])C([H])(C79C([H])([H])C5([H])C(=C([H])C([H])(C%10([H])C([H])([H])C([H])([H])C([H])([H])C%10([H])[H])C([H])([H])C4([H])C%11(OC(=O)C=%12C%11=C([H])C([H])=C([H])C%12C([H])([H])C([H])([H])C([H])([H])N([H])[H])C23C([H])([H])C6([H])[H])C([H])([H])C9([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])C%13([H])N8C([H])([H])C%14([H])C%15([H])N(C%16([H])C%17(C([H])([H])C%18(C([H])([H])C%17([H])[H])C([H])([H])C([H])([H])C([H])([H])C%18([H])[H])C([H])([H])C([H])([H])C%15([H])C([H])([H])C1%16[H])C([H])([H])C%13([H])C%14([H])[H]" %>%
     parse.smiles() %>% .[[1]] %>%
    extractDrugLongestAliphaticChain()

#> Error: segfault from C stack overflow

Then, if you don't run extractDrugLongestAliphaticChain but run with other random Rcpi functions, the entire R session crashes

"[H]OC1=C2OC(=O)C34C5=C6C7([H])C8=C(C([H])([H])C([H])(C79C([H])([H])C5([H])C(=C([H])C([H])(C%10([H])C([H])([H])C([H])([H])C([H])([H])C%10([H])[H])C([H])([H])C4([H])C%11(OC(=O)C=%12C%11=C([H])C([H])=C([H])C%12C([H])([H])C([H])([H])C([H])([H])N([H])[H])C23C([H])([H])C6([H])[H])C([H])([H])C9([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])C%13([H])N8C([H])([H])C%14([H])C%15([H])N(C%16([H])C%17(C([H])([H])C%18(C([H])([H])C%17([H])[H])C([H])([H])C([H])([H])C([H])([H])C%18([H])[H])C([H])([H])C([H])([H])C%15([H])C([H])([H])C1%16[H])C([H])([H])C%13([H])C%14([H])[H]" %>%
     parse.smiles() %>% .[[1]] %>%
     extractDrugXLogP()

 *** caught segfault ***
address 0x311000006, cause 'memory not mapped'

Traceback:
 1: .jcheck()
 2: .jcall(dval, "Lorg/openscience/cdk/qsar/result/IDescriptorResult;",     "getValue")
 3: FUN(X[[i]], ...)
 4: lapply(descvals, .get.desc.values, nexpected = length(dnames))
 5: eval.desc(molecules, "org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor",     verbose = !silent)
 6: extractDrugXLogP(.)
 7: "[H]OC1=C2OC(=O)C34C5=C6C7([H])C8=C(C([H])([H])C([H])(C79C([H])([H])C5([H])C(=C([H])C([H])(C%10([H])C([H])([H])C([H])([H])C([H])([H])C%10([H])[H])C([H])([H])C4([H])C%11(OC(=O)C=%12C%11=C([H])C([H])=C([H])C%12C([H])([H])C([H])([H])C([H])([H])N([H])[H])C23C([H])([H])C6([H])[H])C([H])([H])C9([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])C%13([H])N8C([H])([H])C%14([H])C%15([H])N(C%16([H])C%17(C([H])([H])C%18(C([H])([H])C%17([H])[H])C([H])([H])C([H])([H])C([H])([H])C%18([H])[H])C([H])([H])C([H])([H])C%15([H])C([H])([H])C1%16[H])C([H])([H])C%13([H])C%14([H])[H]" %>%     parse.smiles() %>% .[[1]] %>% extractDrugXLogP()

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

The first issue may be CDK java issue, but can we do something in the second case to prevent R crash?

[nanxstats]

I would recommend checking JDK and rJava configurations. Normally, this would return a proper NA:

library(magrittr)

"CCCC" %>%
  rcdk::parse.smiles() %>%
  .[[1]] %>%
  Rcpi::extractDrugLongestAliphaticChain()

#> nAtomLAC
#> 1        4

x <- "[H]OC1=C2OC(=O)C34C5=C6C7([H])C8=C(C([H])([H])C([H])(C79C([H])([H])C5([H])C(=C([H])C([H])(C%10([H])C([H])([H])C([H])([H])C([H])([H])C%10([H])[H])C([H])([H])C4([H])C%11(OC(=O)C=%12C%11=C([H])C([H])=C([H])C%12C([H])([H])C([H])([H])C([H])([H])N([H])[H])C23C([H])([H])C6([H])[H])C([H])([H])C9([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])C%13([H])N8C([H])([H])C%14([H])C%15([H])N(C%16([H])C%17(C([H])([H])C%18(C([H])([H])C%17([H])[H])C([H])([H])C([H])([H])C([H])([H])C%18([H])[H])C([H])([H])C([H])([H])C%15([H])C([H])([H])C1%16[H])C([H])([H])C%13([H])C%14([H])[H]"

x %>%
  rcdk::parse.smiles() %>%
  .[[1]] %>%
  Rcpi::extractDrugLongestAliphaticChain()

#> nAtomLAC
#> 1       NA

If that's really not possible, perhaps wrapping calls with callr could be a workaround to avoid crashing the main process and to allow exception handling. See an example at https://nanx.me/blog/post/disposable-computing-with-callr/.

[lz100]

Thanks for the recommendation. I suspect this is OS related. Both my attempts on Centos 7 and Ubuntu 20 crashed. I wonder if you are using a non-Linux system?

[nanxstats]

Just tested on macOS with Oracle JDK installed via homebrew cask and Windows 10 with Amazon Corretto JDK installed via chocolatey. They all work ok out of the box.