Comments (10)
Hi @varungiri,
Can you replicate the error and provide the output of sessionInfo()
please? I can use your code fine.
Thanks,
zach cp
from cdkr.
library(rcdk, fingerprint)
Loading required package: fingerprint
a <- get.fingerprint(parse.smiles('CCCO')[[1]])
b <- get.fingerprint(parse.smiles('CCCC')[[1]])
distance(a,b)
[1] 0.375
sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=de_DE.UTF-8
[9] LC_ADDRESS=de_DE.UTF-8 LC_TELEPHONE=de_DE.UTF-8
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=de_DE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rcdk_3.3.8 fingerprint_3.5.4
loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0 parallel_3.4.0 rcdklibs_2.0
[5] iterators_1.0.8 itertools_0.1-3 rJava_0.9-8 png_0.1-7
distance(a,b)
Segmentation fault (core dumped)
I will meanwhile try to reinstall R and check.
from cdkr.
I can confirm it works for me as well.
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.5 (Sierra)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rcdk_3.4.1 dplyr_0.4.3 plyr_1.8.3 reshape2_1.4.2 ggplot2_2.1.0 ncgcdb_1.0.0 ROracle_1.2-2 DBI_0.5-1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.4.5 png_0.1-7 assertthat_0.1 grid_3.3.1 R6_2.1.2 gtable_0.2.0 magrittr_1.5 scales_0.4.0 itertools_0.1-3 stringi_1.1.2
[11] iterators_1.0.8 tools_3.3.1 stringr_1.1.0 fingerprint_3.5.3 munsell_0.4.3 rcdklibs_2.0 parallel_3.3.1 colorspace_1.2-6 rJava_0.9-8
from cdkr.
@varungiri can you try installing rcdk off of Rajarshi's branch? I see you are using rcdk 3.3.8 but we are using 3.4.1 (now 3.4.2)
from cdkr.
I was in between also trying the cran version; but I get some error none the less.
a <- get.fingerprint(parse.smiles('CCCO')[[1]])
b <- get.fingerprint(parse.smiles('CCCOC')[[1]])
distance(a,b)
[1] 0.7
sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=de_DE.UTF-8
[9] LC_ADDRESS=de_DE.UTF-8 LC_TELEPHONE=de_DE.UTF-8
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=de_DE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rcdk_3.4.2 rcdklibs_2.0 rJava_0.9-8 devtools_1.13.2
[5] fingerprint_3.5.4
loaded via a namespace (and not attached):
[1] png_0.1-7 digest_0.6.10 withr_1.0.2 R6_2.2.1
[5] git2r_0.18.0 httr_1.2.1 itertools_0.1-3 curl_2.6
[9] iterators_1.0.8 tools_3.4.0 parallel_3.4.0 compiler_3.4.0
[13] tcltk_3.4.0 memoise_1.1.0
distance(a,b)
Segmentation fault (core dumped)
I tried installing R again, but in vain. May be I have some broken dependency somewhere. On other machines I tried it also worked for me. Any guess what I can check?
from cdkr.
from cdkr.
Works for me too :
library(fingerprint)
a <- get.fingerprint(parse.smiles('CCCO')[[1]])
b <- get.fingerprint(parse.smiles('CCCC')[[1]])
distance(a,b)
[1] 0.375
distance(a,b)
[1] 0.375
distance(a,b)
[1] 0.375
sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fingerprint_3.5.4 rcdk_3.4.2 rcdklibs_2.0 rJava_0.9-8 RMassBankData_1.8.0
[6] RMassBank_2.3.1 Rcpp_0.12.9
from cdkr.
I checked calls to fp.sim.matrix run without any issue. Even multiple calls to it does not break anything. But the second call to distance still has the issue. --> Does not look like it is C code!
library(rcdk)
Loading required package: rcdklibs
Loading required package: rJava
library(fingerprint)
a <- get.fingerprint(parse.smiles('CCCC')[[1]])
b <- get.fingerprint(parse.smiles('CCCO')[[1]])
c <- get.fingerprint(parse.smiles('CCCN')[[1]])
fingerprint::fp.sim.matrix(c(a,b,c))
[,1] [,2] [,3]
[1,] 1.000 0.375 0.375
[2,] 0.375 1.000 0.400
[3,] 0.375 0.400 1.000
fingerprint::fp.sim.matrix(c(a,b,c))
[,1] [,2] [,3]
[1,] 1.000 0.375 0.375
[2,] 0.375 1.000 0.400
[3,] 0.375 0.400 1.000
fingerprint::fp.sim.matrix(c(a,b,c))
[,1] [,2] [,3]
[1,] 1.000 0.375 0.375
[2,] 0.375 1.000 0.400
[3,] 0.375 0.400 1.000
fingerprint::fp.sim.matrix(c(a,b,c))
[,1] [,2] [,3]
[1,] 1.000 0.375 0.375
[2,] 0.375 1.000 0.400
[3,] 0.375 0.400 1.000
fingerprint::fp.sim.matrix(c(a,b,c))
[,1] [,2] [,3]
[1,] 1.000 0.375 0.375
[2,] 0.375 1.000 0.400
[3,] 0.375 0.400 1.000
fingerprint::distance(a,b)
[1] 0.375
fingerprint::distance(a,c)
Segmentation fault (core dumped)
from cdkr.
Unfortunately, I still can't reproduce this
from cdkr.
Looks like a system specific error. I could not isolate the source of error.
from cdkr.
Related Issues (20)
- Having problem with "eval.desc" HOT 1
- failed to load rcdk HOT 3
- view.molecule.2D not working on Rstudio HOT 5
- get.volume giving error HOT 8
- Major Changes to JDK17 HOT 7
- If possible, provide more verbose messaging on parse.smiles failures
- `get.formula` fails if elements has length one
- library(rcdk) crashes Rstudio HOT 2
- eval.desc return error : "segfault from C stack overflow"
- generate.formula for charged species: window not correctly calculated?
- rcdk::matches() function bugs HOT 3
- cdk implementation in R::depict HOT 3
- InChIKey functionality crashes with "Exception: java.lang.StackOverflowError thrown from the UncaughtExceptionHandler in thread "process reaper"" HOT 6
- How to use HOSEcode HOT 1
- Remove atoms with CDK HOT 1
- Partial charge not-supported for element: 'B'
- Only "0" returned for AromaticAtomsCountDescriptor and AromaticBondsCountDescriptor HOT 4
- Update to CDK 2.9 HOT 2
- Isotope labels for get.isotope.pattern HOT 1
- visualization with `view.molecule.2d` fails with an `<init>` error message HOT 11
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cdkr.