Open ricoderks opened 3 years ago
Hi,
Small update. It fails on this line in getCD()
:
descs_x_loop <- rcdk::eval.desc(mols_x1, descNames)
Cheers, Rico
Hi, It seems to a compatibility problem with last version of Ubuntu and Rstudio
See this:
https://community.rstudio.com/t/rstudio-is-crashing-after-update-on-ubuntu-20-04-focal/66682
They are working to fix it in a update of Rstudio. Hope it will be released soon!
Thanks! Paolo
A possible solution found in the link before:
“Just thought I'd add a finding on this: I'm running Lubuntu 20.04 and have freshly installed R (4.0.2) and R Studio (1.3.59), display=1920x1080.
I ran into the same problems as others have described. The problem may be associated with the nouveau driver for Nvidia cards.
Switching to the NVidia proprietary driver (under additional drivers as suggested by this post on askubuntu ) fixed the issue and RStudio runs just fine now.”
Maybe this help
Hi Paolo,
I'am using Rstudio 1.3.1056.
Just to be sure I ran the same code in just R and it stops with this error:
[1] "Computing Chemical Descriptors 1 of 970 ... Please wait"
Error: segfault from C stack overflow
If I want to run some other command I get:
*** caught segfault ***
address (nil), cause 'unknown'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Cheers, Rico
A possible solution found in the link before:
“Just thought I'd add a finding on this: I'm running Lubuntu 20.04 and have freshly installed R (4.0.2) and R Studio (1.3.59), display=1920x1080.
I ran into the same problems as others have described. The problem may be associated with the nouveau driver for Nvidia cards.
Switching to the NVidia proprietary driver (under additional drivers as suggested by this post on askubuntu ) fixed the issue and RStudio runs just fine now.”
Maybe this help
I'll look into this. Thanks.
Cheers, Rico
A possible solution found in the link before: “Just thought I'd add a finding on this: I'm running Lubuntu 20.04 and have freshly installed R (4.0.2) and R Studio (1.3.59), display=1920x1080. I ran into the same problems as others have described. The problem may be associated with the nouveau driver for Nvidia cards. Switching to the NVidia proprietary driver (under additional drivers as suggested by this post on askubuntu ) fixed the issue and RStudio runs just fine now.” Maybe this help
I'll look into this. Thanks.
Cheers, Rico
I have ATI Radeon Pro WX 2100 card.
Cheers, Rico
I've been playing around in getCD()
and if I leave the descriptor "org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor"
(index 20) out, it goes fine.
The modified function looks like this:
function (x) {
print(paste0("Converting SMILES..."))
for (i in 1:nrow(x)) {
smi <- rcdk::parse.smiles(as.character(unlist(x[i, "SMILES"])))[[1]]
smi1 <- rcdk::generate.2d.coordinates(smi)
smi1 <- rcdk::get.smiles(smi, smiles.flavors(c("CxSmiles")))
x$SMILES[i] <- smi1
print(paste0(i, " of ", nrow(x)))
}
descNames <- rcdk::get.desc.names(type = "all")
descNames1 <- c("org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor")
print(paste0("Checking for compound errors..."))
mols_x <- rcdk::parse.smiles(as.character(unlist(x[1, "SMILES"])))
descs1_x <- rcdk::eval.desc(mols_x, descNames1)
for (i in 2:nrow(x)) {
mols1 <- rcdk::parse.smiles(as.character(unlist(x[i, "SMILES"])))
descs1_x[i, ] <- rcdk::eval.desc(mols1, descNames1)
print(paste0(i, " of ", nrow(x)))
}
x_na <- data.frame(descs1_x, x)
x_na_rem <- x_na[stats::complete.cases(x_na), ]
x_na_rem <- x_na_rem[, -c(1:6)]
print(paste0("Computing Chemical Descriptors 1 of ", nrow(x_na_rem),
" ... Please wait"))
mols_x1 <- rcdk::parse.smiles(as.character(unlist(x_na_rem[1, "SMILES"])))[[1]]
rcdk::convert.implicit.to.explicit(mols_x1)
# leave out "org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor"
descs_x_loop <- rcdk::eval.desc(mols_x1, descNames[-20])
for (i in 2:nrow(x_na_rem)) {
mols <- rcdk::parse.smiles(as.character(unlist(x_na_rem[i, "SMILES"])))[[1]]
rcdk::convert.implicit.to.explicit(mols)
# leave out "org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor"
descs_x_loop[i, ] <- rcdk::eval.desc(mols, descNames[-20])
print(paste0(i, " of ", nrow(x_na_rem)))
}
datadesc <- data.frame(x_na_rem, descs_x_loop)
return(datadesc)
}
Cheers, Rico
I looked deeper in rcdk::eval.desc()
and it goes wrong here:
descvals <- lapply(molecules, function(a, check) {
val <- tryCatch({
.jcall(desc, "Lorg/openscience/cdk/qsar/DescriptorValue;",
"calculate", a, check = check)
})
}, check = FALSE)
and if you have only 1 descriptor:
descvals <- lapply(molecules, function(a, b) {
val <- tryCatch({
.jcall(b, "Lorg/openscience/cdk/qsar/DescriptorValue;",
"calculate", a)
}, warning = function(e) return(NA), error = function(e) return(NA))
}, b = desc)
Hope this is helpfull. Don't know how to go further. Never worked with rJava stuff.
cheers, Rico
Hi, It seems to a compatibility problem with last version of Ubuntu and Rstudio
See this:
https://community.rstudio.com/t/rstudio-is-crashing-after-update-on-ubuntu-20-04-focal/66682
They are working to fix it in a update of Rstudio. Hope it will be released soon!
Mmm, I get the exact same error in R (command line), so I bet Rstudio is not part of the problem.
If I run getCD(HILIC)
immediately after loading the library, I get
Error: segfault from C stack overflow
Warning messages:
1: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
2: In FUN(X[[i]], ...) : The AtomType null could not be found
3: In FUN(X[[i]], ...) : Molecule must have 3D coordinates
on R version 4.2.3 (2023-03-15) running in Docker with an image generated with
ARG R_VERSION=latest
FROM rocker/verse:${R_VERSION}
RUN apt-get update && \
apt-get install -y --no-install-recommends \
build-essential \
libomp-dev \
default-jdk && \
git clone \
--recursive \
--branch stable \
--depth 1 https://github.com/Microsoft/LightGBM && \
cd ./LightGBM && \
sh build-cran-package.sh --no-build-vignettes && \
R CMD INSTALL ./lightgbm_*.tar.gz && \
cd .. && \
rm -rf ./LightGBM
RUN R -e 'install.packages(c("devtools", "reticulate"))'
RUN R -e 'library(reticulate); install_miniconda()'
RUN R -e 'devtools::install_github("Paolobnn/Retiplib")'
RUN R -e 'devtools::install_github("Paolobnn/Retip")'
RUN R -e 'library(keras); install_keras()'
the first RUN
is taken from https://github.com/microsoft/LightGBM/blob/master/docker/dockerfile-r that is the official Microsoft Dockerfile for LightGBM.
The problem persists also with older version, I've attempted to build with docker build --build-arg R_VERSION=3.6.3-ubuntu18.04
and it crashes in the exact same way.
Hi,
I wanted to try the Retip package, but running your example it made R crash when it wants to compute the chemical descriptors.
In Rstudio I get this output:
It outputs the line
[80786:80786:20200826,091229.024746:ERROR elf_dynamic_array_reader.h:61] tag not found
many many times. I also tried without parallel computing, but same issue. Can you help me with this?My sessioninfo:
I have openjdk-11 installed. I also tried with openjdk-8, but same issue.
Cheers, Rico