Question

chemmineOB install help

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jrbald04 • 0

@f3fd86b6

Last seen 20 months ago

United States

I'm having difficulty installing chemmineOB. I was able to install biocmanager and chemmineR without much difficulty. I installed openbabel using brew and found that it exists in ~/local/include/openbabel-2.0/openbabel/ in my directories. It is version 3.1.0. I am running r version 4.4.0 and I have bioconductor version 3.19 (all current). I have been running:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChemmineOB")

and I get:

ChemmineOB.cpp:1569:10: fatal error: 'openbabel/obutil.h' file not found
#include <openbabel/obutil.h>
         ^~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [ChemmineOB.o] Error 1

I'm not sure why it won't recognize .obutil.h as this file exists in that directory.

ChemmineOB Install • 1.4k views

ADD COMMENT • link updated 17 days ago by Jeremy • 0 • written 20 months ago by jrbald04 • 0

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I resinstalled openbabel and was successful in doing so. I also downloaded the .tgz file from the website for chemmineOB and am now getting this error. Could it possibly be that I am running it on an M2 chip and it is not compatible with it? I've also confirmed that the /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ChemmineOB/libs/ChemmineOB.so filepath does exist.

Error: package or namespace load failed for ChemmineOB:
 .onLoad failed in loadNamespace() for ChemmineOB, details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ChemmineOB/libs/ChemmineOB.so:
 (mach-o file, but is an incompatible architecture (have x86_64, need arm64e or arm64))

ADD REPLY • link 20 months ago jrbald04 • 0

score 1 · Answer 1 · 2024-06-10

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khoran ▴ 10

@khoran-10774

Last seen 20 months ago

Canada

ChemmineOB has never been tested on arm64 and is unlikely to work as-is. Since I don't have access to an M2, I'm afraid I can't be much help.

ADD COMMENT • link 20 months ago khoran ▴ 10

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Gotcha! thanks for the reply

ADD REPLY • link 20 months ago jrbald04 • 0

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I could install ChemmineOB on my MacBook Pro M1 Max using this procedure

1. Install open-babel and eigen using homebrew and create a custom link

brew install open-babel

brew install eigen

sudo ln -s /opt/homebrew/include/eigen3/Eigen /opt/homebrew/include/Eigen

2. Add this to your ~/.R/Makevars (or create the file if it does not exist), you may want to remove this after installing successfully

CXX=clang++ -arch arm64

CXX11STD = -std=c++11

CPPFLAGS+=-I/opt/homebrew/include -I/opt/homebrew/include/openbabel3 -I/opt/homebrew/include/eigen3

LDFLAGS+=-L/opt/homebrew/lib

LIBS += -L/opt/homebrew/lib -lopenbabel

3. Install ChemmineOB

BiocManager::install("ChemmineOB", type="source", force=T)

(I was actually interested in volcalc, this package installed effortlessly after successfully installing ChemmineOB) pak::pkg_install("Meredith-Lab/volcalc")

R version 4.5.2 (2025-10-31) Platform: aarch64-apple-darwin20 Running under: macOS Tahoe 26.2

ADD REPLY • link 17 days ago Jeremy • 0