[Bioc-devel] ChemmineOB build failures

[Jennifer Wokaty]

Hi Kevin,

I have not been able to figure out the configuration for open-babel on Apple Silicon. The release branch is frozen as of this week and undergoing its last build. However, I see that on devel that the Intel mac is passing. I can try to revisit this likely after the release.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Kevin Horan <khoran using cs.ucr.edu>
Sent: Thursday, October 17, 2024 1:14 PM
To: Jennifer Wokaty <Jennifer.Wokaty using sph.cuny.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Thomas Girke <thomas.girke using ucr.edu>
Subject: Re: [Bioc-devel] ChemmineOB build failures


Jennifer,


Any progress on this? I see ChemmineOB is not building on either mac right now.


Kevin


On 10/1/24 8:37 AM, Kevin Horan wrote:

Jennifer,

Great, thanks.


Regarding mac arm64, I'm not familiar with that platform, and I don't have access to it to test on. However, there is an open issue on github with several folks working with OpenBabel on arm64, they might be able to help. Perhaps you could post your question here: https://github.com/girke-lab/ChemmineOB/issues/35<https://urldefense.com/v3/__https://github.com/girke-lab/ChemmineOB/issues/35__;!!LRXxDv2l!T07mOwwMuY2-qQjwZktyWTpdjWaxb6w-RUSf2Bq0T1ufZuE1kq3PkCiCW7rHUR4hX7mGfxXqov5_wZKjuFpzwIP8jMwk$>


The issue is regarding getting ChemmineOB working on arm64, but since that requires OpenBabel as well, the issues are related.


Kevin


On 10/1/24 8:00 AM, Jennifer Wokaty wrote:
Hi Kevin,

I've reinstalled OpenBabel on the Windows release builder, palomino7. However, I need additional guidance to set up on Mac ARM64 as it must be compiled. On the Intel macs, we brew install OpenBabel, so I tried the same with the Mac ARM64 machines; however, running R CMD build with the brewed version gives the missing header error. If you could provide more guidance, I can try compiling it.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org><mailto:bioc-devel-bounces using r-project.org> on behalf of Kevin Horan <khoran using cs.ucr.edu><mailto:khoran using cs.ucr.edu>
Sent: Thursday, September 26, 2024 11:21 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org><mailto:bioc-devel using r-project.org>
Subject: [Bioc-devel] ChemmineOB build failures

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My package ChemmineOB is failing to build on Windows and mac arm64
(kjohnson1). They both show the same error, that a header file is
missing from the OpenBabel installation.

clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3    -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ChemmineOB.cpp -o ChemmineOB.o
ChemmineOB.cpp:1569:10: fatal error: 'openbabel/obutil.h' file not found
#include <openbabel/obutil.h>
          ^~~~~~~~~~~~~~~~~~~~
1 error generated.



Here is the build report:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FChemmineOB%2Fpalomino7-install.html__%3B!!PxiZbSOawA!IoRSgkcxOph1i6RrC5vHOKp5RSfWoFdI30XdtBA0JO6BtHFTCriOSf7f4fF5tJrD0fs6t9kEYFHG4-9KYTrk6wH_gLta%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C1c238f6a100543fa6bb708dcde3ef985%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638629609273870937%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=3WWApsB2%2F6QehII6qR0RYgFObft3KZq1yTH1yGFVzeY%3D&reserved=0<https://urldefense.com/v3/__https://www.bioconductor.org/checkResults/3.19/bioc-LATEST/ChemmineOB/palomino7-install.html__;!!PxiZbSOawA!IoRSgkcxOph1i6RrC5vHOKp5RSfWoFdI30XdtBA0JO6BtHFTCriOSf7f4fF5tJrD0fs6t9kEYFHG4-9KYTrk6wH_gLta$>

It is saying that the file openbabel/obutil.h is missing. That file
appears normally when I install OpenBabel myself, so could you check
that OpenBabel is installed on those machines and confirm whether or not
that file is present? Could you also let me know what directory
openbabel is installed in? Thank you.

Kevin

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