[Bioc-devel] ChemmineOB build failures

[Jennifer Wokaty]

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> on behalf of Kevin Horan <khoran using cs.ucr.edu>
Sent: Thursday, September 26, 2024 11:21 AM
To: bioc-devel using r-project.org <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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