[Bioc-devel] ChemmineOB build failures

[Kevin Horan]

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


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> 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
> * This email originates from a sender outside of CUNY. Verify the 
> sender before replying or clicking on links and attachments. *
>
> 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 
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>
> 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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