[Bioc-devel] ChemmineOB build failures

[Kevin Horan]

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
>
>
> 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 
>> <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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>>
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