[Bioc-devel] ChemmineOB build failures

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