[Bioc-devel] Build error: missing perl xml module
Hi Spencer, Thanks for your message. I've installed the missing Perl modules on nebbiolo2. This is machine is coming back online after some updates and may take a few builds to get back on track. I recommend checking next week to see if the error resolved. I originally installed MEME suite for another package that is being reviewed, but it should be installed on all the builders for memes. I'll document my progress at https://github.com/Bioconductor/BBS/issues/421. 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 Spencer Nystrom <nystromdev at gmail.com>
Sent: Tuesday, September 24, 2024 10:16 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Build error: missing perl xml module
Sent: Tuesday, September 24, 2024 10:16 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Build error: missing perl xml module
* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *
Hi all,
I maintain the `{memes}` package that interfaces with the MEME Suite
toolkit. I just noticed a failing build in devel because the meme suite was
installed on the builders (thank you!!), and it is missing a perl module.
```
Can't locate XML/Parser/Expat.pm in @INC (you may need to install the
XML::Parser::Expat module) (@INC entries checked: /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.38.2
/usr/local/share/perl/5.38.2 /usr/lib/x86_64-linux-gnu/perl5/5.38
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base
/usr/lib/x86_64-linux-gnu/perl/5.38 /usr/share/perl/5.38
/usr/local/lib/site_perl) at
/opt/meme/libexec/meme-5.5.5/tomtom_xml_to_html line 21.
BEGIN failed--compilation aborted at
/opt/meme/libexec/meme-5.5.5/tomtom_xml_to_html
```
There are some more detailed instructions about the perl modules required
at this link:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmeme-suite.org%2Fmeme%2Fdoc%2Finstall.html%3Fman_type%3Dweb*quick_src__%3BIw!!PxiZbSOawA!NCQV0BW7Os87zbcvm3b9qWmMA_O3r91hl199fHrRRQ8R_oQA2_qqaq3NRs8oQKaPMB_f5W_AJWO1XS_nsE1CeUmpzaVlNQ%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C45284af7af034c3c4b8908dcdca383fa%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638627842093790707%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=I5pfYqhUm6RFQ9cYaDvOikrsOGcfpcinnRQe%2BtfDfWg%3D&reserved=0<https://urldefense.com/v3/__https://meme-suite.org/meme/doc/install.html?man_type=web*quick_src__;Iw!!PxiZbSOawA!NCQV0BW7Os87zbcvm3b9qWmMA_O3r91hl199fHrRRQ8R_oQA2_qqaq3NRs8oQKaPMB_f5W_AJWO1XS_nsE1CeUmpzaVlNQ$>
I'm a bit out of the loop on how the builders work these days, but I've
done my fair share of troubleshooting installing the meme suite so if I can
be of any help debugging this feel free to reach out.
Thanks again for adding this to the builders, I had no idea that had
happened!
Cheers,
- Spencer
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