[Bioc-devel] Build error: missing perl xml module

[Jennifer Wokaty]

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 using r-project.org> on behalf of Spencer Nystrom <nystromdev using gmail.com>
Sent: Tuesday, September 24, 2024 10:16 AM
To: bioc-devel using r-project.org <bioc-devel using 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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