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

[Spencer Nystrom]

Thanks so much! The build is working now!

Cheers!
  - Spencer


On Thu, Sep 26, 2024, 4:03 PM Jennifer Wokaty <Jennifer.Wokaty using sph.cuny.edu>
wrote:

> 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$>
>
> I'm a bit out of the loop on how the builders work these days, but I've
> done my fair share of troubleshooting installing the meme suite so if I can
> be of any help debugging this feel free to reach out.
>
> Thanks again for adding this to the builders, I had no idea that had
> happened!
>
> Cheers,
>   - Spencer
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
>
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!NCQV0BW7Os87zbcvm3b9qWmMA_O3r91hl199fHrRRQ8R_oQA2_qqaq3NRs8oQKaPMB_f5W_AJWO1XS_nsE1CeUmKnabDnA%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C45284af7af034c3c4b8908dcdca383fa%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638627842093808893%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=%2FCpT%2F9KOCUGBwbPNDi8y84cex23r8z6tDuhs%2FJgcDIA%3D&reserved=0
> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!NCQV0BW7Os87zbcvm3b9qWmMA_O3r91hl199fHrRRQ8R_oQA2_qqaq3NRs8oQKaPMB_f5W_AJWO1XS_nsE1CeUmKnabDnA$>
>

	[[alternative HTML version deleted]]