Bug 209653
| Summary: | biology/{htslib,samtools,bcftools}: Update to 1.3.1 | ||||||
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| Product: | Ports & Packages | Reporter: | cartwright | ||||
| Component: | Individual Port(s) | Assignee: | Kurt Jaeger <pi> | ||||
| Status: | Closed FIXED | ||||||
| Severity: | Affects Only Me | CC: | pi | ||||
| Priority: | --- | Keywords: | patch | ||||
| Version: | Latest | ||||||
| Hardware: | Any | ||||||
| OS: | Any | ||||||
| Attachments: |
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Let me know if I need to upload everything separately. testbuilds@work Bump. Do I need to do anything? Thanks. I found some issues with one of the tree ports if built on a loaded system (outside of poudriere) and did not yet find the time to investigate. I'll try to provide details, maybe we find a solution. Here's the build log: http://people.freebsd.org/~pi/logs/bcftools.txt it fails because of issues with the installed port openssl. Fix is: CONFLICTS_BUILD=openssl Thanks for your submission and the patch. But please in the future attach them in plain text as they're easily (re)viewable here in bugzilla which speeds up resolution. :) I'm not sure where to begin with this issue. BCFTools doesn't link directly against OpenSSL. It links with libhts, which links to lubcurl, which links to libssl. Samtools does a similar thing, and it seems weird that it wouldn't also fail to link. The issue appears to be triggered if OPENSSL_NO_SCTP was defined when building the library and not defined when linking/compiling against it. I don't know if this is an biology/htslib issue, a curl issue, or an openssl issue. A commit references this bug: Author: pi Date: Thu May 26 20:28:56 UTC 2016 New revision: 415914 URL: https://svnweb.freebsd.org/changeset/ports/415914 Log: biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer) Changes: head/biology/bcftools/Makefile head/biology/bcftools/distinfo head/biology/bcftools/pkg-plist head/biology/htslib/Makefile head/biology/htslib/distinfo head/biology/samtools/Makefile head/biology/samtools/distinfo head/biology/samtools/files/patch-Makefile (In reply to cartwright from comment #8) I committed the updates now, most of the time the ports will be build using poudriere. I have not analyzed the root cause of the issue. If you find the time, try to find it -- and I know, it's not easy! |
Created attachment 170492 [details] tar archive containing three patches and pounderie testport output Update the following package to 1.3.1 biology/htslib biology/samtools biology/bcftools