Created attachment 235067 [details] patch Changes: * add test target * remove TEST option since it isn't needed * change PORTVERSION to DISTVERSION * impove Makefile format to make it more readable 3.4.0 is c++20 compatible (3.3.9 isn't). I've tested several dependencies and they worked. All dependencies should be tested.
Created attachment 235068 [details] patch
Moin moin Thanks for the patch, let's take it for an exp-run. mfg Tobias
New failure log: http://package22.nyi.freebsd.org/data/130amd64-default-foo/2022-07-05_08h38m37s/logs/errors/gcta-1.26.0_3.log
(In reply to Antoine Brodin from comment #3) Thanks Antoine. This port is outdated, I'll submit the patch to update it. Yuri
I looked into upgrading biology/gcta but this doesn't appear feasible because new versions now use Intel's closed source MKL library. The right path appears to be to 1) upgrade math/eigen3 with the attached patch 2) leave the current version as math/eigen3-239 3) adjust biology/gcta to use math/eigen3-239 @tcberner, if you would approve the above course of action - I could commit this change.
(In reply to Yuri Victorovich from comment #5) Moin moin It seems a bit much to add a new eigen-port just to satisfy one singular port. As eigen is header-only, could you not just fetch the old eigen as an additional distfile in said port and set CXXFLAGS to include from ${WRKDIR}/eigen-3.2.9? mfg Tobias
(In reply to Tobias C. Berner from comment #6) Sure, this is also doable.
(In reply to Yuri Victorovich from comment #7) Thanks! Feel free to commit the patch once you're ready. mfg Tobias
A commit in branch main references this bug: URL: https://cgit.FreeBSD.org/ports/commit/?id=5fa506511af383c8b1a2f49f861df31966d32493 commit 5fa506511af383c8b1a2f49f861df31966d32493 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2022-07-06 20:23:30 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2022-07-06 20:40:04 +0000 biology/gcta: Use bundled version of eigen3 ... in preparation to upgrading math/eigen to 3.4.0. This version of gcta (1.26.0) doesn't support eigen-3.4.0, and it can't be upgraded because latest versions of gcta use Intel's closed source MKL library. PR: 265032 Suggested by: tcberner@ Approved by: portmgr (interoperability) biology/gcta/Makefile | 16 +++++++++++----- biology/gcta/distinfo | 4 +++- 2 files changed, 14 insertions(+), 6 deletions(-)
A commit in branch main references this bug: URL: https://cgit.FreeBSD.org/ports/commit/?id=b4bb40a4b58ca2930040785937ca086b05c0db50 commit b4bb40a4b58ca2930040785937ca086b05c0db50 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2022-07-06 20:33:29 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2022-07-06 20:40:04 +0000 math/eigen3: Update 3.3.9 -> 3.4.0, add tests and cleanup PR: 265032 Approved by: tcberner@ (from kde@) math/eigen3/Makefile | 34 +++++++++--------- math/eigen3/distinfo | 6 ++-- math/eigen3/pkg-plist | 98 +++++++++++++++++++++++++++++++++++++++------------ 3 files changed, 95 insertions(+), 43 deletions(-)
Committed, thanks!