#41956 closed update (fixed)
bedtools @2.17.0_1: update to 2.18.1, move to GitHub
| Reported by: | arjanvandervelde (Arjan van der Velde) | Owned by: | larryv (Lawrence Velázquez) |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | |
| Keywords: | haspatch maintainer | Cc: | |
| Port: | bedtools |
Description
bedtools has moved off of google code, to github. also, they've released a newer version. please find the patch for the Portfile attached.
-- Arjan
Attachments (2)
Change History (12)
comment:1 Changed 11 years ago by cooljeanius (Eric Gallager)
comment:3 Changed 11 years ago by larryv (Lawrence Velázquez)
| Cc: | vandervelde.ag@… removed |
|---|---|
| Keywords: | haspatch maintainer added |
| Summary: | updated bedtools → bedtools @2.17.0_1: update to 2.18.1, move to GitHub |
| Version: | 2.2.1 |
Thanks for the update. In the future, feel free to use the “maintainer” keyword on tickets for ports you maintain, and “haspatch” when you attach a patch.
comment:4 Changed 11 years ago by larryv (Lawrence Velázquez)
| Owner: | changed from macports-tickets@… to larryv@… |
|---|---|
| Status: | new → assigned |
The BEDTools makefile hard-codes CXX and CXXFLAGS and thus does not use the right compiler.
Do you know whether it is critical for CXXFLAGS to contain -O2 specifically? The default optimization in MacPorts is -Os.
comment:5 follow-up: 6 Changed 11 years ago by arjanvandervelde (Arjan van der Velde)
i don't know. i'd rather not change the makefile if possible. i don't think this has changed from 2.17 to 2.18. can we keep it as is (as was)?
comment:6 Changed 11 years ago by larryv (Lawrence Velázquez)
No, it is not acceptable for the makefile to hard-code g++ as the C++ compiler. It was not acceptable before, and it’s not acceptable now; I expect that Ryan just overlooked it when he submitted the initial commit. The documentation even suggests editing the makefile if an alternate compiler is desired.
I’ll ask upstream about the flags.
comment:7 Changed 11 years ago by arjanvandervelde (Arjan van der Velde)
ok. i have created a patch to comment out the relevant lines in the Makefile. instead, the compiler and flags are now passed from the Portfile. additionally i have set the optimization flag to -O2 in the Portfile. for bedtools we do not care about code size but we do care a lot about performance -- i would consider this critical. is this acceptable?
Thanks.
-- Arjan
Changed 11 years ago by arjanvandervelde (Arjan van der Velde)
| Attachment: | Portfile-bedtools.diff added |
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Changed 11 years ago by arjanvandervelde (Arjan van der Velde)
| Attachment: | patch-Makefile.diff added |
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comment:8 Changed 11 years ago by arjanvandervelde (Arjan van der Velde)
Hello. Could you please have another look at this? Thank you very much.
-- Arjan
comment:9 Changed 11 years ago by larryv (Lawrence Velázquez)
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
r115738. The Makefile patch is unnecessary, as providing CXX and CXXFLAGS as command-line arguments overrides the internal variable definitions.
comment:10 Changed 11 years ago by arjanvandervelde (Arjan van der Velde)
thank you very much.
-- Arjan
If it is now on GitHub, consider using the GitHub portgroup: browser:trunk/dports/_resources/port1.0/group/github-1.0.tcl