[MacPorts] #41956: updated bedtools
#41956: updated bedtools ------------------------------+-------------------------------- Reporter: vandervelde.ag@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: bedtools ------------------------------+-------------------------------- 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 -- Ticket URL: <https://trac.macports.org/ticket/41956> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: updated bedtools -------------------------------+-------------------------------- Reporter: vandervelde.ag@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: bedtools | -------------------------------+-------------------------------- Comment (by egall@…): If it is now on GitHub, consider using the GitHub portgroup: browser:trunk/dports/_resources/port1.0/group/github-1.0.tcl -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: updated bedtools -------------------------------+-------------------------------- Reporter: vandervelde.ag@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: bedtools | -------------------------------+-------------------------------- Comment (by vandervelde.ag@…): i have updated the patch. -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Changes (by larryv@…): * cc: vandervelde.ag@… (removed) * keywords: => haspatch maintainer * version: 2.2.1 => Comment: 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. -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: larryv@… Type: update | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Changes (by larryv@…): * status: new => assigned * owner: macports-tickets@… => larryv@… Comment: The [https://github.com/arq5x/bedtools2/blob/v2.18.1/Makefile BEDTools makefile] hard-codes `CXX` and `CXXFLAGS` and thus does not [[UsingTheRightCompiler|use the right compiler]]. Do you know whether it is critical for `CXXFLAGS` to contain `-O2` specifically? The default optimization in MacPorts is `-Os`. -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: larryv@… Type: update | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Comment (by vandervelde.ag@…): 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)? -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: larryv@… Type: update | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Comment (by larryv@…): 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 [http://bedtools.readthedocs.org/en/latest/content/installation.html #compiling-from-source-via-google-code suggests editing the makefile] if an alternate compiler is desired. I’ll ask upstream about the flags. -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: larryv@… Type: update | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Comment (by vandervelde.ag@…): 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 -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: larryv@… Type: update | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Comment (by vandervelde.ag@…): Hello. Could you please have another look at this? Thank you very much. -- Arjan -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: larryv@… Type: update | Status: closed Priority: Normal | Milestone: Component: ports | Version: Resolution: fixed | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Changes (by larryv@…): * status: assigned => closed * resolution: => fixed Comment: r115738. The Makefile patch is unnecessary, as providing `CXX` and `CXXFLAGS` as command-line arguments overrides the internal variable definitions. -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
#41956: bedtools @2.17.0_1: update to 2.18.1, move to GitHub -------------------------------+--------------------------------- Reporter: vandervelde.ag@… | Owner: larryv@… Type: update | Status: closed Priority: Normal | Milestone: Component: ports | Version: Resolution: fixed | Keywords: haspatch maintainer Port: bedtools | -------------------------------+--------------------------------- Comment (by vandervelde.ag@…): thank you very much. -- Arjan -- Ticket URL: <https://trac.macports.org/ticket/41956#comment:10> MacPorts <http://www.macports.org/> Ports system for OS X
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