[Debian-med-packaging] Bug#783354: phylip: The phylip package is compiled with wrong flags and as a result is very slow

Atanas Kumbarov kumbarov at gmail.com
Sun Apr 26 11:05:27 UTC 2015

Package: phylip
Version: 1:3.696+dfsg-1
Severity: important
Tags: upstream

Dear Maintainer,
The make file for the phylip package does not set any optimization level by
default. It contains a line which sets some recommended CFLAGS for building
the package on Linux, including optimization flags, but it is commented.

Compiling the package without optimization causes significant performance
loss - it runs twice as slow as when compiled with the suggested CFLAGS for
Linux. Note that some programs from the phylip package may run for many
hours and even days depending on the input data so reducing the
computational time by 50% is a significant improvement.

Please consider building this package with optimization flags:

--- Makefile.unx        2015-04-26 12:32:25.000000000 +0200
+++ Makefile.unx        2015-04-26 12:35:55.158504466 +0200
@@ -92,13 +92,13 @@
 #A minimal one
 # A basic one for debugging
 #CFLAGS  = -g
 # An optimized one for gcc
-#CFLAGS  = -O3 -DUNX -fomit-frame-pointer
+CFLAGS  = -O3 -DUNX -fomit-frame-pointer
 # For some serious debugging using Gnu gcc

Best regards,
Atanas Kumbarov

-- System Information:
Debian Release: 8.0
  APT prefers stable
  APT policy: (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages phylip depends on:
ii  libc6  2.19-18

phylip recommends no packages.

Versions of packages phylip suggests:
pn  phylip-doc  <none>

-- no debconf information
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