Package: bowtie
Version: 0.12.7-2
Severity: normal
Tags: patch

Dear Maintainer,

The LDFLAGS/CPPFLAGS hardening flags are missing because the
build system ignores them. For more hardening information please
have a look at [1], [2] and [3].

The attached patch fixes the issue, if possible it should be sent
to upstream.

To check if all flags were correctly enabled you can use
`hardening-check` from the hardening-includes package and check
the build log (for example with blhc [4]) (hardening-check
doesn't catch everything):

    $ hardening-check /usr/bin/bowtie-inspect /usr/bin/bowtie-build 
/usr/bin/bowtie ...
    /usr/bin/bowtie-inspect:
     Position Independent Executable: no, normal executable!
     Stack protected: yes
     Fortify Source functions: no, only unprotected functions found!
     Read-only relocations: yes
     Immediate binding: no not found!
    /usr/bin/bowtie-build:
     Position Independent Executable: no, normal executable!
     Stack protected: yes
     Fortify Source functions: no, only unprotected functions found!
     Read-only relocations: yes
     Immediate binding: no not found!
    /usr/bin/bowtie:
     Position Independent Executable: no, normal executable!
     Stack protected: yes
     Fortify Source functions: yes (some protected functions found)
     Read-only relocations: yes
     Immediate binding: no not found!
    ...

(Position Independent Executable and Immediate binding is not
enabled by default.)

Use find -type f \( -executable -o -name \*.so\* \) -exec
hardening-check {} + on the build result to check all files.

Regards,
Simon

[1]: https://wiki.debian.org/ReleaseGoals/SecurityHardeningBuildFlags
[2]: https://wiki.debian.org/HardeningWalkthrough
[3]: https://wiki.debian.org/Hardening
[4]: http://ruderich.org/simon/blhc/
-- 
+ privacy is necessary
+ using gnupg http://gnupg.org
+ public key id: 0x92FEFDB7E44C32F9
Description: Use build flags from environment (dpkg-buildflags).
 Necessary for hardening flags.
Author: Simon Ruderich <[email protected]>
Last-Update: 2012-04-24

--- bowtie-0.12.7.orig/Makefile
+++ bowtie-0.12.7/Makefile
@@ -177,7 +177,7 @@ define checksum
   cat $^ | md5sum | awk '{print $$1}' > [email protected]
 endef
 
-ALL_FLAGS=$(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
+ALL_FLAGS=$(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
 DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
 RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
 

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