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Make sure that eqmake4 is run by the ebuild so that doxygen's Makefiles don't get to call qmake directly. Remove old doxygen versions and patches.
(Portage version: 2.2_rc62-r4/hg/Linux x86_64)
(Unsigned Manifest commit)

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AUX bsd-configure.patch 504 RMD160 4d3321c677bbfcae2c25c7937ef015ff41812594 SHA1 df68c4be15c41b02c822364b5f54214ce65b3fc0 SHA256 8aa47622750701cd492b35e8037b3b8a5ed1c13e564d0a0081a09877717b9cf1
AUX doxygen-1.5-dot-eps.patch 2247 RMD160 b34b332df8b6769f73613ba11f98b3c5bdee40c6 SHA1 ab5c78d0599661e82a9ac1f4bf0117318e54712e SHA256 6dc47978298a39bc520a1f48206be26f76657842f14aba3413768352c7e87d45
AUX doxygen-1.5-legacy-patches.diff 7242 RMD160 0100a2305101b392764eaf867a32e0d14dcf9208 SHA1 bb564532f157e72436e0c8ecbbed163d96db3674 SHA256 f696c10fe571d281ed8178e7a07864c7a5bba9cc21ac723ee9669ac32e43e114
AUX doxygen-1.5-system-libpng.patch 5332 RMD160 cfa7709a0f867609cf149407d19df2ecf53af750 SHA1 9b0547b64fd9b15406a72b18fe19673f784c50f9 SHA256 5800013e75e3fdb4a6dbc513a25393ec9cef0dfa412032c1c3de562829ddaeab
AUX doxygen-1.5.6-prefix-misc-alt.patch 2017 RMD160 fba979abf6b0db3c32a1a9509c0a98d7e452a86f SHA1 3bb95cd36289a46d7ba221319421c82e5433e60e SHA256 ee4b8c11c8af9bc3dfb365eff06addf3d7ec73931a234ac3651be2ba28ad3b44
AUX doxygen-1.5.8-kdedocs.patch 854 RMD160 945e07ab7f5f168d63f5a99423a56d9b12477df8 SHA1 5e987c64b95500441a668fd4912db32714de495d SHA256 48703fc843633e774e05c64e6903badfd74f456f7099399d44b3150f9b964e6c
AUX doxygen-gcc4.patch 267 RMD160 f96f301331db451247fc1fb061f35e173ec1cff8 SHA1 ac7ed139251d87876e67b3e5ce04652b3ac27795 SHA256 df914a5303499c5293c0fcec3e126260157a15bbdc605040d4161ef9599fa2ce
AUX doxywizard.png 4231 RMD160 b194049b42aad3466a5ef9c69ff3504536223dae SHA1 0902260c7169e60a504b29feec419b3a4183081f SHA256 eb648ebd3a194a56d9ed6e47cc8dbf1af2e124d83c2c42af9bf86bd837984209
DIST doxygen-1.5.8.src.tar.gz 4125837 RMD160 e392cd00960c4036661c8cda3ec6bc6ee3fe300c SHA1 a55b1c41417be8acb3ac5e1553a711ffa437cba2 SHA256 01540aaf7e929e7784e3392331f2c915480acb174a16e8652855d90965f44ff8
DIST doxygen-1.5.9.src.tar.gz 4141375 RMD160 51d79c0f8846f47e9aa8c37cd0eb9db630491885 SHA1 6211b850bdaa2198e35546e4299a27774c957ece SHA256 89c3d1102e9e5c63ff735dee88b595bc986fbb2b5944b28ba5f91d31adf8958e
DIST doxygen-1.6.1.src.tar.gz 3902407 RMD160 0a9c5962dbd076bac418b85b72a4874576c9da4d SHA1 31f861841eba1ebdded1b4bf70bdecb42441dafd SHA256 4c5aedf052a14a0f7fe8c126140ff1c5c50887c74814a4804181c61625d539d3
EBUILD doxygen-1.5.8-r1.ebuild 5595 RMD160 27f83c683eccbe835d0639e3d72f9382c175270c SHA1 c0346fdc2ed0f609a901b77794de063960f54c53 SHA256 97db981432bd0c0432a11ccc272f0b51913869d1ebc73a4e99da1d0e16fdf375
EBUILD doxygen-1.5.9.ebuild 5393 RMD160 3b0fcfb62e47acc69a88012c572096aaf7d8a01e SHA1 699126289a600197b6c0768f06979c9afdcd7c01 SHA256 a4893be42a65463170f70d0275ed54db72a056dfc61a50171dfdbc0f395a4a4d
EBUILD doxygen-1.6.1.ebuild 5587 RMD160 96c5af4fffd4300f699f653b1516d5085b5e84b9 SHA1 7f6537e8f73100f4337d916c614f2f450b3cdcc1 SHA256 6702116e1ad87e711f2e2d863aa702d5a6cf2a0261f17b71509134d0874e0b5d
MISC ChangeLog 29688 RMD160 adbad11a188df92f9471a8c9527072cc465454fa SHA1 d20de9c622aaf40fc946da7f4408ddcbffc20ce0 SHA256 88aeea7349c3daf2012b5e22c513974a085ef59ef3a1679e939356d5427200f5
MISC metadata.xml 740 RMD160 288a23989773f251e7acccaf77ae390ca2376c3a SHA1 8fc5f720b18d2952fd0519fd73e3dcb66aa94ee4 SHA256 90abffce7a6f2d24635ea2cf3cb7e64c9374304d9f9daacf5f963e0d8bfcb4f8