reinit the tree, so we can have metadata

11 files changed, 538 insertions, 0 deletions

diff --git a/sci-geosciences/gmt/Manifest b/sci-geosciences/gmt/Manifest
new file mode 100644
index 000000000000..67756d6f86d4
--- /dev/null
+++ b/sci-geosciences/gmt/Manifest
@@ -0,0 +1,25 @@
+AUX gmt-4.5.0-no-strip.patch 1963 SHA256 c08daec9357087e52026faeec2398a888fc0b7c145511f01016734e41bbc1fea SHA512 8ef2ca6acf17b092989ce7b8c91a3f42b82b074d606d2635c7b5a03355fcd3f83b3d08ef83747e51f5eb6e6ed9cb9a683208797d49da7b8f0714ed0c8f2e6155 WHIRLPOOL 6d10111b14637f020d529dedcb248a240a09218e2a06ad43f593400a4ec98763f182c0c8cbf34c53359d15391aeef13a7b0f3e34a4a888af4d056efa95c1bf44
+AUX gmt-4.5.6-respect-ldflags.patch 2396 SHA256 c690c160cd7fad23a0ce0171aae47a4a275ff03203418de27d77fbab5d2b525a SHA512 c2cc4986a1211a75856391cd0c731f37d9cf8e2ad28fdf29f532ed03308f2ef7f309a0bc525bb08c976c4535e8cbe77789546eb8585ddcedf016af32769e5420 WHIRLPOOL 868c7c567f69c1e54dc56b26723e9cef09e03a1cdfd86ad2f2f821dff96aa3f37fe20064c2495bf15cb84f60cec3ddec3fcfbef5712270fe70ce1307d0b6f45b
+AUX gmt-4.5.8-bfr-overflow.patch 1576 SHA256 61602cbdd6d233882b9bda79f96897a1dcd82e5a572267102c61d6b68ec084a2 SHA512 fd2c137047333ef4494bba28339c1f8a34e83acc2646db514e0d2289e60acca5f6ac360d1dab27d84a088ce4a1c8c3af5f5cd4ae57485bb14eb08a668ea8ecc9 WHIRLPOOL 4ae526a59b2776cb54da27b377fdad47d8af344bc44e75bc9a8f21c3eeeca31401abb508f6ec777186bdc27c27744c09e6e8d92770c16b2b27640201c343a131
+AUX gmt-4.5.8-impl-dec.patch 291 SHA256 b244567f01a35515249f85c5a8a4142aa2c1765c51a2b1315860574ba75ee67b SHA512 ed977bd1a19024a60682d6e422c202cb3c29ed5da1450d85558544d6aa300ac967595811c90143a4858213a6b60b8fffee453de8351666c55676371e00b144ad WHIRLPOOL 24b0d923e7f02a521c3692feb8774fde4794d71a91e10ba83fa86bf874ac711eb37844a0b421312635e5cf6e7344cf0ff8e4d7346b27fc45911913529eed6a6b
+AUX gmt-4.5.9-no-strip.patch 1246 SHA256 b72d6528aacd8869bc4d9f00e4d4bc72c1dab8aada2d911f72a36f03ff322b5a SHA512 271be4c32607bd4776cace933ed0a81a76fb5ea8ccc0c92f0f11cdf17f6b4f8740e2345323236af94dd4eb52323625cc82e5c661e22a008dcdc85f4d1d452b23 WHIRLPOOL 485c01f259dca075bbba6f709995488277af410f6adf4a63f2699cee0e8c8dd88ca6e4717a027068b21fb9f5b2908be0b64b7822faa7d8708f115fba03a225f4
+AUX gmt-4.5.9-unistd.h.patch 358 SHA256 396acb0dcc6990f91a2f29391bcd15fa448ad905c7fe5eedf935ada07f410639 SHA512 877e73b161d9fbb1fe17d5f575852be67cfd9eec31ff8b74ffeb7b00569e3061d5a85c55e6633c06f12147bf7e3ab2838ab2738c5fe4adf93065ce55e7884df6 WHIRLPOOL b04e63e5dd486b6d1f2116da89592e9b6786906c8e51940859f635358638b971eb037a853c7fb891686a2759180f88673d855dedc4d616c37571b920a9e21455
+DIST gmt-4.5.6-doc.tar.bz2 25230761 SHA256 9fbdf427ef06e666d83871c9e1241e5b578906b82e5c382d38fe75dfb40645dd SHA512 97d3ab39b8f015c7488d039af1578c9187f8fdd82e8492729150afb1ec658b2e5221d92145e0776348ecfd1a720004e9766760e3a20337b00f43f309150ae302 WHIRLPOOL 36a13a4a5bfae1f660fb684c5ebb6b2785cb3bef89d2840360f0cd61e4228c7ae4f147a1fcbd83f1dcb4d40f7d1afdfad1303ae354291424ccd630ae6f1aafd1
+DIST gmt-4.5.6-share.tar.bz2 43704 SHA256 364fcd62e1ed422d40399b92815e1196e916ea86f5a460cc799406754220234d SHA512 7b1ca938a291f06be83421d1324612851da74a2156bc7568da01b05f2a235eb2f36854abd4fac5c357f9e22df4f98a69410fc3e2e2117f72994db60c00780fc0 WHIRLPOOL a30b9b3bff58a0db9f70529c262c3db0a73a39aed962063f0299f3147973eae952f6edd0bbb58e4cfdb9b8530213bf16661d8970391852267354284f81a515d0
+DIST gmt-4.5.6-src.tar.bz2 1134118 SHA256 f58b24320e9ffd2a2196aa68689dbc8b3bf01a13c4efc30a28aba2dd5b65e7b4 SHA512 0cb06f6be7cf6a3f586f7d9b4579d5520fb15f6ef14eec216c60aa4b3fa9a3ca3308bf4683c8cc0bcf71f3c02ba74a0f9bf296fec4c1980d10adc4ba4a12024e WHIRLPOOL e58762ee4c2dd4cc553e8e1eb0e6a972f1060221944e1cebfe712bfbda19b579e5937a4ce1937d0743978989b087246b63c2fcad730b69e5685ef63e16107edc
+DIST gmt-4.5.6-suppl.tar.bz2 4137369 SHA256 572d23252055ed1e1d72f07e7aee86d92c4cd15b47fd55b0ecf39bfb7f014bee SHA512 7e1cd35da0a7f75800074cac4dd7f82ce17721953251c951c4f585f0cf159af6c2450fba20d9c02fad69ec7a689483de55cc652fcc600535255cf17ab528a027 WHIRLPOOL 55abc1471e582385420392a81c4d46c045cf85c94cbade0db6f6c9c0bb88e2a0cba7182125c686e1b4464f74ce8a06d99d4f57f55ebcccf62f538cbd29e8b646
+DIST gmt-4.5.6-triangle.tar.bz2 103426 SHA256 0ef5ca66eebd1386b1f59e2577cedb2d7e68c8bff83d4b57a648d1b04026a05c SHA512 3daabba610a50e72c2e9e5dd7fb22ff02547c598ff22f40f145f3f794447cde995ddbdcd2560954478806fc5edc2af4fb59615e405622daa4292e6dc2f0e4f5e WHIRLPOOL de80a48ddfa9edb82a4312843ec604c2e78e73b756212293f88d0ae4cdaf259f6de5eae5c0178b7fed53c7f640147f1705b4f685c21f2e4840f66330eea12b0d
+DIST gmt-4.5.8-non-gpl.tar.bz2 109125 SHA256 f68c9ee5d0376f0931643be9afc34f21f2f8752117c7fdfb46a7239c1acdc98f SHA512 04b3eefd1490b194d7797af86fc726dd84960d65dd955e5ddefaf6ea4ec5a98f6f00085acc0cc846aa70e986facf65221256dd6a625f918c6abe6ba0b6b06f64 WHIRLPOOL 882789617e091bd844ae2e30e80d328492d5b2a5b033ec2ac876ea2a95c0b1fb8e2b75f0d5529c4d9d20a74a2c782ebff4a8c61d53c0a651a96f0e0cb37df1e8
+DIST gmt-4.5.8.tar.bz2 39350328 SHA256 de3398acaf3ecb34f48c8a61a916c6037276793bd4b13bef376282a7731e54d4 SHA512 5bc3be1f7963df6a3035195e2123645d8a8b7a8a9aa17c89a6dd50560485706c628e0e0aca779930c4a28f2305fcc184981db728085d3373b2cad89e59d5c6fd WHIRLPOOL 2e09cd006818c3b656bacd54b9f28642993f26a5ada6d92ce52026bf0530746705fdba4a46aa44bd30855784b3f8cebc0047b2e3c683d24bdcb8d7c0025ffc69
+DIST gmt-4.5.9-non-gpl.tar.bz2 103494 SHA256 29103015063d61b5b6103775a1bd7cc56b053018bb2fa680213839a98215897b SHA512 a41cd94acbd014bed780797be1ac1b492388c7c8e0fcfc5e773e894e803a024bdc60b897589ad4db9af973f20606a87ac9cff606f0391641236bca95c0b7a4c5 WHIRLPOOL d59d894b2d6b5822a71501e51ab0e328c2fe9367c1d1c64591971004c594554fe8a692d84a1a76b84f614556f8c8d31ae83245a1c6fbc9a70aed53934272c7c1
+DIST gmt-4.5.9.tar.bz2 39325492 SHA256 9b13be96ccf4bbd38c14359c05dfa7eeeb4b5f06d6f4be9c33d6c3ea276afc86 SHA512 1edda71787fa2e1434a6891618d4523c39d04c2db285dadc66c1d52b425cfff6866c492926cae41d78d2a4e5118e8d003ef3d71d164e0c0695d71aaddb598242 WHIRLPOOL ca890bc544f0861bf722f623773d41fac294874be76b25222a71ac0f9ef725069982ca9f77c5ca7558eadcd2a8b8e8bd1a934bf467ba1ef873ccbbc1f9a024fb
+DIST gshhs-2.1.1-coast.tar.bz2 4322743 SHA256 9d78154cc316553e7ade8c79792d15e97469615f67e256e91b35da4bf0e64730 SHA512 6009139cc4760925817e789e0c9980ec6bde1310f521e6f43e5643b9eba1e859bb9a23bdc4bb661e66d32f4886ad3ad93f5af76ca93ac847307f9acd37eeb332 WHIRLPOOL 6658cd37fe2db73baa629566765e1657f5ecb214ccfad88c2cff7dd0524b45f89897f87ca7a8d1698e9ebd3a7592c437764a99c333c0967fa6bc18058381f653
+DIST gshhs-2.1.1-full.tar.bz2 29916230 SHA256 a81f6cdf64cad78c36b71c550079f11ebc11305b399f2c5354dc0d4087977938 SHA512 f4759d21514a63b1cf3a65c75aeab951740091235e3f19d832ad2c09416d2ab8d516a8f5bf0f6068c81f6c18f76734c4bf3772c37406c1df5abd4ae445f3d375 WHIRLPOOL acb9edd5d4d468b8903646155a6d85f80bdebd54debc7af0f04934010fb211b4da8c94396177de7410a9c92caef02e3a3dddc9e89075dfcda34843f45b1543f8
+DIST gshhs-2.1.1-high.tar.bz2 9712697 SHA256 a19e1e4b205419d56ae3dca98a71dd0001eb5aab2ebc5f436c1d7e6e741945c7 SHA512 a9c22d7ce285320d4ae22a1a446e7d7d446d1b0641abeb39d50e358d65011fd3e39761a61a41820a373df4d4ef950160f5aab71d2df899a8425caf7d162e6e0e WHIRLPOOL da74e96a61c3458591f196b15a48da79e8296d4a4475834c2c9f07bd98eab60676f4e04d0ecc6a5bfa95cda0b28c84fc982396438dd7a3fbcf7cad99341ba20a
+DIST gshhs-2.2.0.tar.bz2 47021761 SHA256 e6c6c93ae10c9476c33934d46f5fb54a4d12463bdfb46f8e1c2f189ed4a4dfd2 SHA512 a9c1550f24feeefbc7ae633cce41e737f8153bb7df974e942fb5b9f0c931a49707c737f34bf6316ac89aa9bf487a091ada08ca8d798e2a5385e75f3dc05fdf83 WHIRLPOOL 125aa0f8e4da1b1f62b0380250cd06ec2f5d1e0f7b8c2316feebd6a49bb229a8608156d1555e2e241772c716fc452f6c7cc38d64877e7ee44c1e76f0b09d3c59
+EBUILD gmt-4.5.6.ebuild 2311 SHA256 9a4afc47713d0b3b436c928faa432a34865b5d49ccca5a05de55af8bad7c8371 SHA512 c3ce34dbd2e000416eae85e98b582e4729de4ee4b1e09107e8930c9802970207b35a56c76e918bf89bbff4f582f8310b6dc8bc3d89a346b25cd4ac20e021cf8c WHIRLPOOL 9433b458546700976cc2809696891d11b4b5a4bebf39c91d9ed7fe291f3cd0ec98b71c396917f94eaf2d0694e22979d8aa5aa3ef1ee760afbd68bf449e2f4821
+EBUILD gmt-4.5.8.ebuild 1972 SHA256 b64eda7cd96ac020c9f838691d42af38e9bca4c5e41626403de634f93e9dfad5 SHA512 c8f810de340e6205c5b97a6e9c2accccda2f589941c435b2f09670761960858c43ab6fb42b20fdf62895052c96f6e59969036c71df3ee2f551e51f7dd110bee1 WHIRLPOOL b27c799664b55474319b76c22b6ec21fcdca8ecefac8d289d6418dcc6ed1865ed161a608998ac03c96c1a62aff399c2848d1b68cdfbb39f11ad9edae9c1a60b7
+EBUILD gmt-4.5.9.ebuild 1954 SHA256 c24c98721ea55cad38702e2106f600df8896394eb5636e6283c9bda0113d0401 SHA512 31974c6a7e26f02cf457aa4b178e32a5c556b1fce8226162b7178211e73569a2eb9df0f0e14d45c878a7c561a26e04a8e8d7e917aab9f7379c9dfba7dc1ab996 WHIRLPOOL 7e23131cfdcb6d76c86dad99759e228eec6656cc78b87b4ee4b13a2d736f14d4618fbd25090df0f63ee09af2d011188629f06f7e794fcdca2e921676d1fea5e2
+MISC ChangeLog 2893 SHA256 d7d764c1332a2c9f5258cbb8e7cee8d0e81ced06d19a55be78743c395c952dc3 SHA512 fccefde6c4004eda9ea5df3786dedfaa0a6bbf0e3a9635d1e342db1a4d6311c474453e37b623799feb589ec94c8483d814e6ea57bb15a16d2b887e83326639fe WHIRLPOOL 34343c77f6196ee007514887ee3dfd8da9645817ddaa59f65479039c4499ddc2b9dc80116ca99c24fa8e2125232d81295a4b9dd92f45c094fcb081813d94544d
+MISC ChangeLog-2015 6318 SHA256 f631a875a68936d4136cbe668f235b4e50ad1a3f49ecbd864c6124423d119c62 SHA512 1428f4a137e70b40a0b9650822c5189ea54efa66887a10d816c4f203d6dc118e829011a40063c6a69cb6b42b7f0f162d666cb524f0f722a3eeda4c337c166bc2 WHIRLPOOL d5035ac4944a45d5198d7380eaf8afc5c058cc8b8f5731758be247ee0c9ad4f9a9cf24b8d7616bf2e248024d476496723b7fafb4619f9ac7356d7a3eba638d87
+MISC metadata.xml 810 SHA256 a957f58792350fa5c2a312c2c7a6363a2728d5b424ff9ebb1753ce9a6d13df10 SHA512 647d1a082313d0894a6203cde5afbe729d084e3ed923a9f22850022acb632b0af1fe2dd14aaba6801b5656d1277be39559fa5f76a03e621a88eb6634fa2ec645 WHIRLPOOL 81a670d740be75cf6f9ed65d4d6e905da11c733e019252c9402573f5543ad28e9b8597cc052ed31e674d62ece0fe3eb7bb7b708c3032f307c1b6cae7fe1f44ad
diff --git a/sci-geosciences/gmt/files/gmt-4.5.0-no-strip.patch b/sci-geosciences/gmt/files/gmt-4.5.0-no-strip.patch
new file mode 100644
index 000000000000..f0fe4c3e833e
--- /dev/null
+++ b/sci-geosciences/gmt/files/gmt-4.5.0-no-strip.patch
@@ -0,0 +1,62 @@
+Drop manipulation of several flags:
+
+* stripping of -g from CFLAGS, as it interferes with deliberate
+  generation of debug symbols and breaks on flags like -ggdb.
+* Addition of -s resp. -Wl,-x to LDFLAGS, as stipping of binaries is
+  done as a separate step on Gentoo (and many other distros) in order
+  to faciliate retention or splitting of debug symbols.
+* Setting of optimization flags, as the user should be free to choose
+  them.
+
+2009-07-27 Martin von Gagern
+
+Reference: http://bugs.gentoo.org/279268
+
+Index: GMT4.5.0/configure
+===================================================================
+--- GMT4.5.0.orig/configure
++++ GMT4.5.0/configure
+@@ -10665,19 +10665,6 @@ if test "X$enable_debug" = "Xyes" ; then
+ echo "${ECHO_T}yes" >&6; }
+ 	CFLAGS="$CFLAGS -g"
+ else
+-	CFLAGS=`echo $CFLAGS | sed 's/-g//'`
+-	if test "$os" = "Darwin" ; then
+-		LDFLAGS="$LDFLAGS -Wl,-x"
+-	else
+-		LDFLAGS="$LDFLAGS -s"
+-	fi
+-	if test "$GCC" = "yes" || test "$os" = "Linux" || test "$os" = "AIX"; then
+-		CFLAGS="$CFLAGS -O2"
+-	elif test "$chip" = "alpha" || test "$os" = "AUX" || test "$os" = "HP-UX"; then
+-		CFLAGS="$CFLAGS"
+-	else
+-		CFLAGS="$CFLAGS -O"
+-	fi
+ 	{ echo "$as_me:$LINENO: result: no" >&5
+ echo "${ECHO_T}no" >&6; }
+ fi
+Index: GMT4.5.0/configure.ac
+===================================================================
+--- GMT4.5.0.orig/configure.ac
++++ GMT4.5.0/configure.ac
+@@ -527,19 +527,6 @@ if test "X$enable_debug" = "Xyes" ; then
+ 	AC_MSG_RESULT(yes)
+ 	CFLAGS="$CFLAGS -g"
+ else
+-	CFLAGS=`echo $CFLAGS | sed 's/-g//'`
+-	if test "$os" = "Darwin" ; then
+-		LDFLAGS="$LDFLAGS -Wl,-x"
+-	else
+-		LDFLAGS="$LDFLAGS -s"
+-	fi
+-	if test "$GCC" = "yes" || test "$os" = "Linux" || test "$os" = "AIX"; then
+-		CFLAGS="$CFLAGS -O2"
+-	elif test "$chip" = "alpha" || test "$os" = "AUX" || test "$os" = "HP-UX"; then
+-		CFLAGS="$CFLAGS"
+-	else
+-		CFLAGS="$CFLAGS -O"
+-	fi
+ 	AC_MSG_RESULT(no)
+ fi
+ dnl -----------------------------------------------------------------
diff --git a/sci-geosciences/gmt/files/gmt-4.5.6-respect-ldflags.patch b/sci-geosciences/gmt/files/gmt-4.5.6-respect-ldflags.patch
new file mode 100644
index 000000000000..07494380fdfb
--- /dev/null
+++ b/sci-geosciences/gmt/files/gmt-4.5.6-respect-ldflags.patch
@@ -0,0 +1,56 @@
+diff -urN GMT4.5.6/src/Makefile GMT4.5.6.new/src/Makefile
+--- GMT4.5.6/src/Makefile	2011-03-03 22:02:50.000000000 +0100
++++ GMT4.5.6.new/src/Makefile	2011-06-07 14:48:00.969500019 +0200
+@@ -195,13 +195,13 @@
+ 		$(RANLIB) $@
+ 
+ libpsl.$(SL):	libpsl.a
+-		$(LD) $(LD_OPT) pslib.o $(LIBS) -o $@
++		$(LD) $(LD_OPT) $(LDFLAGS) pslib.o $(LIBS) -o $@
+ 
+ libgmt.$(SL):	libgmt.a
+-		$(LD) $(LD_OPT) $(LIB_O) $(TRIANGLE_O) $(ALPHA_SINCOS_O) $(NETCDF_LIB) $(GDAL_LIB) $(LIBS) -o $@
++		$(LD) $(LD_OPT) $(LDFLAGS) $(LIB_O) $(TRIANGLE_O) $(ALPHA_SINCOS_O) $(NETCDF_LIB) $(GDAL_LIB) $(LIBS) -o $@
+ 
+ libgmtps.$(SL):	libgmtps.a libgmt.$(SL) libpsl.$(SL)
+-		$(LD) $(LD_OPT) $(LIBPS_O) libgmt.$(SL) libpsl.$(SL) $(LIBS) -o $@
++		$(LD) $(LD_OPT) $(LDFLAGS) $(LIBPS_O) libgmt.$(SL) libpsl.$(SL) $(LIBS) -o $@
+ 
+ #-------------------------------------------------------------------------------
+ #	program rules
+diff -urN GMT4.5.6/src/mgd77/Makefile GMT4.5.6.new/src/mgd77/Makefile
+--- GMT4.5.6/src/mgd77/Makefile	2010-11-01 23:39:16.000000000 +0100
++++ GMT4.5.6.new/src/mgd77/Makefile	2011-06-07 14:53:46.394181616 +0200
+@@ -93,7 +93,7 @@
+ 		$(RANLIB) $@
+ 
+ libmgd77.$(SL):	libmgd77.a
+-		$(LD) $(LD_OPT) $(LIB_O) $(GMT_LIB) $(NETCDF_LIB) $(LIBS) -o $@
++		$(LD) $(LD_OPT) $(LDFLAGS) $(LIB_O) $(GMT_LIB) $(NETCDF_LIB) $(LIBS) -o $@
+ 
+ #-------------------------------------------------------------------------------
+ #	program rules
+diff -urN GMT4.5.6/src/mgg/Makefile GMT4.5.6.new/src/mgg/Makefile
+--- GMT4.5.6/src/mgg/Makefile	2010-11-01 23:39:16.000000000 +0100
++++ GMT4.5.6.new/src/mgg/Makefile	2011-06-07 14:54:48.096410233 +0200
+@@ -95,7 +95,7 @@
+ 		$(RANLIB) $@
+ 
+ libgmt_mgg.$(SL):	libgmt_mgg.a
+-		$(LD) $(LD_OPT) $(LIB_O) $(GMT_LIB) $(NETCDF_LIB) $(LIBS) -o $@
++		$(LD) $(LD_OPT) $(LDFLAGS) $(LIB_O) $(GMT_LIB) $(NETCDF_LIB) $(LIBS) -o $@
+ 
+ #-------------------------------------------------------------------------------
+ #	program rules
+diff -urN GMT4.5.6/src/x2sys/Makefile GMT4.5.6.new/src/x2sys/Makefile
+--- GMT4.5.6/src/x2sys/Makefile	2010-11-01 23:39:16.000000000 +0100
++++ GMT4.5.6.new/src/x2sys/Makefile	2011-06-07 14:54:15.124822433 +0200
+@@ -83,7 +83,7 @@
+ 		$(RANLIB) $@
+ 
+ libx2sys.$(SL):	libx2sys.a
+-		$(LD) $(LD_OPT) x2sys.o $(ALLLIB) -o $@
++		$(LD) $(LD_OPT) $(LDFLAGS) x2sys.o $(ALLLIB) -o $@
+ 
+ #-------------------------------------------------------------------------------
+ #	program rules
diff --git a/sci-geosciences/gmt/files/gmt-4.5.8-bfr-overflow.patch b/sci-geosciences/gmt/files/gmt-4.5.8-bfr-overflow.patch
new file mode 100644
index 000000000000..216149d93f78
--- /dev/null
+++ b/sci-geosciences/gmt/files/gmt-4.5.8-bfr-overflow.patch
@@ -0,0 +1,27 @@
+diff --git a/src/mgd77/mgd77.c b/src/mgd77/mgd77.c
+index b27b1d9..6a25576 100644
+--- a/src/mgd77/mgd77.c
++++ b/src/mgd77/mgd77.c
+@@ -854,7 +854,7 @@ int MGD77_Decode_Header_m77t (struct MGD77_HEADER_PARAMS *P, char *record)
+ 			case  3:	strcpy (P->Parameters_Surveyed_Code, word);			break;
+ 			case  4:	strncpy (P->File_Creation_Year, word, 4);
+ 					strncpy (P->File_Creation_Month, &word[4], 2);
+-					strncpy (P->File_Creation_Day, &word[6], 4);			break;
++					strncpy (P->File_Creation_Day, &word[6], 2);			break;
+ 			case  5:	strcpy (P->Source_Institution, word);				break;
+ 			case  6:	strcpy (P->Country, word);					break;
+ 			case  7:	strcpy (P->Platform_Name, word);				break;
+@@ -865,11 +865,11 @@ int MGD77_Decode_Header_m77t (struct MGD77_HEADER_PARAMS *P, char *record)
+ 			case 12:	strcpy (P->Funding, word);					break;
+ 			case 13:	strncpy (P->Survey_Departure_Year, word, 4);
+ 					strncpy (P->Survey_Departure_Month, &word[4], 2);
+-					strncpy (P->Survey_Departure_Day, &word[6], 4);			break;
++					strncpy (P->Survey_Departure_Day, &word[6], 2);			break;
+ 			case 14:	strcpy (P->Port_of_Departure, word);				break;
+ 			case 15:	strncpy (P->Survey_Arrival_Year, word, 4);
+ 					strncpy (P->Survey_Arrival_Month, &word[4], 2);
+-					strncpy (P->Survey_Arrival_Day, &word[6], 4);			break;
++					strncpy (P->Survey_Arrival_Day, &word[6], 2);			break;
+ 			case 16:	strcpy (P->Port_of_Arrival, word);				break;
+ 			case 17:	strcpy (P->Navigation_Instrumentation, word);			break;
+ 			case 18:	strcpy (P->Geodetic_Datum_Position_Determination_Method, word);	break;
diff --git a/sci-geosciences/gmt/files/gmt-4.5.8-impl-dec.patch b/sci-geosciences/gmt/files/gmt-4.5.8-impl-dec.patch
new file mode 100644
index 000000000000..5c63bb209578
--- /dev/null
+++ b/sci-geosciences/gmt/files/gmt-4.5.8-impl-dec.patch
@@ -0,0 +1,16 @@
+diff --git a/src/gmt.h b/src/gmt.h
+index d4c9c20..ea6ddc5 100644
+--- a/src/gmt.h
++++ b/src/gmt.h
+@@ -34,9 +34,11 @@ extern "C" {
+ 
+ /*  GMT is POSIX.1 COMPLIANT  */
+ 
++/*
+ #ifndef _POSIX_SOURCE
+ #define _POSIX_SOURCE 1
+ #endif
++*/
+ 
+ /* Declaration modifiers for DLL support (MSC et al) */
+ 
\ No newline at end of file
diff --git a/sci-geosciences/gmt/files/gmt-4.5.9-no-strip.patch b/sci-geosciences/gmt/files/gmt-4.5.9-no-strip.patch
new file mode 100644
index 000000000000..f57f1d811b05
--- /dev/null
+++ b/sci-geosciences/gmt/files/gmt-4.5.9-no-strip.patch
@@ -0,0 +1,38 @@
+Drop manipulation of several flags:
+
+* stripping of -g from CFLAGS, as it interferes with deliberate
+  generation of debug symbols and breaks on flags like -ggdb.
+* Addition of -s resp. -Wl,-x to LDFLAGS, as stipping of binaries is
+  done as a separate step on Gentoo (and many other distros) in order
+  to faciliate retention or splitting of debug symbols.
+* Setting of optimization flags, as the user should be free to choose
+  them.
+
+2009-07-27 Martin von Gagern
+
+Reference: http://bugs.gentoo.org/279268
+
+Index: GMT4.5.0/configure.ac
+===================================================================
+--- GMT4.5.0.orig/configure.ac
++++ GMT4.5.0/configure.ac
+@@ -527,19 +527,6 @@ if test "X$enable_debug" = "Xyes" ; then
+ 	AC_MSG_RESULT(yes)
+ 	CFLAGS="$CFLAGS -g"
+ else
+-	CFLAGS=`echo $CFLAGS | sed 's/-g//'`
+-	if test "$os" = "Darwin" ; then
+-		LDFLAGS="$LDFLAGS -Wl,-x"
+-	else
+-		LDFLAGS="$LDFLAGS -s"
+-	fi
+-	if test "$GCC" = "yes" || test "$os" = "Linux" || test "$os" = "AIX"; then
+-		CFLAGS="$CFLAGS -O2"
+-	elif test "$chip" = "alpha" || test "$os" = "AUX" || test "$os" = "HP-UX"; then
+-		CFLAGS="$CFLAGS"
+-	else
+-		CFLAGS="$CFLAGS -O"
+-	fi
+ 	AC_MSG_RESULT(no)
+ fi
+ dnl -----------------------------------------------------------------
diff --git a/sci-geosciences/gmt/files/gmt-4.5.9-unistd.h.patch b/sci-geosciences/gmt/files/gmt-4.5.9-unistd.h.patch
new file mode 100644
index 000000000000..e724b4ceab79
--- /dev/null
+++ b/sci-geosciences/gmt/files/gmt-4.5.9-unistd.h.patch
@@ -0,0 +1,19 @@
+Fix "gmtdigitize.c:77:2: error: unknown type name 'gid_t'"
+build failure; patch from upstream version 4.5.11
+
+https://bugs.gentoo.org/show_bug.cgi?id=543624
+
+--- a/src/misc/gmtdigitize.c
++++ b/src/misc/gmtdigitize.c
+@@ -37,6 +37,11 @@
+  *
+  */
+  
++#define _XOPEN_SOURCE
++#ifdef HAVE_UNISTD_H
++#include <unistd.h>
++#endif
++
+ #include "gmt.h"
+ 
+ #ifndef WIN32
diff --git a/sci-geosciences/gmt/gmt-4.5.6.ebuild b/sci-geosciences/gmt/gmt-4.5.6.ebuild
new file mode 100644
index 000000000000..9e73c830b201
--- /dev/null
+++ b/sci-geosciences/gmt/gmt-4.5.6.ebuild
@@ -0,0 +1,95 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit multilib autotools eutils
+
+GSHHS="gshhs-2.1.1"
+
+DESCRIPTION="Powerful map generator"
+HOMEPAGE="http://gmt.soest.hawaii.edu/"
+SRC_URI="mirror://gmt/legacy/${P}-src.tar.bz2
+	mirror://gmt/legacy/${P}-share.tar.bz2
+	mirror://gmt/legacy/${GSHHS}-coast.tar.bz2
+	mirror://gmt/legacy/${P}-suppl.tar.bz2
+	doc? ( mirror://gmt/legacy/${P}-doc.tar.bz2 )
+	gmtfull? ( mirror://gmt/legacy/${GSHHS}-full.tar.bz2 )
+	gmthigh? ( mirror://gmt/legacy/${GSHHS}-high.tar.bz2 )
+	gmttria? ( mirror://gmt/legacy/${P}-triangle.tar.bz2 )"
+
+LICENSE="GPL-2 gmttria? ( Artistic )"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="doc debug gmtfull gmthigh gmttria +metric mex +netcdf octave postscript"
+
+RDEPEND="
+	!sci-biology/probcons
+	netcdf? ( >=sci-libs/netcdf-4.1 )
+	octave? ( sci-mathematics/octave )
+"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror" # for the gmttria
+
+S="${WORKDIR}/GMT${PV}"
+
+# mex can use matlab too which i can't test
+REQUIRED_USE="
+	mex? ( octave )
+	gmthigh? ( !gmtfull ) gmtfull? ( !gmthigh )
+"
+
+# hand written make files that are not parallel safe
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+	mv -f "${WORKDIR}/share/"* "${S}/share/" || die
+
+	epatch \
+		"${FILESDIR}/${PN}-4.5.0-no-strip.patch" \
+		"${FILESDIR}/${PN}-4.5.6-respect-ldflags.patch" \
+		"${FILESDIR}"/${PN}-4.5.9-unistd.h.patch
+
+	eautoreconf
+}
+
+src_configure() {
+	# triangle disabled due to non-comercial license
+	econf \
+		--libdir=/usr/$(get_libdir)/${P} \
+		--includedir=/usr/include/${P} \
+		--datadir=/usr/share/${P} \
+		--docdir=/usr/share/doc/${PF} \
+		--disable-update \
+		--disable-debug \
+		--disable-gdal \
+		--disable-matlab \
+		--disable-xgrid \
+		--enable-shared \
+		$(use_enable netcdf) \
+		$(use_enable octave) \
+		$(use_enable debug devdebug) \
+		$(use_enable !metric US) \
+		$(use_enable postscript eps) \
+		$(use_enable mex) \
+		$(use_enable gmttria triangle)
+}
+
+src_install() {
+	emake \
+		DESTDIR="${D}" \
+		install-gmt install-data install-suppl install-man
+
+	# remove static libs
+	find "${D}/usr/$(get_libdir)" -name '*.a' -exec rm -f {} +
+
+	dodoc README
+	use doc && dodoc -r "${S}"/share/doc/${PN}/*
+
+	cat << _EOF_ > "${T}/99gmt"
+GMTHOME=${EPREFIX}/usr/share/${P}
+GMT_SHAREDIR=${EPREFIX}/usr/share/${P}
+_EOF_
+	doenvd "${T}/99gmt"
+}
diff --git a/sci-geosciences/gmt/gmt-4.5.8.ebuild b/sci-geosciences/gmt/gmt-4.5.8.ebuild
new file mode 100644
index 000000000000..69ac9baca347
--- /dev/null
+++ b/sci-geosciences/gmt/gmt-4.5.8.ebuild
@@ -0,0 +1,91 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils multilib
+
+GSHHS="gshhs-2.2.0"
+
+DESCRIPTION="Powerful map generator"
+HOMEPAGE="http://gmt.soest.hawaii.edu/"
+SRC_URI="
+	mirror://gmt/legacy/${P}.tar.bz2
+	mirror://gmt/legacy/${GSHHS}.tar.bz2
+	gmttria? ( mirror://gmt/legacy/${P}-non-gpl.tar.bz2 )"
+
+LICENSE="GPL-2 gmttria? ( Artistic )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug +gdal gmttria +metric mex +netcdf octave postscript"
+
+RDEPEND="
+	!sci-biology/probcons
+	gdal? ( sci-libs/gdal )
+	netcdf? ( >=sci-libs/netcdf-4.1 )
+	octave? ( sci-mathematics/octave )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/GMT${PV}"
+
+# mex can use matlab too which i can't test
+REQUIRED_USE="
+	mex? ( octave )
+"
+
+# hand written make files that are not parallel safe
+MAKEOPTS+=" -j1"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.5.0-no-strip.patch
+	"${FILESDIR}"/${PN}-4.5.6-respect-ldflags.patch
+	"${FILESDIR}"/${P}-bfr-overflow.patch
+	"${FILESDIR}"/${P}-impl-dec.patch
+	)
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+	mv -f "${WORKDIR}/share/"* "${S}/share/" || die
+
+	tc-export AR RANLIB
+
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		--libdir=/usr/$(get_libdir)/${P}
+		--includedir=/usr/include/${P}
+		--datadir=/usr/share/${P}
+		--docdir=/usr/share/doc/${PF}
+		--disable-update
+		--disable-matlab
+		--disable-xgrid
+		--disable-debug
+		$(use_enable gdal)
+		$(use_enable netcdf)
+		$(use_enable octave)
+		$(use_enable debug devdebug)
+		$(use_enable !metric US)
+		$(use_enable postscript eps)
+		$(use_enable mex)
+		$(use_enable gmttria triangle)
+		)
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install install-all
+
+	# remove static libs
+	find "${ED}/usr/$(get_libdir)" -name '*.a' -exec rm -f {} +
+
+	cat <<- _EOF_ > "${T}/99gmt"
+	GMTHOME="${EPREFIX}/usr/share/${P}"
+	GMT_SHAREDIR="${EPREFIX}/usr/share/${P}"
+	_EOF_
+	doenvd "${T}/99gmt"
+}
diff --git a/sci-geosciences/gmt/gmt-4.5.9.ebuild b/sci-geosciences/gmt/gmt-4.5.9.ebuild
new file mode 100644
index 000000000000..7aefd90eb08c
--- /dev/null
+++ b/sci-geosciences/gmt/gmt-4.5.9.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils multilib
+
+GSHHS="gshhs-2.2.0"
+
+DESCRIPTION="Powerful map generator"
+HOMEPAGE="http://gmt.soest.hawaii.edu/"
+SRC_URI="
+	mirror://gmt/legacy/${P}.tar.bz2
+	mirror://gmt/legacy/${GSHHS}.tar.bz2
+	gmttria? ( mirror://gmt/legacy/${P}-non-gpl.tar.bz2 )"
+
+LICENSE="GPL-2 gmttria? ( Artistic )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug +gdal gmttria +metric mex +netcdf octave postscript"
+
+RDEPEND="
+	!sci-biology/probcons
+	gdal? ( sci-libs/gdal )
+	netcdf? ( >=sci-libs/netcdf-4.1 )
+	octave? ( sci-mathematics/octave )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/GMT${PV}"
+
+# mex can use matlab too which i can't test
+REQUIRED_USE="
+	mex? ( octave )
+"
+
+# hand written make files that are not parallel safe
+MAKEOPTS+=" -j1"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.5.9-no-strip.patch
+	"${FILESDIR}"/${PN}-4.5.6-respect-ldflags.patch
+	"${FILESDIR}"/${PN}-4.5.9-unistd.h.patch
+	)
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+	mv -f "${WORKDIR}/share/"* "${S}/share/" || die
+
+	tc-export AR RANLIB
+
+	autotools-utils_src_prepare
+
+	eautoreconf
+}
+
+src_configure() {
+	local myeconfargs=(
+		--libdir=/usr/$(get_libdir)/${P}
+		--includedir=/usr/include/${P}
+		--datadir=/usr/share/${P}
+		--docdir=/usr/share/doc/${PF}
+		--disable-update
+		--disable-matlab
+		--disable-xgrid
+		--disable-debug
+		$(use_enable gdal)
+		$(use_enable netcdf)
+		$(use_enable octave)
+		$(use_enable debug devdebug)
+		$(use_enable !metric US)
+		$(use_enable postscript eps)
+		$(use_enable mex)
+		$(use_enable gmttria triangle)
+		)
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install install-all
+
+	# remove static libs
+	find "${ED}/usr/$(get_libdir)" -name '*.a' -exec rm -f {} +
+
+	cat <<- _EOF_ > "${T}/99gmt"
+	GMTHOME="${EPREFIX}/usr/share/${P}"
+	GMT_SHAREDIR="${EPREFIX}/usr/share/${P}"
+	_EOF_
+	doenvd "${T}/99gmt"
+}
diff --git a/sci-geosciences/gmt/metadata.xml b/sci-geosciences/gmt/metadata.xml
new file mode 100644
index 000000000000..c31969b5f364
--- /dev/null
+++ b/sci-geosciences/gmt/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-geosciences@gentoo.org</email>
+    <name>Gentoo Geosciences Project</name>
+  </maintainer>
+  <use>
+    <flag name="gdal">Enable <pkg>sci-libs/gdal</pkg> library support</flag>
+    <flag name="gmtfull">Full resolution bathymetry database</flag>
+    <flag name="gmthigh">Add high resolution bathymetry database</flag>
+    <flag name="gmttria">Non GNU triangulation method, more efficient</flag>
+    <flag name="metric">Use SI (cm) units instead of US (inches) ones</flag>
+    <flag name="mex">Enable compilation of mex supplement which requires Octave/Matlab</flag>
+    <flag name="octave">Enable octave support</flag>
+  </use>
+</pkgmetadata>