[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/, sci-chemistry/xcrysden/files/
commit: f97bb147c9e7d1ae7a0cafae40ab2d891b970dc8 Author: Patrick J Taylor gmail com> AuthorDate: Tue Sep 13 18:25:51 2022 + Commit: Ronny Gutbrod tastytea de> CommitDate: Tue Sep 13 18:27:24 2022 + URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=f97bb147 sci-chemistry/xcrysden: edit Makefiles to respect LDFLAGS Closes: https://bugs.gentoo.org/869947 Signed-off-by: Patrick J Taylor gmail.com> .../xcrysden/files/xcrysden-1.6.2-LDFLAGS.patch| 171 + sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild | 1 + 2 files changed, 172 insertions(+) diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-LDFLAGS.patch b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-LDFLAGS.patch new file mode 100644 index 0..1ae39ae5e --- /dev/null +++ b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-LDFLAGS.patch @@ -0,0 +1,171 @@ +diff --git a/C/Makefile b/C/Makefile +index 2aa0307..452e0f1 100644 +--- a/C/Makefile b/C/Makefile +@@ -12,7 +12,7 @@ include make-objects + + .SUFFIXES: .o .c + .c.o: +- $(CC) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $< ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $< + + objects = $(XC_OBJS) $(EXTERNAL_OBJS) + +@@ -24,18 +24,18 @@ compile: + #objects: $(objects) + # + #$(objects): %.o: %.c +-# $(CC) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $< ++# $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $< + + xcrys: $(XC_OBJS) $(EXTERNAL_OBJS) +- $(CC) $(CFLAGS) $(XC_OBJS) $(EXTERNAL_OBJS) \ ++ $(CC) $(LDFLAGS) $(CFLAGS) $(XC_OBJS) $(EXTERNAL_OBJS) \ + -o xcrys $(FFTW3_LIB) $(MESCHACH_LIB) $(TK_LIB) $(TCL_LIB) $(TOGL_LIB) $(GLU_LIB) $(GL_LIB) $(X_LIB) $(MATH) $(LDLIB) $(EXT_LIB) + + xctclsh: xcTclsh.o +- $(CC) $(CFLAGS) xcTclsh.o -o xctclsh $(TCL_LIB) $(MATH) $(LDLIB) ++ $(CC) $(LDFLAGS) $(CFLAGS) xcTclsh.o -o xctclsh $(TCL_LIB) $(MATH) $(LDLIB) + + XFS_OBJS = xsf2xsf.o + xsf2xsf: $(XFS_OBJS) +- $(CC) $(CFLAGS) $(XFS_OBJS) -o xsf2xsf $(MATH) $(LDLIB) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(XFS_OBJS) -o xsf2xsf $(MATH) $(LDLIB) + + + install: +diff --git a/F/Makefile b/F/Makefile +index 3f8270e..92f17d1 100644 +--- a/F/Makefile b/F/Makefile +@@ -4,10 +4,10 @@ include ../Make.sys + .SUFFIXES : .o .f .f90 + + .f90.o: +- $(FC) $(FFLAGS) -c $< ++ $(FC) $(LDFLAGS) $(FFLAGS) -c $< + + .f.o: +- $(FC) $(FFLAGS) -c $< ++ $(FC) $(LDFLAGS) $(FFLAGS) -c $< + + OBJ = gengeom.o \ + multhexa.o \ +@@ -73,70 +73,70 @@ spaghetti: + cd SRC_spaghetti; $(MAKE) + + gengeom: $(OBJ) +- $(FC) $(FFLAGS) -o gengeom $(OBJ) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o gengeom $(OBJ) + + calplane: $(OBJ2) +- $(FC) $(FFLAGS) -o calplane $(OBJ2) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o calplane $(OBJ2) + + atomlab: $(OBJ3) +- $(FC) $(FFLAGS) -o atomlab $(OBJ3) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o atomlab $(OBJ3) + + recvec: recvec.o auxil.o +- $(FC) $(FFLAGS) -o recvec recvec.o auxil.o ++ $(FC) $(LDFLAGS) $(FFLAGS) -o recvec recvec.o auxil.o + + str2xcr: $(OBJ5) +- $(FC) $(FFLAGS) -o str2xcr $(OBJ5) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o str2xcr $(OBJ5) + + fracCoor: fracCoor.o auxil.o readf1.o +- $(FC) $(FFLAGS) -o fracCoor fracCoor.o auxil.o readf1.o ++ $(FC) $(LDFLAGS) $(FFLAGS) -o fracCoor fracCoor.o auxil.o readf1.o + + multislab: $(OBJ6) +- $(FC) $(FFLAGS) -o multislab $(OBJ6) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o multislab $(OBJ6) + + savestruct: $(OBJ7) +- $(FC) $(FFLAGS) -o savestruct $(OBJ7) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o savestruct $(OBJ7) + + ftnunit: ftnunit.o +- $(FC) $(FFLAGS) -o ftnunit ftnunit.o ++ $(FC) $(LDFLAGS) $(FFLAGS) -o ftnunit ftnunit.o + + kPath: $(OBJ8) +- $(FC) $(FFLAGS) -o kPath $(OBJ8) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o kPath $(OBJ8) + + pwKPath: $(OBJ88) +- $(FC) $(FFLAGS) -o pwKPath $(OBJ88) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o pwKPath $(OBJ88) + + fhi_inpini2ftn34: fhi_inpini2ftn34.o +- $(FC) $(FFLAGS) -o fhi_inpini2ftn34 fhi_inpini2ftn34.o ++ $(FC) $(LDFLAGS) $(FFLAGS) -o fhi_inpini2ftn34 fhi_inpini2ftn34.o + + fhi_coord2xcr: fhi_coord2xcr.o +- $(FC) $(FFLAGS) -o fhi_coord2xcr fhi_coord2xcr.o ++ $(FC) $(LDFLAGS) $(FFLAGS) -o fhi_coord2xcr fhi_coord2xcr.o + + wn_readbands: $(OBJ9) +- $(FC) $(FFLAGS) -o wn_readbands $(OBJ9) $(OBJ10) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o wn_readbands $(OBJ9) $(OBJ10) + + wn_readbakgen: wn_readbakgen.o +- $(FC) $(FFLAGS) -o wn_readbakgen wn_readbakgen.o ++ $(FC) $(LDFLAGS) $(FFLAGS) -o wn_readbakgen wn_readbakgen.o + + pw: pwi2xsf pwi2xsf_old pwo_xsf2xsf + + + pwi2xsf_old: $(OBJ11) +- $(FC) $(FFLAGS) -o pwi2xsf_old $(OBJ11) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o pwi2xsf_old $(OBJ11) + + pwi2xsf: $(OBJ111) +- $(FC) $(FFLAGS) -o pwi2xsf $(OBJ111) ++ $(FC) $(LDFLAGS) $(FFLAGS) -o pwi2xsf $(OBJ111) + + pwo_xsf2xsf: $(OBJ13) +- $(FC) $(FFLAGS) -o pwo_xsf2xsf
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/files/, sci-chemistry/xcrysden/
commit: ae3ffad2c35d356a7f5b05daf3eb1799e1000d56
Author: Patrick J Taylor gmail com>
AuthorDate: Sat Sep 10 20:17:37 2022 +
Commit: Florian Schmaus gentoo org>
CommitDate: Sat Sep 10 20:19:04 2022 +
URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=ae3ffad2
sci-chemistry/xcrysden: replace patch with flag-o-matic to set -fcommon
Signed-off-by: Patrick J Taylor gmail.com>
.../xcrysden/files/xcrysden-1.6.2-gcc_flags.patch | 14 --
sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild | 4 ++--
2 files changed, 2 insertions(+), 16 deletions(-)
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch
b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch
deleted file mode 100644
index ef231827e..0
--- a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Adds -fcommon to CFLAGS to allow compilation on more recent GCC.
-diff --git a/system/Make.sys-shared b/system/Make.sys-shared
-index 51891e7..f89f876 100644
a/system/Make.sys-shared
-+++ b/system/Make.sys-shared
-@@ -19,7 +19,7 @@ MAKE = make
- # C-preprocessor flags
- CPPFLAGS ?=
- # C-compiler flags
--CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall
-+CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall -fcommon
-
- CC = gcc
- #LDLIB = -ldl
diff --git a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
index c6ecb73d0..b243f1a06 100644
--- a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
+++ b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-inherit desktop xdg
+inherit desktop flag-o-matic xdg
DESCRIPTION="For the visualisation of molecular and crystal structures."
@@ -28,7 +28,6 @@ BDEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}/${P}-ext-bwidget.patch"
- "${FILESDIR}/${P}-gcc_flags.patch"
"${FILESDIR}/${P}-Togl_lib.patch"
"${FILESDIR}/${P}-wrapper_paths.patch"
)
@@ -39,6 +38,7 @@ src_prepare() {
}
src_compile() {
+ append-cflags "-fcommon"
emake xcrysden
}
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/
commit: 4dcefd003b68a8e91ff7febad71989613f4c2858 Author: Patrick J Taylor gmail com> AuthorDate: Sat Sep 10 23:26:39 2022 + Commit: Florian Schmaus gentoo org> CommitDate: Sat Sep 10 23:26:39 2022 + URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=4dcefd00 sci-chemistry/xcrysden: add missing dependencies Signed-off-by: Patrick J Taylor gmail.com> sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild index f8b459ae2..b76f8a0a1 100644 --- a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild +++ b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild @@ -17,7 +17,9 @@ SLOT="0" KEYWORDS="~amd64" -RDEPEND=">=dev-lang/tcl-8.6.12 +RDEPEND=">=x11-base/xorg-server-21.1.4 + >=virtual/glu-9.0-r2 + >=dev-lang/tcl-8.6.12 >=dev-lang/tk-8.6.12 >=dev-tcltk/togl-2.0-r3 >=dev-tcltk/bwidget-1.9.14
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/
commit: cba32fbe5315194e22ea3919f3831e7fa98ad2c6
Author: Patrick J Taylor gmail com>
AuthorDate: Sat Sep 10 21:11:29 2022 +
Commit: Florian Schmaus gentoo org>
CommitDate: Sat Sep 10 21:11:29 2022 +
URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=cba32fbe
sci-chemistry/xcrysden: BDEPEND->DEPEND
Signed-off-by: Patrick J Taylor gmail.com>
sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
index 99ad16333..f8b459ae2 100644
--- a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
+++ b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
@@ -24,7 +24,7 @@ RDEPEND=">=dev-lang/tcl-8.6.12
>=media-libs/mesa-22.1.3
>=sci-libs/fftw-3.3.10"
-BDEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}/${P}-ext-bwidget.patch"
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/, sci-chemistry/xcrysden/files/
commit: c6a2a87c15be29578d3ce20dc49f0e324b797782
Author: Patrick J Taylor gmail com>
AuthorDate: Sat Sep 10 20:18:37 2022 +
Commit: Florian Schmaus gentoo org>
CommitDate: Sat Sep 10 20:19:04 2022 +
URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=c6a2a87c
sci-chemistry/xcrysden: rename patches to match established convention
Signed-off-by: Patrick J Taylor gmail.com>
.../{xcrysden-1.6.2-Togl_lib.patch => xcrysden-1.6.2-Togl-lib.patch} | 0
...n-1.6.2-wrapper_paths.patch => xcrysden-1.6.2-wrapper-paths.patch} | 0
sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild | 4 ++--
3 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl_lib.patch
b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl-lib.patch
similarity index 100%
rename from sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl_lib.patch
rename to sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl-lib.patch
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper_paths.patch
b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper-paths.patch
similarity index 100%
rename from sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper_paths.patch
rename to sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper-paths.patch
diff --git a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
index b243f1a06..99ad16333 100644
--- a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
+++ b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
@@ -28,8 +28,8 @@ BDEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}/${P}-ext-bwidget.patch"
- "${FILESDIR}/${P}-Togl_lib.patch"
- "${FILESDIR}/${P}-wrapper_paths.patch"
+ "${FILESDIR}/${P}-Togl-lib.patch"
+ "${FILESDIR}/${P}-wrapper-paths.patch"
)
src_prepare() {
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/
commit: 6ec032dc40cd80668fc874aea01f61da09a29bcf Author: Patrick J Taylor gmail com> AuthorDate: Fri Sep 9 22:23:09 2022 + Commit: Ronny Gutbrod tastytea de> CommitDate: Fri Sep 9 22:23:42 2022 + URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=6ec032dc sci-chemistry/xcrysden: fix missing metadata Signed-off-by: Patrick J Taylor gmail.com> sci-chemistry/xcrysden/metadata.xml | 8 1 file changed, 8 insertions(+) diff --git a/sci-chemistry/xcrysden/metadata.xml b/sci-chemistry/xcrysden/metadata.xml new file mode 100644 index 0..50dcf2837 --- /dev/null +++ b/sci-chemistry/xcrysden/metadata.xml @@ -0,0 +1,8 @@ + +https://www.gentoo.org/dtd/metadata.dtd'> + + + patrick.joseph.tay...@gmail.com + Patrick J Taylor + +
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/
commit: fef1b3cef4e78333e8a2627ad33a6d9431725a89
Author: Patrick J Taylor gmail com>
AuthorDate: Fri Sep 9 22:22:28 2022 +
Commit: Ronny Gutbrod tastytea de>
CommitDate: Fri Sep 9 22:23:41 2022 +
URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=fef1b3ce
sci-chemistry/xcrysden: use xdg over xdg-utils
Signed-off-by: Patrick J Taylor gmail.com>
sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild | 11 +--
1 file changed, 1 insertion(+), 10 deletions(-)
diff --git a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
index 4d9e97a87..c6ecb73d0 100644
--- a/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
+++ b/sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild
@@ -3,8 +3,7 @@
EAPI=8
-inherit desktop
-inherit xdg-utils
+inherit desktop xdg
DESCRIPTION="For the visualisation of molecular and crystal structures."
@@ -57,11 +56,3 @@ src_install() {
/usr/share/doc/${P}/examples/FermiSurface \
/usr/share/man/
}
-
-pkg_postinst() {
- xdg_icon_cache_update
-}
-
-pkg_postrm() {
- xdg_icon_cache_update
-}
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/files/
commit: 49f61b1d314069b7b6dca1ad29cf40729559b576 Author: Patrick J Taylor gmail com> AuthorDate: Thu Sep 8 22:09:03 2022 + Commit: Ronny Gutbrod tastytea de> CommitDate: Thu Sep 8 22:09:03 2022 + URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=49f61b1d sci-chemistry/xcrysden: fixed path to icon in desktop file Signed-off-by: Patrick J Taylor gmail.com> sci-chemistry/xcrysden/files/xcrysden.desktop | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-chemistry/xcrysden/files/xcrysden.desktop b/sci-chemistry/xcrysden/files/xcrysden.desktop index 1f0128280..6880af143 100644 --- a/sci-chemistry/xcrysden/files/xcrysden.desktop +++ b/sci-chemistry/xcrysden/files/xcrysden.desktop @@ -4,5 +4,5 @@ Type=Application Comment=For the visualisation of molecular and crystal structures. Exec=xcrysden TryExec=xcrysden -Icon=/usr/share/icons/hicolor/96x96/apps/xcrysden.png +Icon=/usr/share/icons/hicolor/32x32/apps/xcrysden.png Categories=Science;
[gentoo-commits] repo/proj/guru:master commit in: sci-chemistry/xcrysden/files/, sci-chemistry/xcrysden/files/icons/, ...
commit: 7911079d4e3a5d8f1c18ac258508766ad148a2a7
Author: Patrick Taylor gmail com>
AuthorDate: Thu Sep 8 19:41:15 2022 +
Commit: Ronny Gutbrod tastytea de>
CommitDate: Thu Sep 8 19:41:54 2022 +
URL:https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=7911079d
sci-chemistry/xcrysden: new package, add 1.6.2
Signed-off-by: Patrick Taylor gmail.com>
sci-chemistry/xcrysden/Manifest| 1 +
sci-chemistry/xcrysden/files/icons/xcrysden.png| Bin 0 -> 11920 bytes
.../xcrysden/files/xcrysden-1.6.2-Togl_lib.patch | 14 +
.../files/xcrysden-1.6.2-ext-bwidget.patch | 14 +
.../xcrysden/files/xcrysden-1.6.2-gcc_flags.patch | 14 +
.../files/xcrysden-1.6.2-wrapper_paths.patch | 16 +
sci-chemistry/xcrysden/files/xcrysden.desktop | 8 +++
sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild | 67 +
8 files changed, 134 insertions(+)
diff --git a/sci-chemistry/xcrysden/Manifest b/sci-chemistry/xcrysden/Manifest
new file mode 100644
index 0..a5d3d6532
--- /dev/null
+++ b/sci-chemistry/xcrysden/Manifest
@@ -0,0 +1 @@
+DIST xcrysden-1.6.2.tar.gz 2460277 BLAKE2B
f0b7c2c5aeff51db97b29c8052273ed44bb9c183e0df62c406eee327c4c5d86d141d8adfd05df70b97661a8cbddbf052c233c288f1f30b308e4c877539c06a84
SHA512
9ed1b7fc11674509a3f2bf6604aa11e087fd77a971afb93039ca542cb9abb62b2553c7f386b845f004df5d3d340bdf1fe673552319788f006fd031efb6a4ad67
diff --git a/sci-chemistry/xcrysden/files/icons/xcrysden.png
b/sci-chemistry/xcrysden/files/icons/xcrysden.png
new file mode 100644
index 0..f41eddceb
Binary files /dev/null and b/sci-chemistry/xcrysden/files/icons/xcrysden.png
differ
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl_lib.patch
b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl_lib.patch
new file mode 100644
index 0..533c50650
--- /dev/null
+++ b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl_lib.patch
@@ -0,0 +1,14 @@
+Ensures that Togl is linked properly.
+diff --git a/system/Make.sys-shared b/system/Make.sys-shared
+index 51891e7..ba478fa 100644
+--- a/system/Make.sys-shared
b/system/Make.sys-shared
+@@ -48,7 +48,7 @@ X_INCDIR =
+
+ TCL_LIB = -ltcl$(TCL_VER2)
+ TK_LIB = -ltk$(TCL_VER2)
+-TOGL_LIB = -lTogl
++TOGL_LIB = -Wl,-rpath,"/usr/lib64/Togl2.0" -L/usr/lib64/Togl2.0 -lTogl2.0
+ GLU_LIB = -lGLU
+ GL_LIB = -lGL
+ FFTW3_LIB= -lfftw3
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch
b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch
new file mode 100644
index 0..0ca1f69b6
--- /dev/null
+++ b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch
@@ -0,0 +1,14 @@
+Prevents bwidget from being automatically downloaded when it is already
required as a build/run-time dependency.
+diff --git a/Makefile b/Makefile
+index cfdc14a..d0f7e6c 100644
+--- a/Makefile
b/Makefile
+@@ -18,7 +18,7 @@ what:
+
+ all: tcl tk mesa togl fftw xcrysden
+ # meschach
+-xcrysden: usage bwidget bindir src-C src-F src-Tcl
++xcrysden: usage bindir src-C src-F src-Tcl
+
+ usage: $(TOPDIR)/docs/xcrysden.1
+ man $(TOPDIR)/docs/xcrysden.1 | awk 'BEGIN {lprint=0; print "## do not
edit changes will be lost (file automatically generated)\n"; } /SYNOPSIS/ {
lprint=1; } /SEE ALSO/ { lprint=0; } /a*/ { if (lprint) print; }' > usage
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch
b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch
new file mode 100644
index 0..ef231827e
--- /dev/null
+++ b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch
@@ -0,0 +1,14 @@
+Adds -fcommon to CFLAGS to allow compilation on more recent GCC.
+diff --git a/system/Make.sys-shared b/system/Make.sys-shared
+index 51891e7..f89f876 100644
+--- a/system/Make.sys-shared
b/system/Make.sys-shared
+@@ -19,7 +19,7 @@ MAKE = make
+ # C-preprocessor flags
+ CPPFLAGS ?=
+ # C-compiler flags
+-CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall
++CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall -fcommon
+
+ CC = gcc
+ #LDLIB = -ldl
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper_paths.patch
b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper_paths.patch
new file mode 100644
index 0..8cc8b247a
--- /dev/null
+++ b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper_paths.patch
@@ -0,0 +1,16 @@
+Ensures that wrapper scripts account for live filesystem merge.
+diff --git a/sys_utils/wrappers.sh b/sys_utils/wrappers.sh
+index 1fa3cc6..e078b22 100755
+--- a/sys_utils/wrappers.sh
b/sys_utils/wrappers.sh
+@@ -5,8 +5,8 @@ do
+ #!/bin/sh -f
+
+ # simple wrapper to run $cmd
+-XCRYSDEN_TOPDIR="$prefix/share/$xcrysden"
+-XCRYSDEN_LIB_BINDIR="$prefix/lib/$xcrysden"
++XCRYSDEN_TOPDIR="/usr/share/$xcrysden"
++XCRYSDEN_LIB_BINDIR="/usr/lib/$xcrysden"
+ export XCRYSDEN_TOPDIR
+ export XCRYSDEN_LIB_BINDIR
+
diff --git
