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openbabel: upgrade 2.4.1 -> 3.0.0

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This should build without python2

Signed-off-by: Andreas Müller <schnitzeltony@gmail.com>
This commit is contained in:
Andreas Müller
2019-12-04 10:54:53 +01:00
parent dda1238647
commit 3e2bc54d88
3 changed files with 37 additions and 63 deletions
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30
recipes-misc/recipes-chemistry/openbabel/files/0001-Workaround-xdr-linker-error.patch Normal file
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@@ -0,0 +1,30 @@
From fce5f3a38a62dd4927adaa8372b73eedeeffbe46 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20M=C3=BCller?= <schnitzeltony@gmail.com>
Date: Tue, 3 Dec 2019 19:25:03 +0100
Subject: [PATCH] Workaround xdr linker error
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Upstream-Status: Pending
Signed-off-by: Andreas Müller <schnitzeltony@gmail.com>
---
CMakeLists.txt | 1 -
1 file changed, 1 deletion(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 33bf2da29..178231b62 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -224,7 +224,6 @@ check_include_file(conio.h HAVE_CONIO_H)
check_include_file(sys/time.h HAVE_SYS_TIME_H)
check_include_file(time.h HAVE_TIME_H)
check_include_file(strings.h HAVE_STRINGS_H)
-check_include_file(rpc/xdr.h HAVE_RPC_XDR_H)
check_include_file(regex.h HAVE_REGEX_H)
check_include_file_cxx(sstream HAVE_SSTREAM)
--
2.21.0

58
recipes-misc/recipes-chemistry/openbabel/files/0001-take-care-for-ARM-s-unsigned-char.patch
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@@ -1,58 +0,0 @@
From 52851a453a1da3452d55e44f13323389b3a689c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20M=C3=BCller?= <schnitzeltony@googlemail.com>
Date: Fri, 16 Dec 2016 18:39:34 +0100
Subject: [PATCH] take care for ARM's unsigned char
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Stolen from [1]
[1] http://pkgs.fedoraproject.org/cgit/rpms/openbabel.git/tree/openbabel-narrowing-conversion.patch
Upstream-Status: Pending
Signed-off-by: Andreas Müller <schnitzeltony@googlemail.com>
---
src/formats/pngformat.cpp | 2 +-
src/formats/yasaraformat.cpp | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/formats/pngformat.cpp b/src/formats/pngformat.cpp
index 49bff17..375d42c 100644
--- a/src/formats/pngformat.cpp
+++ b/src/formats/pngformat.cpp
@@ -218,7 +218,7 @@ bool PNGFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
_count=0;
_hasInputPngFile=true;
}
- const char pngheader[] = {-119,80,78,71,13,10,26,10,0};
+ const signed char pngheader[] = {-119,80,78,71,13,10,26,10,0};
char readbytes[9];
ifs.read(readbytes, 8);
diff --git a/src/formats/yasaraformat.cpp b/src/formats/yasaraformat.cpp
index cfc0a53..5a4d413 100644
--- a/src/formats/yasaraformat.cpp
+++ b/src/formats/yasaraformat.cpp
@@ -472,7 +472,7 @@ bool YOBFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
// bool hetatom;
char buffer[32],/*resname[4],*/atomname[5];
- char double1[8]={0,0,0,0,0,0,-16,0x3f};
+ const signed char double1[8]={0,0,0,0,0,0,-16,0x3f};
// char *str;
int i,j,/*m,q,*/pos;
int /*resno,chainNum,link,linktype,*/atoms,element,links/*,chain*/;
@@ -500,7 +500,7 @@ bool YOBFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
mem_set(buffer,0,8);
for (i=0;i<4;i++)
{ for (j=0;j<4;j++)
- { if (i==j) ofs.write(double1,8);
+ { if (i==j) ofs.write(reinterpret_cast<const char*>(double1),8);
else ofs.write(buffer,8); } }
storeint32le(buffer,MOB_INFOEND);
storeint32le(&buffer[4],MOB_INFOENDSIZE);
--
2.5.5

12
recipes-misc/recipes-chemistry/openbabel/openbabel_2.4.1.bb → recipes-misc/recipes-chemistry/openbabel/openbabel_git.bb
View File

@@ -9,15 +9,17 @@ DEPENDS = " \
cairo \
libxml2 \
zlib \
libtirpc \
"
SRC_URI = " \
${SOURCEFORGE_MIRROR}/project/${BPN}/${BPN}/${PV}/${BPN}-${PV}.tar.gz \
git://github.com/openbabel/openbabel.git \
file://0001-Workaround-xdr-linker-error.patch \
file://openbabel-gui.desktop \
file://0001-take-care-for-ARM-s-unsigned-char.patch \
"
SRC_URI[md5sum] = "d9defcd7830b0592fece4fe54a137b99"
SRC_URI[sha256sum] = "204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc"
SRCREV = "49f9cfb32bd0bc6ea440639d338123eb27accbe2"
S = "${WORKDIR}/git"
PV = "3.0.0"
do_install_append() {
install -d ${D}${datadir}/applications
@@ -27,4 +29,4 @@ do_install_append() {
convert.im7 ${S}/src/GUI/babel.xpm -transparent white ${D}${datadir}/pixmaps/babel.png
}
FILES_${PN} += "${libdir}/cmake"
FILES_${PN}-dev += "${libdir}/cmake"