Comments (37)
iamleot
commented on July 17, 2024
Hello pin,
if you would like start packaging I suggest to dig in `The pkgsrc guide'
and request an account for pkgsrc-wip:
https://www.pkgsrc.org/wip/users
Usually, to start it's an:
% cd pkgsrc/wip
% mkdir <pkg> && cd <pkg>
% url2pkg <URL>
...and then adjusting the corresponding `Makefile'.
If you get stuck both #pkgsrc IRC channel at Freenode and tech-pkg@ ML
are good places to get more help!
Have fun!
from pkgsrc-wip.
commented on July 17, 2024
Thx!
I'll dig into it and see how far I get, it would be nice to contribute and maintain a few packades ;)
Back in a week or so, have some reading to do :)
from pkgsrc-wip.
commented on July 17, 2024
Hi,
Tried to build the package locally, but failed :(
Installed cmake and the qt5-5.13.1 meta-package. Running cmake fails because it can not find the required packages, which from the CMakeList.txt file are the following...
57 set(Qt5RequiredPackages
58 Core
59 Widgets
60 Gui
61 PrintSupport
62 Svg
63 Network
64 )
I've tried looking for a different name for these packages, found that Qt5Svg is called qt5-qtsvg, but couldn't find Core or the others. Maybe I'm still not advanced enough to start packaging :(
Edit: I'll give it another try using url2pkg and pkglint as described in chapter 12 of the pkgsrc guide... should read first.
from pkgsrc-wip.
commented on July 17, 2024
Ok guys, just sharing my experience...
Initially I had problems with checksums. The sourceforge link was not working and the directlink caused a mismatch in the checksums. I've downloaded the .tar.gz file and hosted it on my github under a temporary repository.
This solved the issue with the checksums. Running bmake proceeds fine untill the Qt5 dependencies above are not found :(
Obviously, the build fails....
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iamleot
commented on July 17, 2024
Hello @voidpin!
Can you please share the WIP package on pkgsrc-wip and maybe populate a TODO file with the build errors? (also if it still has some prolem it's perfectly fine to share it on pkgsrc-wip!)
In that way it will be easier to investigate/work on it collaboratevily!
Thanks for working on it!
from pkgsrc-wip.
commented on July 17, 2024
No, thank you for your interest, I've now requested commit access to pkgsrc-wip.
Unfortunately, I've cleaned the build directory, but don't worry, as soon as I have commit access, I'll repeat the procedure and report on the build errors.
Looking forward to learn :) I'm not a programmer....
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krytarowski
commented on July 17, 2024
I can package it but I am disoriented as inside https://sourceforge.net/projects/molsketch/files/Molsketch/ there are several catalogues like nitrogen, hydrogen.. Please point exact tarball to fetch and package.
from pkgsrc-wip.
commented on July 17, 2024
The latest release is the one in the Nitrogen folder, 0.6.0. https://sourceforge.net/projects/molsketch/files/Molsketch/Nitrogen%200.6.0/Molsketch-0.6.0-src.tar.gz/download
That would be awesome, thanks!!
Promisse to look at the details and learn.
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krytarowski
commented on July 17, 2024
Please check: wip/molsketch
It builds, installs and runs for me.
from pkgsrc-wip.
commented on July 17, 2024
Wow! Amazing, thx!
Call it noob mistake if you wish...
I did figure that you needed USE_LANGUAGES= c c++ as initially I had only c++
My Makefile was missing these three lines
.include "../../biology/openbabel/buildlink3.mk"
.include "../../x11/qt5-qtbase/buildlink3.mk"
.include "../../x11/qt5-qtsvg/buildlink3.mk"
:( How did you find this? I'm here to learn and hope to be able to build packages myself soon!
I was obviously, also missing cmake path detection and PLIST, as I didn't get that far...
Let me ask you, was the cmake path expecting Linux or, was it something different?
Once again thank you! I'll be building the package tomorrow as I left my NetBSD machine at work this evening.
Finally, one more noob question... should I use bmake, cmake or just make to build the package now that the Makefile is fixed?
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krytarowski
commented on July 17, 2024
I did figure that you needed USE_LANGUAGES= c c++ as initially I had only c++
USE_LANGUAGES is typically try and fail.
How did you find this?
grep -r Svg ../../x11/qt5*/
And adding relative path to buildlink3.mk of dependencies.
Most of packaging is grepping.
bmake only if you run bootstrap yourself, on NetBSD native make is fine. Never run directly cmake as it is a tool inside a package.
Does molsketch work? If so, I will import it into pkgsrc.
from pkgsrc-wip.
commented on July 17, 2024
Thank you!
I'll build the package tomorrow morning (Sweden) and let you know.
I did guess qt5-qtsvg, but couldn't figure that all others were included in qt5-qtbase
Let you know how it works once I've tried it. Chemistry is no problem for me ;)
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commented on July 17, 2024
Trying to build the package. First I had to ALLOW_VULNERABLE_PACKAGES= in mk.conf to build libmolsketch
But later it fails to build openbabel with the following
===> Building for openbabel-2.3.2nb9
[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
In file included from /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:19:0,
from /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/alias.cpp:17:
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/shared_ptr.h:33:17: error: 'std::tr1' has not been declared
using std::tr1::shared_ptr;
^
In file included from /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/alias.cpp:17:0:
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:118:47: error: 'shared_ptr' was not declared in this scope
typedef std::vector< std::pair<std::string, shared_ptr<OBSmartsPattern> > > SmartsTable;
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:118:73: error: template argument 2 is invalid
typedef std::vector< std::pair<std::string, shared_ptr<OBSmartsPattern> > > SmartsTable;
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:118:75: error: template argument 1 is invalid
typedef std::vector< std::pair<std::string, shared_ptr<OBSmartsPattern> > > SmartsTable;
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:118:75: error: template argument 2 is invalid
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:118:77: error: expected unqualified-id before '>' token
typedef std::vector< std::pair<std::string, shared_ptr<OBSmartsPattern> > > SmartsTable;
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/alias.h:119:24: error: 'SmartsTable' has not been declared
static bool LoadFile(SmartsTable& smtable);
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/alias.cpp:239:26: error: 'bool OpenBabel::AliasData::LoadFile' is not a static data member of 'class OpenBabel::AliasData'
bool AliasData::LoadFile(SmartsTable& smtable)
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/alias.cpp:239:26: error: 'SmartsTable' was not declared in this scope
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/alias.cpp:239:39: error: 'smtable' was not declared in this scope
bool AliasData::LoadFile(SmartsTable& smtable)
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/alias.cpp:240:1: error: expected ',' or ';' before '{' token
{
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/alias.cpp:396:1: error: expected '}' at end of input
}//namespace
^
*** Error code 1
Stop.
make[2]: stopped in /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2
*** Error code 1
Stop.
make[1]: stopped in /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2
*** Error code 1
Stop.
make[2]: stopped in /usr/pkgsrc/biology/openbabel
*** Error code 1
Stop.
make[1]: stopped in /usr/pkgsrc/biology/openbabel
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/wip/molsketch
EDIT: Crazy thought... Could download the tarball of openbabel for NetBSD-7.1, unpack and manually move the contents into place.
from pkgsrc-wip.
krytarowski
commented on July 17, 2024
https://github.com/NetBSD/pkgsrc/blob/trunk/biology/openbabel/Makefile#L14
Please experiment and try to change this line to: c gnu++03. If nothing will help, report to @jsonn as he added this line.
from pkgsrc-wip.
commented on July 17, 2024
:( Unfortunately it doesn't work... openbabel still fails to build. @jsonn
Would be nice to know what's the difference between the builds for 8.1 and 7.1, the binary was successfully built and is available through pkgin for 7.1, but fails for 8.1?!
Edit: Looking back, it was already the case back in 2019Q2 release of pkgsrc.
Bulk build report for 2019Q2 for 7.1
...
Build failures
Package Breaks Maintainer
-------------------------------------------------------------------------
audio/audacity pkgsrc-users%NetBSD.org@localhost
audio/fasttracker2 fox%NetBSD.org@localhost
audio/gst-plugins1-spc pkgsrc-users%NetBSD.org@localhost
audio/libopenmpt pkgsrc-users%NetBSD.org@localhost
audio/musicpd pkgsrc-users%NetBSD.org@localhost
audio/squeezeboxserver pkgsrc-users%NetBSD.org@localhost
benchmarks/dnsperf pkgsrc-users%NetBSD.org@localhost
benchmarks/glmark2 prlw1%cam.ac.uk@localhost
benchmarks/google-benchmark 7 minskim%NetBSD.org@localhost
benchmarks/phoronix-test-suite jym%NetBSD.org@localhost
biology/fastp bacon%NetBSD.org@localhost
cad/fastcap dmcmahill%NetBSD.org@localhost
...
...
Bulk build report for 2019Q2 for 8.0
...
Build failures
Package Breaks Maintainer
-------------------------------------------------------------------------
audio/gst-plugins1-spc pkgsrc-users%NetBSD.org@localhost
audio/squeezeboxserver pkgsrc-users%NetBSD.org@localhost
benchmarks/dnsperf pkgsrc-users%NetBSD.org@localhost
benchmarks/phoronix-test-suite jym%NetBSD.org@localhost
biology/canu bacon%NetBSD.org@localhost
biology/openbabel 1 pkgsrc-users%NetBSD.org@localhost
cad/dinotrace-mode dmcmahill%NetBSD.org@localhost
...
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krytarowski
commented on July 17, 2024
https://github.com/openbabel/openbabel/releases/tag/openbabel-3-0-0
Probably the best way forward is to upgrade openbabel to 3.0. The pkgsrc version uses compiler extension for, at that time, unreleased C++ standard.
from pkgsrc-wip.
krytarowski
commented on July 17, 2024
I will give it a try.
from pkgsrc-wip.
commented on July 17, 2024
Great stuff! Thank you so much!!!
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krytarowski
commented on July 17, 2024
How about building the pkgsrc openbabel with c gnu++11? It was already patched for this version.
from pkgsrc-wip.
commented on July 17, 2024
At least it start the building of openbabel, but still fails at 20% with
[ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/sort.o
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/ops/sort.cpp: In member function 'virtual bool OpenBabel::OpSort::ProcessVec(std::vector<OpenBabel::OBBase*>&)':
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/ops/sort.cpp:117:99: error: no matching function for call to 'make_pair(OpenBabel::OBBase*&, double)'
valvec.push_back(std::make_pair<OBBase*,double>(*iter, _pDesc->Predict(*iter, &_pDescOption)));
^
In file included from /usr/include/g++/bits/stl_algobase.h:64:0,
from /usr/include/g++/bits/char_traits.h:39,
from /usr/include/g++/string:40,
from /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/op.h:23,
from /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/ops/sort.cpp:19:
/usr/include/g++/bits/stl_pair.h:276:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
make_pair(_T1&& __x, _T2&& __y)
^
/usr/include/g++/bits/stl_pair.h:276:5: note: template argument deduction/substitution failed:
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/ops/sort.cpp:117:99: note: cannot convert 'iter.__gnu_cxx::__normal_iterator<_Iterator, _Container>::operator*<OpenBabel::OBBase**, std::vector<OpenBabel::OBBase*> >()' (type 'OpenBabel::OBBase*') to type 'OpenBabel::OBBase*&&'
valvec.push_back(std::make_pair<OBBase*,double>(*iter, _pDesc->Predict(*iter, &_pDescOption)));
^
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/ops/sort.cpp:147:68: error: no matching function for call to 'make_pair(OpenBabel::OBBase*&, std::string&)'
valvec.push_back(std::make_pair<OBBase*,std::string>(*iter, s));
^
In file included from /usr/include/g++/bits/stl_algobase.h:64:0,
from /usr/include/g++/bits/char_traits.h:39,
from /usr/include/g++/string:40,
from /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/include/openbabel/op.h:23,
from /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/ops/sort.cpp:19:
/usr/include/g++/bits/stl_pair.h:276:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
make_pair(_T1&& __x, _T2&& __y)
^
/usr/include/g++/bits/stl_pair.h:276:5: note: template argument deduction/substitution failed:
^
/usr/include/g++/bits/stl_pair.h:276:5: note: template argument deduction/substitution failed:
/usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2/src/ops/sort.cpp:147:68: note: cannot convert 'iter.__gnu_cxx::__normal_iterator<_Iterator, _Container>::operator*<OpenBabel::OBBase**, std::vector<OpenBabel::OBBase*> >()' (type 'OpenBabel::OBBase*') to type 'OpenBabel::OBBase*&&'
valvec.push_back(std::make_pair<OBBase*,std::string>(*iter, s));
^
*** Error code 1
Stop.
make[2]: stopped in /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2
*** Error code 1
Stop.
make[1]: stopped in /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/biology/openbabel/work/openbabel-2.3.2
*** Error code 1
Stop.
make[2]: stopped in /usr/pkgsrc/biology/openbabel
*** Error code 1
Stop.
make[1]: stopped in /usr/pkgsrc/biology/openbabel
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/wip/molsketch
:(
from pkgsrc-wip.
krytarowski
commented on July 17, 2024
Please upgrade pkgsrc/biology/openbabel and try to build it.
I will need to try to patch molsketch to build against it.
from pkgsrc-wip.
commented on July 17, 2024
Ok, will do!
Should I try to upgrade to 3.0.0 or 2.4.1?
from pkgsrc-wip.
krytarowski
commented on July 17, 2024
pkgsrc/biology/openbabel is upgraded now to 3.0.0
I am trying to build molsketch with it.
Please try to build pkgsrc openbabel version 3.0.0.
from pkgsrc-wip.
krytarowski
commented on July 17, 2024
OK: pkgsrc/biology/openbabel 3.0.0nb1
- molsketch from pkgsrc-wip work for me
commit 9a725bc110e331bbf46df8fca3b71e5b28bc43c0 (HEAD -> master, origin/master, origin/HEAD)
Author: Kamil Rytarowski <[email protected]>
Date: Wed Nov 20 19:06:06 2019 +0100
molsketch: Fix build with openbabel 3.0.0
I have ported it to openbabel.
Please build openbabel 3.0.0nb1 and the newest version of molsketch.
from pkgsrc-wip.
commented on July 17, 2024
Thank you so much for this!
I'll give it a go again tomorrow morning with openbabel 3.0.0 from pkgsrc-HEAD and report back.
from pkgsrc-wip.
commented on July 17, 2024
@krytarowski I must be doing something wrong :(
I'm on NetBSD-8.1_STABLE so, I've rm -r pkgsrc/, cloned the git-repo of pkgsrc-HEAD, followed by clone of pkgsrc-wip into place. Everything built and installed, including openbabel, until this point...
Sorry!
=> Bootstrap dependency digest>=20010302: found digest-20190127
===> Patching for molsketch-0.6.0
=> Applying pkgsrc patches for molsketch-0.6.0
**************************************
Ignoring patch file /usr/pkgsrc/wip/molsketch/patches/patch-CMakeLists.txt: invalid checksum
**************************************
Ignoring previously applied (or reversed) patch.
1 out of 1 hunks ignored--saving rejects to cmake/modules/FindOpenBabel2.cmake.rej
Patch /usr/pkgsrc/wip/molsketch/patches/patch-cmake_modules_FindOpenBabel2.cmake failed
Ignoring previously applied (or reversed) patch.
3 out of 3 hunks ignored--saving rejects to obabeliface/obabeliface.cpp.rej
Patch /usr/pkgsrc/wip/molsketch/patches/patch-obabeliface_obabeliface.cpp failed
ERROR: Patching failed due to modified or broken patch file(s):
ERROR: /usr/pkgsrc/wip/molsketch/patches/patch-CMakeLists.txt
ERROR: /usr/pkgsrc/wip/molsketch/patches/patch-cmake_modules_FindOpenBabel2.cmake
ERROR: /usr/pkgsrc/wip/molsketch/patches/patch-obabeliface_obabeliface.cpp
*** Error code 1
Stop.
make[1]: stopped in /usr/pkgsrc/wip/molsketch
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/wip/molsketch
from pkgsrc-wip.
krytarowski
commented on July 17, 2024
Please update pkgsrc-wip and retry. I have regenerated the checksum.
from pkgsrc-wip.
commented on July 17, 2024
Just saw you had pushed an update :) Cheers!!
I'm out this evening ;), but I'll re-build it asap (I can).
from pkgsrc-wip.
commented on July 17, 2024
@krytarowski It works! Thank you very much!!!!
The program work fine and let me tell you, its probably the best open source molecule editor I've tried. Thanks!!!!
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krytarowski
commented on July 17, 2024
OK, so homework:
- please get in touch with openbabel people and upstream patches for it in pkgsrc
- fix .pc file not upgraded since openbabel2
- add missing includes for
std::sort(<algorithm>)
- please get in touch with molsketch people and upstream patches for new openbabel
from pkgsrc-wip.
commented on July 17, 2024
Ok, I've dropped a message to openbabel and molsketch people and waiting an answer.
The other,
fix .pc file not upgraded since openbabel2
add missing includes for std::sort (<algorithm>)
I'm not sure what you're asking me to do??
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krytarowski
commented on July 17, 2024
That was a comment what is done by the patches, to be forwarded to upstream.
from pkgsrc-wip.
commented on July 17, 2024
Pull-request for Molesketch, hvennekate/Molsketch#4
Working on the one for openbabel sooooon....
Edit: for openbabel, openbabel/openbabel#2093
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commented on July 17, 2024
@krytarowski #2093 merged into master for openbabel ;)
from pkgsrc-wip.
commented on July 17, 2024
@krytarowski
Can Molsketch be merged?
from pkgsrc-wip.
krytarowski
commented on July 17, 2024
I prefer to do it after merging local patches into Molsketch and releasing a new version of Molsketch, so pkgsrc will ship with 0 local patches.
from pkgsrc-wip.
commented on July 17, 2024
Fair enough, I agree with that. Its for sure cleaner.
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