Package Details: molden 6.7-1

Git Clone URL: https://aur.archlinux.org/molden.git (read-only, click to copy)
Package Base: molden
Description: A program for molecular and electronic structure visualization
Upstream URL: http://www.cmbi.ru.nl/molden/
Keywords: molecular visualisation
Licenses: custom
Provides: molden
Submitter: dan.maftei
Maintainer: dan.maftei
Last Packager: dan.maftei
Votes: 6
Popularity: 0.000001
First Submitted: 2016-06-07 09:53 (UTC)
Last Updated: 2021-02-15 18:37 (UTC)

Latest Comments

berquist commented on 2020-11-07 16:54 (UTC)

@mib1982 If you apply the diff, that problem is solved.

mib1982 commented on 2020-11-07 14:36 (UTC) (edited on 2020-11-07 14:39 (UTC) by mib1982)

Hi everyone,

I think the path for 'ambfor' and 'surf' has changed. I get the following error during packaging:

cannot stat 'src/ambfor/ambfor': No such file or directory
cannot stat 'src/surf/surf': No such file or directory

Both these subfolders are not created by the build-process. I found binaries with these filenames in the same folders as molden, though.

berquist commented on 2020-09-28 03:01 (UTC)

I was having a bunch of problems unrelated to GCC 10; here's the diff for the changes:

diff --git a/PKGBUILD b/PKGBUILD
index f3eeaf7..6325166 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,57 +1,44 @@
 # Maintainer: Dan Maftei <dan.maftei@gmail.com>
 pkgname="molden"
 pkgver=6.5
-pkgrel=1
+pkgrel=2
 pkgdesc="A program for molecular and electronic structure visualization"
 arch=('i686' 'x86_64')
 url="http://www.cmbi.ru.nl/molden/"
 license=('custom')
-groups=()
-depends=('mesa' 'glu')
-makedepends=(
-    'vi'
-    'gcc-fortran'
-    'xorgproto'
-    'libx11'
-    'mesa'
-    'glu'
-)
+depends=('gcc-libs' 'glu' 'libx11' 'libxmu')
+makedepends=('gcc-fortran' 'xorgproto' 'vi')
 optdepends=(
    'openbabel: to create 2D images of the molecules in a .sdf file'
    'wget: to fetch PDB from rcsb.org'
 )
 provides=('molden')
-conflicts=()
-replaces=()
-backup=()
-options=()
-install=
-changelog=
 source=(
     "ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/$pkgname$pkgver.tar.gz"
 )
-noextract=()
 md5sums=('97bfffd55e166ca3a9fbddee111993ff')

-build() {
+prepare() {
   cd "molden$pkgver"
-  # Patch Makefile for surf utility to reflect 
-  # the replacement of missing makedepend 
+  # Patch Makefile for surf utility to reflect
+  # the replacement of missing makedepend
   sed -i 's/@.*makedepend.*$/@ \$(CC) \$(INCLUDE) -M \$(SRCS) \> makedep/' src/surf/Makefile
-  
+
   # Patch to compile with gfortran 10
   # Contributed by Panadestein on 5/31/2020
   sed -i 's/FFLAGS = -g ${AFLAG}/& -fallow-argument-mismatch/g' makefile
   sed -i 's/FFLAGS = -c -g -ffast-math -funroll-loops -O3/& -fallow-argument-mismatch/g' src/ambfor/makefile
+}
+
+build() {
+  cd "molden$pkgver"
   make
 }

 package() {
   cd "molden$pkgver"
   install -t "$pkgdir/usr/bin/"  -Dm755 bin/{molden,gmolden}
-  install -t "$pkgdir/usr/lib/$pkgname/" -Dm755 src/ambfor/ambfor src/ambfor/ambmd src/surf/surf  
-  install -t "$pkgdir/usr/share/doc/$pkgname" -Dm755 doc/figures.ps.Z  doc/manual.ps.Z doc/manual.txt.Z  
-  install -t "$pkgdir/usr/share/licenses/$pkgname/" -Dm755 CopyRight COMMERCIAL_LICENSE REGISTER     
+  install -t "$pkgdir/usr/lib/$pkgname/" -Dm755 bin/{ambfor,ambmd,surf}
+  install -t "$pkgdir/usr/share/doc/$pkgname" -Dm755 doc/figures.ps.Z  doc/manual.ps.Z doc/manual.txt.Z
+  install -t "$pkgdir/usr/share/licenses/$pkgname/" -Dm755 CopyRight COMMERCIAL_LICENSE REGISTER
 }
-
-

Panadestein commented on 2020-05-31 21:46 (UTC) (edited on 2020-05-31 22:53 (UTC) by Panadestein)

Hi everyone.

In case you are facing compilations errors due to some new features introduced in GCC 10, I suggest you to add the -fallow-argument-mismatch compilation flag to gfortran. This action needs to be performed in the main makefile and in the ambfor makefile. The issue is partially explained in the GCC 10 release notes:

https://gcc.gnu.org/gcc-10/changes.html

I guess a patch to the PKGBUILD file can be written, parsing both makefiles and adding the compilation flag.

Nice day to all of you.

Edit

These are the lines that need to be added to the build() function of the PKGBUILD:

sed -i 's/FFLAGS = -g ${AFLAG}/& -fallow-argument-mismatch/g' makefile
sed -i 's/FFLAGS = -c -g -ffast-math -funroll-loops -O3/& -fallow-argument-mismatch/g' ambfor/makefile

mvondomaros commented on 2020-03-28 03:00 (UTC)

Hi, Dan!

xproto is now called xorgproto. Could you please change?

Thanks a bunch!

dan.maftei commented on 2019-10-20 16:15 (UTC)

Package just upgraded, Thank you!

c0r3dump3d commented on 2019-10-20 11:26 (UTC)

Hello, It's seems that the md5sum of the package for version 6.1 it's wrong:

md5sum molden6.1.tar.gz 7bc693baddd615f554a08f452c5282dd molden6.1.tar.gz

mykhal commented on 2018-07-21 15:38 (UTC)

if download fails, s/ftp.cmbi.ru.nl/ftp.cmbi.umcn.nl/ might help.

3yan commented on 2018-05-28 03:44 (UTC)

New version in the upstream (5.8) is fixed. I do not know if anybody wrote to the developers but they've released it 2018-05-24. Flagging "out of date." Tested the build. Only thing that is needed is to change pkgver and pkgrel to 5.8 and 1 respectively in the PKGBUILD.

3yan commented on 2018-05-16 08:15 (UTC)

arjun_karol - thx, solution works. Did anybody wrote to the Molden developer team?

Panadestein commented on 2018-05-15 15:34 (UTC) (edited on 2018-05-15 15:35 (UTC) by Panadestein)

Thanks arjun_karol I did as suggested and it is now working. I patched the original source.

arjun_karol commented on 2018-05-15 14:42 (UTC)

Hello, I found out simple way to prevent mentioned call flth(jat,icnn2,inb,iconn) error. In the rdchx.f file, in flth subroutine delete +1 from icoon declarations mxcon+1 -> mxcon.

After that change molden compiles, and I didn't noticed any problems yet.

Panadestein commented on 2018-05-07 12:45 (UTC) (edited on 2020-05-31 22:49 (UTC) by Panadestein)

Hello.

A new update of molden and gcc-fortran. There is a checksum mismatch, so I edited the PKGBUILD adding the correct md5sum. After this, there are some compilation errors (I guess related to the new gcc-fortran version):

gfortran -g -m64 -c -o rdchx.o rdchx.f rdchx.f:6097:29:

            call flth(jat,icnn2,ibnds2,iconn)
                         1

Error: Actual argument contains too few elements for dummy argument ‘icnn’ (10/11) at (1) rdchx.f:6102:39:

                      call flth(kat,icnn2,ibnds2,iconn)
                                   1

Error: Actual argument contains too few elements for dummy argument ‘icnn’ (10/11) at (1) rdchx.f:6129:29:

            call flth(jat,icnn2,ibnds2,iconn)
                         1

Error: Actual argument contains too few elements for dummy argument ‘icnn’ (10/11) at (1) rdchx.f:6144:33:

            call flth(icnn(i),icnn2,ibnds2,iconn)
                             1

Error: Actual argument contains too few elements for dummy argument ‘icnn’ (10/11) at (1) rdchx.f:6175:38:

                     call flth(jat,icnn2,ibnds2,iconn)
                                  1

Error: Actual argument contains too few elements for dummy argument ‘icnn’ (10/11) at (1) rdchx.f:6190:35:

                  call flth(jat,icnn2,inb,iconn)
                               1

Error: Actual argument contains too few elements for dummy argument ‘icnn’ (10/11) at (1) make: *** [<builtin>: rdchx.o] Error 1 ==> ERROR: A failure occurred in build(). Aborting... 2018-05-07 14:39:59,646 - wrappers - makepkg - ERROR - makepkg query makepkg -cf --noconfirm failed

Panadestein commented on 2017-10-05 13:04 (UTC)

Hello. Again a checksum mismatch, can you please correct the PKGBUILD? Your idea of the cronjob is a good one, I think it must be implemented. Greetings

dan.maftei commented on 2017-06-06 15:36 (UTC)

Symlink-ing libraries is NOT a good idea, even if it works sometimes. In your case, further updates of gcc-fortran will fail with pacman complaining that "file ... exists in the filesystem...". However, the issue doesn't relate to molden. Since you've upgraded the dependencies (gcc-gfortran and maybe others), you should recompile molden too, to link against newly-installed libs: yaourt -Syyua (to upgrade all packages, including those from AUR) or, to upgrade only molden: yaourt -Sa molden

Panadestein commented on 2017-06-02 20:24 (UTC) (edited on 2017-06-02 20:52 (UTC) by Panadestein)

Hello! I have detected a new issue on the package. After upgrading the system, in particular gcc-fortran "libgfortran.so" to version 4.0.0, Molden stopped working, with the following error message: molden: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory I thought it could be a dependencies issue and effectively, it was, so I tried this: sudo ln -s /usr/lib/libgfortran.so.4 /usr/lib/libgfortran.so.3 But of course, there's no reason for this to work properly, and then I got this error messages: molden: /usr/lib/libgfortran.so.3: version `GFORTRAN_1.0' not found (required by molden) molden: /usr/lib/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by molden) So at this point, what could be a good solution, to downgrade libgfortran.so.4? Greetings! Edit: Just uninstalled and rebuilt the package and now works flawlessly! Maybe this is an stupid question but, do I have to rebuilt the package any time the compiler is upgraded? I mean, it seems to me that you can't really have issues executing binaries compiled with to closer versions of the compiler. But again, I'm just a noob.

dan.maftei commented on 2017-05-22 16:21 (UTC)

Thank you for signaling the checksum mismatch! Indeed, the developers of molden inadvertently update the source while keeping the archive name (i.e. molden5.7.tar.gz). It happened in the past and most likely will happen again. For now, I've just updated the PKGBUILD with the current checksum. In the future, I intend to fire a cronjob to periodically check for such updates...

Panadestein commented on 2017-05-21 11:35 (UTC) (edited on 2017-05-21 11:54 (UTC) by Panadestein)

I'm getting this error when trying to build the package: ==> Making package: molden 5.7-2 (Sun May 21 12:42:09 CEST 2017) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> Retrieving sources... -> Downloading molden5.7.tar.gz... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 5214k 100 5214k 0 0 94329 0 0:00:56 0:00:56 --:--:-- 371k ==> Validating source files with md5sums... molden5.7.tar.gz ... FAILED ==> ERROR: One or more files did not pass the validity check! Edit: I checked the md5sum of the package in ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz, and it's different to the one in the PKGBUILD, so I think it has to be updated. After editing it, everything works perfectly.