Bug 741626 (packmol)

*** Bug 531605 has been marked as a duplicate of this bug. ***

- The way you build it breaks the debuginfo package:
  extracting debug info from /home/tom/rpmbuild/BUILDROOT/packmol-1.1.1.258-1.fc15.x86_64/usr/bin/packmol
  cpio: packmol/ser/gencan.i: Cannot stat: No such file or directory
  cpio: packmol/ser/molpa.i: Cannot stat: No such file or directory
  cpio: packmol/ser/sizes.i: Cannot stat: No such file or directory

  The files are in packmol/*.i directly.

Is there a CMake possibility to put them into the ser directory instead?
Running "mv *.i ser/" after building works, but looks rather hackish...



- Why are GPLv3 headers -> GPL+?
  I'd expect GPLv3+ (or GPLv3only) here:
  (minimal) version = version in COPYING.

  It would be best to ask upstream to clarify it.

(In reply to comment #2)
> Is there a CMake possibility to put them into the ser directory instead?
> Running "mv *.i ser/" after building works, but looks rather hackish...

Maybe. But these are include files...

> - Why are GPLv3 headers -> GPL+?
>   I'd expect GPLv3+ (or GPLv3only) here:
>   (minimal) version = version in COPYING.
> 
>   It would be best to ask upstream to clarify it.

.. where do you see gplv3 headers?

(In reply to comment #3)
> (In reply to comment #2)
> > Is there a CMake possibility to put them into the ser directory instead?
> > Running "mv *.i ser/" after building works, but looks rather hackish...
> 
> Maybe. But these are include files...

How about a complete cp then?
e.g.
mkdir ser; cd ser
cp ../* .
%cmake... etc
cd ..

Do you intend to build both serial and parallel versions?
How do you want to name them?
par/ppackmol would only be a script that calls packmol with OMP_THREADS

With copying around anything from above, it would be possible to install par/packmol as ppackmol and get a backtrace of the segfault with abrt.

> > - Why are GPLv3 headers -> GPL+?
> >   I'd expect GPLv3+ (or GPLv3only) here:
> >   (minimal) version = version in COPYING.
> > 
> >   It would be best to ask upstream to clarify it.
> 
> .. where do you see gplv3 headers?

GPL+ for me is any GPL version, that exists and that will come in the future.

When adding a GPLv3 COPYING, I either want to have the program licensed under GPLv3 or GPLv3+, but not with GPLv2. But I'm not a lawyer, so asking upstream to clarify it is the best way to be sure.

(In reply to comment #4)
> (In reply to comment #3)
> > (In reply to comment #2)
> > > Is there a CMake possibility to put them into the ser directory instead?
> > > Running "mv *.i ser/" after building works, but looks rather hackish...
> > 
> > Maybe. But these are include files...
> 
> How about a complete cp then?
> e.g.
> mkdir ser; cd ser
> cp ../* .
> %cmake... etc
> cd ..
 
I'll copy the inc files.

My reason for writing the CMake scripts was to get out-of-tree builds to work, and also make SMP make work correctly.

> Do you intend to build both serial and parallel versions?
> How do you want to name them?
> par/ppackmol would only be a script that calls packmol with OMP_THREADS
> 
> With copying around anything from above, it would be possible to install
> par/packmol as ppackmol and get a backtrace of the segfault with abrt.

I might in the future. Packmol allocates everything statically (gah!), since it has been written in Fortran 77 (double gah! - Fortran 90 is a *lot* better in every aspect).

The segfault is due to the stack memory limit being broken.

I don't see a need for a wrapper script.
 
> > > - Why are GPLv3 headers -> GPL+?
> > >   I'd expect GPLv3+ (or GPLv3only) here:
> > >   (minimal) version = version in COPYING.
> > > 
> > >   It would be best to ask upstream to clarify it.
> > 
> > .. where do you see gplv3 headers?
> 
> GPL+ for me is any GPL version, that exists and that will come in the future.
> 
> When adding a GPLv3 COPYING, I either want to have the program licensed under
> GPLv3 or GPLv3+, but not with GPLv2. But I'm not a lawyer, so asking upstream
> to clarify it is the best way to be sure.

Please read

https://fedoraproject.org/wiki/Licensing:FAQ#How_do_I_figure_out_what_version_of_the_GPL.2FLGPL_my_package_is_under.3F

I have asked the author to add license boilerplates already a couple of weeks ago, and to port the code to allocate the memory dynamically.

I take this one. The package looks good to me -- I just recommend to explicitly remove cenmass.o in %prep in order to prevent linking this object file.

Also, upstream has released a new version of packmol. Maybe you'd like to update the package. The license headers are still missing but there's a file LICENSE present now which refers to GPLv2 only while COPYING still contains the GPLv3 license text. Upstream should definitely fix this. The license tag GPL+ is nonetheless correct, though.


$ rpmlint  *.rpm
packmol.src: W: spelling-error %description -l en_US lamellar -> Carmella, Mallarme, Marcella
packmol.src:58: W: macro-in-comment %{buildroot}
packmol.src:58: W: macro-in-comment %{_bindir}
packmol.src:68: W: macro-in-comment %{_bindir}
packmol.src: W: invalid-url Source0: http://packmol.googlecode.com/files/packmol-1.1.1.258.tar.gz HTTP Error 404: Not Found
packmol.x86_64: W: spelling-error %description -l en_US lamellar -> Carmella, Mallarme, Marcella
packmol.x86_64: W: no-manual-page-for-binary packmol
packmol.x86_64: W: no-manual-page-for-binary packmol_solvate
3 packages and 0 specfiles checked; 0 errors, 8 warnings.

The above warnings can safely be ignored:
- macros in comments are expected
- invalid url warning is false positive
- spelling errors are false positive
- no manual pages available for the binaries

---------------------------------
key:

[+] OK
[.] OK, not applicable
[X] needs work
---------------------------------

[+] MUST: The package must be named according to the Package Naming Guidelines.
[+] MUST: The spec file name must match the base package %{name}.
[+] MUST: The package must meet the Packaging Guidelines.
[+] MUST: The package must be licensed with a Fedora approved license.
    - GPLv3 license text present
    - no copyright information in sources
    => GPL+

[+] MUST: The License field in the package spec file must match the actual license.
[+] MUST: The file containing the text of the license(s) for the package must be included in %doc.
[+] MUST: The spec file must be written in American English.
[+] MUST: The spec file for the package MUST be legible.
[+] MUST: The sources used to build the package must match the upstream source.
    $ md5sum packmol-1.1.1.258.tar.gz*
    d1b12036b94f48c92595e9c4d3180009  packmol-1.1.1.258.tar.gz
    d1b12036b94f48c92595e9c4d3180009  packmol-1.1.1.258.tar.gz.upstream

[+] MUST: The package MUST successfully compile and build into binary rpms on at least one primary architecture.
[.] MUST: If the package does not successfully compile, build or work on an architecture, ...
[+] MUST: All build dependencies must be listed in BuildRequires.
[+] MUST: When compiling C, C++, or Fortran files, %{optflags} must be applied.
[.] MUST: The spec file MUST handle locales properly.
[.] MUST: Packages storing shared library files (not just symlinks) must call ldconfig in %post and %postun.
[+] MUST: Packages must NOT bundle copies of system libraries.
[.] MUST: If the package is designed to be relocatable, ...
[+] MUST: A package must own all directories that it creates. 
[+] MUST: A Fedora package must not list a file more than once in %files.
[+] MUST: Permissions on files must be set properly.
[+] MUST: Each package must consistently use macros.
[+] MUST: The package must contain code, or permissable content.
[.] MUST: Large documentation files must go in a -doc subpackage.
[+] MUST: Files in %doc must not affect the runtime of the application.
[.] MUST: Header files must be in a -devel package.
[.] MUST: Static libraries must be in a -static package.
[.] MUST: If a package contains library files with a suffix (e.g. libfoo.so.1.1), then library files that end in .so (without suffix) must go in a -devel package.
[.] MUST: devel packages must require the base package using a fully versioned dependency.
[+] MUST: Packages must NOT contain any .la libtool archives.
[.] MUST: Packages containing GUI applications must include a %{name}.desktop file, and that file must be properly installed with desktop-file-install in the %install section. If you feel that your packaged GUI application does not need a .desktop file, you must put a comment in the spec file with your explanation.
[+] MUST: Packages must not own files or directories already owned by other packages.
[+] MUST: All filenames in rpm packages must be valid UTF-8.

EPEL <= 5 only:
[+] MUST: The spec file must contain a valid BuildRoot field.
[+] MUST: At the beginning of %install, each package MUST run rm -rf %{buildroot}.
[+] MUST: Each package must have a %clean section, which contains rm -rf %{buildroot}.
[.] MUST: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig'

[.] SHOULD: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it.
[+] SHOULD: Timestamps of files should be preserved.
[+] SHOULD: The reviewer should test that the package builds in mock.
[+] SHOULD: The reviewer should test that the package functions as described.
[.] SHOULD: If scriptlets are used, those scriptlets must be sane.
[.] SHOULD: Usually, subpackages other than devel should require the base package using a fully versioned dependency.
[.] SHOULD: pkgconfig(.pc) files should be placed in a -devel pkg.
[.] SHOULD: If the package has file dependencies outside of /etc, /bin, /sbin, /usr/bin, or /usr/sbin consider requiring the package which provides the file instead of the file itself.
[X] SHOULD: Your package should contain man pages for binaries/scripts.
    - maybe you can ask upstream to think about adding manpages for the 
      executables

(In reply to comment #6)
> I take this one. The package looks good to me -- I just recommend to explicitly
> remove cenmass.o in %prep in order to prevent linking this object file.

Done.

> Also, upstream has released a new version of packmol. Maybe you'd like to
> update the package. The license headers are still missing but there's a file
> LICENSE present now which refers to GPLv2 only while COPYING still contains the
> GPLv3 license text. Upstream should definitely fix this. The license tag GPL+
> is nonetheless correct, though.

Done; but the correct license tag is now GPLv2.

http://theory.physics.helsinki.fi/~jzlehtol/rpms/packmol.spec
http://theory.physics.helsinki.fi/~jzlehtol/rpms/packmol-1.1.2.017-1.fc16.src.rpm

(In reply to comment #7)
> Done; but the correct license tag is now GPLv2.

Yes, of course. I think, you can drop COPYING as long as it doesn't match the license of the package. Anyway, the package looks good now.

----------------
Package APPROVED
----------------

Sure. Thanks for the review!


New Package SCM Request
=======================
Package Name: packmol
Short Description: Packing optimization for molecular dynamics simulations
Owners: jussilehtola
Branches: F-15 F-16
InitialCC:

Git done (by process-git-requests).

Upstream has added license headers and fixed LICENSE. The license tag has been changed accordingly to GPLv2+.

packmol-1.1.2.023-1.fc15 has been submitted as an update for Fedora 15.
https://admin.fedoraproject.org/updates/packmol-1.1.2.023-1.fc15

packmol-1.1.2.023-1.fc16 has been submitted as an update for Fedora 16.
https://admin.fedoraproject.org/updates/packmol-1.1.2.023-1.fc16

packmol-1.1.2.023-1.fc15 has been pushed to the Fedora 15 testing repository.

Hi,

Is it possible to build it agains CentOs-6 for the epel repo?

I tried on a C6 bix and it works:

rpmbuild --rebuild packmol-1.1.2.023-1.fc16.src.rpm 
Installing packmol-1.1.2.023-1.fc16.src.rpm
warning: user mockbuild does not exist - using root
warning: group mockbuild does not exist - using root
warning: user mockbuild does not exist - using root
warning: group mockbuild does not exist - using root
warning: user mockbuild does not exist - using root
warning: group mockbuild does not exist - using root
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.PT5aQU
+ umask 022
+ cd /root/rpmbuild/BUILD
+ LANG=C
+ export LANG
+ unset DISPLAY
+ cd /root/rpmbuild/BUILD
+ rm -rf packmol
+ /bin/tar -xf -
+ /usr/bin/gzip -dc /root/rpmbuild/SOURCES/packmol-1.1.2.023.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd packmol
+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ cp -a /root/rpmbuild/SOURCES/packmol-CMakeLists.txt CMakeLists.txt
+ find . -name '*.o' -delete
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0yG8KE
+ umask 022
+ cd /root/rpmbuild/BUILD
+ cd packmol
+ LANG=C
+ export LANG
+ unset DISPLAY
+ export FC=gfortran
+ FC=gfortran
+ mkdir ser
+ cd ser
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
+ export FFLAGS
+ /usr/bin/cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DUSE_OPENMP=OFF ..
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
CMake Warning: The variable, 'BUILD_SHARED_LIBS', specified manually, was not used during the generation.
CMake Warning: The variable, 'CMAKE_INSTALL_LIBDIR', specified manually, was not used during the generation.
CMake Warning: The variable, 'INCLUDE_INSTALL_DIR', specified manually, was not used during the generation.
CMake Warning: The variable, 'LIB_INSTALL_DIR', specified manually, was not used during the generation.
CMake Warning: The variable, 'LIB_SUFFIX', specified manually, was not used during the generation.
CMake Warning: The variable, 'SHARE_INSTALL_PREFIX', specified manually, was not used during the generation.
CMake Warning: The variable, 'SYSCONF_INSTALL_DIR', specified manually, was not used during the generation.
-- Build files have been written to: /root/rpmbuild/BUILD/packmol/ser
+ make -j8
/usr/bin/cmake -H/root/rpmbuild/BUILD/packmol -B/root/rpmbuild/BUILD/packmol/ser --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /root/rpmbuild/BUILD/packmol/ser/CMakeFiles /root/rpmbuild/BUILD/packmol/ser/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory `/root/rpmbuild/BUILD/packmol/ser'
make -f CMakeFiles/packmol.dir/build.make CMakeFiles/packmol.dir/depend
make[2]: Entering directory `/root/rpmbuild/BUILD/packmol/ser'
cd /root/rpmbuild/BUILD/packmol/ser && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /root/rpmbuild/BUILD/packmol /root/rpmbuild/BUILD/packmol /root/rpmbuild/BUILD/packmol/ser /root/rpmbuild/BUILD/packmol/ser /root/rpmbuild/BUILD/packmol/ser/CMakeFiles/packmol.dir/DependInfo.cmake --color=
Scanning dependencies of target packmol
make[2]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser'
make -f CMakeFiles/packmol.dir/build.make CMakeFiles/packmol.dir/requires
make[2]: Entering directory `/root/rpmbuild/BUILD/packmol/ser'
make[2]: Nothing to be done for `CMakeFiles/packmol.dir/requires'.
make[2]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser'
make -f CMakeFiles/packmol.dir/build.make CMakeFiles/packmol.dir/build
make[2]: Entering directory `/root/rpmbuild/BUILD/packmol/ser'
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 1
[ 10%] /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 2
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 3
Building Fortran object CMakeFiles/packmol.dir/cenmass.f.o
[ 20%] [ 30%] /usr/bin/gfortran  -o CMakeFiles/packmol.dir/cenmass.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/cenmass.f
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 4
Building Fortran object CMakeFiles/packmol.dir/gencan.f.o
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/gencan.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/gencan.f
Building Fortran object CMakeFiles/packmol.dir/initial.f.o
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/initial.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/initial.f
[ 40%] /usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 5
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 6
[ 50%] Warning: Nonconforming tab character in column 1 of line 2355
[ 60%] Building Fortran object CMakeFiles/packmol.dir/io.f.o
/root/rpmbuild/BUILD/packmol/gencan.f:56.36:

      subroutine evalal(n,x,m,lambda,rho,f,flag)                        
                                    1
Warning: Unused dummy argument 'lambda' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:56.40:

      subroutine evalal(n,x,m,lambda,rho,f,flag)                        
                                        1
Warning: Unused dummy argument 'rho' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:114.37:

      subroutine evalnal(n,x,m,lambda,rho,g,flag)                       
                                     1
Warning: Unused dummy argument 'lambda' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:114.41:

      subroutine evalnal(n,x,m,lambda,rho,g,flag)                       
                                         1
Warning: Unused dummy argument 'rho' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:177.25:

      subroutine evalhd(n)                                              
                         1
Warning: Unused dummy argument 'n' at (1)
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/io.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/io.f
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 7
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 8
Building Fortran object CMakeFiles/packmol.dir/fgcommon.f.o
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/fgcommon.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/fgcommon.f
[ 80%] [ 80%] Building Fortran object CMakeFiles/packmol.dir/packmolnew.f.o
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/packmolnew.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/packmolnew.f
Building Fortran object CMakeFiles/packmol.dir/polartocart.f.o
Building Fortran object CMakeFiles/packmol.dir/heuristics.f.o
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/polartocart.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/polartocart.f
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/heuristics.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/heuristics.f
/root/rpmbuild/BUILD/packmol/polartocart.f:65.72:

      xcart(icart,1) = xbar + xcoor*v1(1) + ycoor*v2(1) + zcoor*v3(1)   
                                                                        1
Warning: Line truncated at (1)
/root/rpmbuild/BUILD/packmol/polartocart.f:66.72:

      xcart(icart,2) = ybar + xcoor*v1(2) + ycoor*v2(2) + zcoor*v3(2)   
                                                                        1
Warning: Line truncated at (1)
/root/rpmbuild/BUILD/packmol/polartocart.f:67.72:

      xcart(icart,3) = zbar + xcoor*v1(3) + ycoor*v2(3) + zcoor*v3(3)   
                                                                        1
Warning: Line truncated at (1)
/root/rpmbuild/BUILD/packmol/io.f:213.2:

25    write(*,*)' ERROR: Output file not (correctly?) specified. '      
  1
Warning: Label 25 at (1) defined but not used
/root/rpmbuild/BUILD/packmol/initial.f:527.39:

     +                   precision,isem)                                
                                       1
Warning: Unused dummy argument 'isem' at (1)
/root/rpmbuild/BUILD/packmol/initial.f:526.59:

      subroutine restmol(itype,ilubar,n,x,fx,solve,movefrac,            
                                                           1
Warning: Unused dummy argument 'movefrac' at (1)
/root/rpmbuild/BUILD/packmol/initial.f:527.34:

     +                   precision,isem)                                
                                  1
Warning: Unused dummy argument 'precision' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:2611.5:

 1003 format(6X,I6,T22,D17.6,T43,D17.6)                                 
     1
Warning: Label 1003 at (1) defined but not used
/root/rpmbuild/BUILD/packmol/gencan.f:2622.40:

     +steabs,epsrel,epsabs,infrel,infabs)                               
                                        1
Warning: Unused dummy argument 'infabs' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:2622.33:

     +steabs,epsrel,epsabs,infrel,infabs)                               
                                 1
Warning: Unused dummy argument 'infrel' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:2622.12:

     +steabs,epsrel,epsabs,infrel,infabs)                               
            1
Warning: Unused dummy argument 'steabs' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:2621.71:

     +fmin,maxfc,iprint,fcnt,inform,xtrial,d,gamma,sigma1,sigma2,sterel,
                                                                       1
Warning: Unused dummy argument 'sterel' at (1)
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 9
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 10
[100%] [100%] /root/rpmbuild/BUILD/packmol/fgcommon.f: In function 'feasyseq':
/root/rpmbuild/BUILD/packmol/fgcommon.f:612: warning: 'flast' may be used uninitialized in this function
Building Fortran object CMakeFiles/packmol.dir/geasy.f.o
Building Fortran object CMakeFiles/packmol.dir/feasy.f.o
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/feasy.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/feasy.f
/usr/bin/gfortran  -o CMakeFiles/packmol.dir/geasy.f.o  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2   -c /root/rpmbuild/BUILD/packmol/geasy.f
/root/rpmbuild/BUILD/packmol/gencan.f:3018.19:

     +epsabs,infrel,infabs)                                             
                   1
Warning: Unused dummy argument 'infrel' at (1)
/root/rpmbuild/BUILD/packmol/packmolnew.f: In function 'packmol':
/root/rpmbuild/BUILD/packmol/packmolnew.f:55: warning: 'iirest' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3856.61:

     +sigma1,sigma2,sterel,steabs,epsrel,epsabs,infrel,infabs)          
                                                             1
Warning: Unused dummy argument 'infabs' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:3856.54:

     +sigma1,sigma2,sterel,steabs,epsrel,epsabs,infrel,infabs)          
                                                      1
Warning: Unused dummy argument 'infrel' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:5216.19:

     +steabs,inform)                                                    
                   1
Warning: Unused dummy argument 'inform' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:5215.52:

      subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel,
                                                    1
Warning: Unused dummy argument 'lambda' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:5215.56:

      subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel,
                                                        1
Warning: Unused dummy argument 'rho' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:5216.12:

     +steabs,inform)                                                    
            1
Warning: Unused dummy argument 'steabs' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:5215.71:

      subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel,
                                                                       1
Warning: Unused dummy argument 'sterel' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:5215.64:

      subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel,
                                                                1
Warning: Unused dummy argument 'xtmp' at (1)
/root/rpmbuild/BUILD/packmol/gencan.f:5699.5:

  110 IF (DABS(DX(I)).LE.XMAX) GO TO 115                                
     1
Warning: Label 110 at (1) defined but not used
/root/rpmbuild/BUILD/packmol/gencan.f:5698.5:

   70 IF (DABS(DX(I)).GT.CUTLO) GO TO 75                                
     1
Warning: Label 70 at (1) defined but not used
/root/rpmbuild/BUILD/packmol/gencan.f:5691.5:

   50 IF (DX(I).EQ.ZERO) GO TO 200                                      
     1
Warning: Label 50 at (1) defined but not used
/root/rpmbuild/BUILD/packmol/gencan.f:5689.5:

   30 IF (DABS(DX(I)).GT.CUTLO) GO TO 85                                
     1
Warning: Label 30 at (1) defined but not used
/root/rpmbuild/BUILD/packmol/io.f: In function 'setrnum':
/root/rpmbuild/BUILD/packmol/io.f:732: warning: 'ireslast' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f: In function 'cg':
/root/rpmbuild/BUILD/packmol/gencan.f:3272: warning: 'alpha' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3272: warning: 'amax1' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3272: warning: 'amax1n' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3273: warning: 'dnorm2' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3273: warning: 'dtr' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3274: warning: 'dtw' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdnegaind' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdnegatype' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdposaind' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3271: warning: 'rbdposatype' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:3275: warning: 'rnorm2prev' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f: In function 'gencan':
/root/rpmbuild/BUILD/packmol/gencan.f:1729: warning: 'sts' may be used uninitialized in this function
/root/rpmbuild/BUILD/packmol/gencan.f:1729: warning: 'sty' may be used uninitialized in this function
Linking Fortran executable packmol
/usr/bin/cmake -E cmake_link_script CMakeFiles/packmol.dir/link.txt --verbose=1
/usr/bin/gfortran    -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -Wall -O2 CMakeFiles/packmol.dir/cenmass.f.o CMakeFiles/packmol.dir/gencan.f.o CMakeFiles/packmol.dir/initial.f.o CMakeFiles/packmol.dir/io.f.o CMakeFiles/packmol.dir/fgcommon.f.o CMakeFiles/packmol.dir/packmolnew.f.o CMakeFiles/packmol.dir/polartocart.f.o CMakeFiles/packmol.dir/heuristics.f.o CMakeFiles/packmol.dir/feasy.f.o CMakeFiles/packmol.dir/geasy.f.o  -o packmol -rdynamic 
make[2]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser'
/usr/bin/cmake -E cmake_progress_report /root/rpmbuild/BUILD/packmol/ser/CMakeFiles  1 2 3 4 5 6 7 8 9 10
[100%] Built target packmol
make[1]: Leaving directory `/root/rpmbuild/BUILD/packmol/ser'
/usr/bin/cmake -E cmake_progress_start /root/rpmbuild/BUILD/packmol/ser/CMakeFiles 0
+ cd ..
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.sktY2F
+ umask 022
+ cd /root/rpmbuild/BUILD
+ '[' /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64 '!=' / ']'
+ rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64
++ dirname /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64
+ mkdir -p /root/rpmbuild/BUILDROOT
+ mkdir /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64
+ cd packmol
+ LANG=C
+ export LANG
+ unset DISPLAY
+ rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64
+ install -D -p -m 755 ser/packmol /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/bin/packmol
+ install -D -p -m 755 solvate.tcl /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/bin/packmol_solvate
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id /root/rpmbuild/BUILD/packmol
extracting debug info from /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/bin/packmol
cpio: packmol/ser/gencan.i: Cannot stat: No such file or directory
cpio: packmol/ser/molpa.i: Cannot stat: No such file or directory
cpio: packmol/ser/sizes.i: Cannot stat: No such file or directory
699 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump
+ /usr/lib/rpm/brp-python-bytecompile
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Processing files: packmol-1.1.2.023-1.el6.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FVKRBJ
+ umask 022
+ cd /root/rpmbuild/BUILD
+ cd packmol
+ DOCDIR=/root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023
+ export DOCDIR
+ rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023
+ /bin/mkdir -p /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023
+ cp -pr AUTHORS LICENSE COPYING /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64/usr/share/doc/packmol-1.1.2.023
+ exit 0
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/tclsh libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgcc_s.so.1()(64bit) libgfortran.so.3()(64bit) libgfortran.so.3(GFORTRAN_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) rtld(GNU_HASH)
Processing files: packmol-debuginfo-1.1.2.023-1.el6.x86_64
Checking for unpackaged file(s): /usr/lib/rpm/check-files /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64
Wrote: /root/rpmbuild/RPMS/x86_64/packmol-1.1.2.023-1.el6.x86_64.rpm
Wrote: /root/rpmbuild/RPMS/x86_64/packmol-debuginfo-1.1.2.023-1.el6.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.dTGsGV
+ umask 022
+ cd /root/rpmbuild/BUILD
+ cd packmol
+ rm -rf /root/rpmbuild/BUILDROOT/packmol-1.1.2.023-1.fc16.x86_64
+ exit 0
Executing(--clean): /bin/sh -e /var/tmp/rpm-tmp.RFSmWZ
+ umask 022
+ cd /root/rpmbuild/BUILD
+ rm -rf packmol
+ exit 0

Very well.

Package Change Request
======================
Package Name: packmol
New Branches: el6
Owners: jussilehtola
InitialCC:

Git done (by process-git-requests).

packmol-1.1.2.023-1.el6 has been submitted as an update for Fedora EPEL 6.
https://admin.fedoraproject.org/updates/packmol-1.1.2.023-1.el6

packmol-1.1.2.023-1.fc15 has been pushed to the Fedora 15 stable repository.

packmol-1.1.2.023-1.fc16 has been pushed to the Fedora 16 stable repository.

packmol-1.1.2.023-1.el6 has been pushed to the Fedora EPEL 6 stable repository.