Bug 1359402 - Review Request: coot - crystallographic macromolecular building toolkit (unretire request)
Summary: Review Request: coot - crystallographic macromolecular building toolkit (unre...
Keywords:
Status: CLOSED NOTABUG
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Antonio T. (sagitter)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard: AwaitingSubmitter
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2016-07-23 18:46 UTC by Tim Fenn
Modified: 2021-04-28 10:53 UTC (History)
1 user (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2021-04-28 10:52:27 UTC
Type: ---
Embargoed:
trpost: fedora-review+


Attachments (Terms of Use)
review log (89.91 KB, text/plain)
2016-11-18 18:49 UTC, Antonio T. (sagitter)
no flags Details

Description Tim Fenn 2016-07-23 18:46:36 UTC
Spec URL: https://drive.google.com/open?id=0BxOz1eBnQT3najl1NDBoVkc2ZUk
SRPM URL: https://drive.google.com/open?id=0BxOz1eBnQT3nTHRGcWFCMm5yMzA
Description: This is a request to unretire coot for rawhide/F24 (there was an error on compilation that needed fixing, it just took me some time to track it down and add the patch - upstream has also been notified and future releases include the patch).  Original review here: https://bugzilla.redhat.com/show_bug.cgi?id=472150

Coot is a toolkit for Macromolecular Crystallography and model-building.  Coot uses OpenGL, together with a new approach to map contouring and importing/creation and other modelling and building operations.  It displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots...

Also see: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Fedora Account System Username: timfenn

Comment 1 Tim Fenn 2016-09-01 21:17:47 UTC
Updated spec/SRPM (for 0.8.6.1 version of the package):

Spec URL: https://drive.google.com/open?id=0BxOz1eBnQT3najl1NDBoVkc2ZUk
SRPM URL: https://drive.google.com/open?id=0BxOz1eBnQT3nTVVJLUxPSUlPZjg

Comment 2 Tim Fenn 2016-09-01 21:21:58 UTC
Sorry, corrupted link.  Updated.

SRPM URL: https://drive.google.com/open?id=0BxOz1eBnQT3nbW5Kb0RhdW1YOVU

Comment 3 Antonio T. (sagitter) 2016-10-03 09:27:28 UTC
Hi Tim.
First of all:

- Leave a comment about what patches do.

- python(2)-sitelib macro is already defined

- Use python2-devel as BR package

- Use macros instead of hardlinks:
  /usr --> %{_prefix}
  /usr/include/ssm --> %{_includedir}/ssm

- 'rm -rf %{buildroot}' and '%defattr(-,root,root,-)' lines are used on epel5 only.

- doc sub-package isn't noarch

- COPYING is not tagged with %license

Comment 4 Tim Fenn 2016-10-14 17:47:16 UTC
(In reply to Antonio Trande from comment #3)
> Hi Tim.
> First of all:
> 
> - Leave a comment about what patches do.
> 

Done.

> - python(2)-sitelib macro is already defined
> 

Removed.

> - Use python2-devel as BR package
> 

Done.

> - Use macros instead of hardlinks:
>   /usr --> %{_prefix}
>   /usr/include/ssm --> %{_includedir}/ssm
> 

Where do you see this in the spec file?

> - 'rm -rf %{buildroot}' and '%defattr(-,root,root,-)' lines are used on
> epel5 only.
> 

Added rhel checks for these lines.

> - doc sub-package isn't noarch
> 

I didn't specify it as such?

> - COPYING is not tagged with %license

Fixed.

New files:

spec: https://drive.google.com/open?id=0BxOz1eBnQT3nOW9XWXZwNzhEY1U
srpm: https://drive.google.com/open?id=0BxOz1eBnQT3nT2FJQjlhYXVTdDA

Comment 5 Antonio T. (sagitter) 2016-10-14 18:46:03 UTC
(In reply to Tim Fenn from comment #4)
> 
> > - doc sub-package isn't noarch
> > 
> 
> I didn't specify it as such?

I don't see any 'BuildArch: noarch' line...

> 
> New files:
> 
> spec: https://drive.google.com/open?id=0BxOz1eBnQT3nOW9XWXZwNzhEY1U
> srpm: https://drive.google.com/open?id=0BxOz1eBnQT3nT2FJQjlhYXVTdDA

'%defattr(-,root,root,-)' and 'rm -rf %{buildroot}' are used for epel5 only.

Why coot-1.spec ?
SPEC file must have same name of src-rpm.

Comment 6 Tim Fenn 2016-10-14 19:55:09 UTC
(In reply to Antonio Trande from comment #5)
> (In reply to Tim Fenn from comment #4)
> > 
> > > - doc sub-package isn't noarch
> > > 
> > 
> > I didn't specify it as such?
> 
> I don't see any 'BuildArch: noarch' line...
> 

OK I'll have that fixed in the next build - sorry, I misread this the first time.

> > 
> > New files:
> > 
> > spec: https://drive.google.com/open?id=0BxOz1eBnQT3nOW9XWXZwNzhEY1U
> > srpm: https://drive.google.com/open?id=0BxOz1eBnQT3nT2FJQjlhYXVTdDA
> 
> '%defattr(-,root,root,-)' and 'rm -rf %{buildroot}' are used for epel5 only.
> 

Is the %if 0%{?rhel} not sufficient around these statements?  Or should it just be removed all together?

> Why coot-1.spec ?
> SPEC file must have same name of src-rpm.

Doh, silly google drive renaming.  I'll fix in the next upload.

Comment 7 Antonio T. (sagitter) 2016-10-14 19:58:37 UTC
(In reply to Tim Fenn from comment #6)
> (In reply to Antonio Trande from comment #5)
> > (In reply to Tim Fenn from comment #4)
> > > 
> > > > - doc sub-package isn't noarch
> > > > 
> > > 
> > > I didn't specify it as such?
> > 
> > I don't see any 'BuildArch: noarch' line...
> > 
> 
> OK I'll have that fixed in the next build - sorry, I misread this the first
> time.
> 
> > > 
> > > New files:
> > > 
> > > spec: https://drive.google.com/open?id=0BxOz1eBnQT3nOW9XWXZwNzhEY1U
> > > srpm: https://drive.google.com/open?id=0BxOz1eBnQT3nT2FJQjlhYXVTdDA
> > 
> > '%defattr(-,root,root,-)' and 'rm -rf %{buildroot}' are used for epel5 only.
> > 
> 
> Is the %if 0%{?rhel} not sufficient around these statements?  Or should it
> just be removed all together?

If this package isn't for epel5, you can remove all.

> 
> > Why coot-1.spec ?
> > SPEC file must have same name of src-rpm.
> 
> Doh, silly google drive renaming.  I'll fix in the next upload.

Why not fedorapeople?

Comment 8 Tim Fenn 2016-10-15 21:42:53 UTC
(In reply to Antonio Trande from comment #7)
> (In reply to Tim Fenn from comment #6)
> > (In reply to Antonio Trande from comment #5)
> > > (In reply to Tim Fenn from comment #4)
> > > > 
> > > > > - doc sub-package isn't noarch
> > > > > 
> > > > 
> > > > I didn't specify it as such?
> > > 
> > > I don't see any 'BuildArch: noarch' line...
> > > 
> > 
> > OK I'll have that fixed in the next build - sorry, I misread this the first
> > time.
> > 
> > > > 
> > > > New files:
> > > > 
> > > > spec: https://drive.google.com/open?id=0BxOz1eBnQT3nOW9XWXZwNzhEY1U
> > > > srpm: https://drive.google.com/open?id=0BxOz1eBnQT3nT2FJQjlhYXVTdDA
> > > 
> > > '%defattr(-,root,root,-)' and 'rm -rf %{buildroot}' are used for epel5 only.
> > > 
> > 
> > Is the %if 0%{?rhel} not sufficient around these statements?  Or should it
> > just be removed all together?
> 
> If this package isn't for epel5, you can remove all.
> 

OK done.

> > 
> > > Why coot-1.spec ?
> > > SPEC file must have same name of src-rpm.
> > 
> > Doh, silly google drive renaming.  I'll fix in the next upload.
> 
> Why not fedorapeople?

Fair enough - new files:

https://timfenn.fedorapeople.org/coot.spec
https://timfenn.fedorapeople.org/coot-0.8.6.1-3.fc24.src.rpm

Comment 9 Antonio T. (sagitter) 2016-10-17 20:38:56 UTC
Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======
- Package unretired
  Package does not use a name that already exists.
  Note: A package with this name already exists. Please check
  https://admin.fedoraproject.org/pkgdb/package/coot
  See:
  https://fedoraproject.org/wiki/Packaging/NamingGuidelines#Conflicting_Package_Names

- hicolr-icon-theme should be a Requires package

- /usr/share/icons/hicolor/* directories are owned by hicolr-icon-theme.
  You must list the coot.* image files only.

- All used licenses (GPLv2+ GPLv3+ LGPLv2+ LGPLv3+) are compatible among them.
  I think you can indicate GPLv3+ only as resultant license.

- Use %python2_sitelib instead of %python_sitelib

- I would split off libcoot-* libraries in a separated libcoot sub-package
  in order to obtain

  coot
  libcoot
  libcoot-devel
  coot-doc

  +
  coot-data for all data files

- Please, leave a comment about additional SourceX

- Spec use %global instead of %define unless justified

- Package should not use obsolete m4 macros
     Note: Some obsoleted macros found, see the attachment.
     See: https://fedorahosted.org/FedoraReview/wiki/AutoTools

- Please, fix unused-direct-shlib-dependency warnings


===== MUST items =====

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig called in %post and %postun if required.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[?]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "LGPL (v2.1 or later) (with incorrect FSF address)", "LGPL",
     "GPL (v2 or later)", "GPL (v3 or later)", "Unknown or generated",
     "MIT/X11 (BSD like)", "LGPL (v3 or later)", "LGPL (v2.1 or later)".
     512 files have unknown license. Detailed output of licensecheck in
     /home/sagitter/1359402-coot/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[?]: If the package is under multiple licenses, the licensing breakdown
     must be documented in the spec.
[!]: Package does not own files or directories owned by other packages.
     Note: Dirs in package are owned also by:
     /usr/share/icons/hicolor/256x256/apps(hicolor-icon-theme, fedora-
     logos), /usr/share/icons/hicolor/96x96/apps(hicolor-icon-theme,
     fedora-logos), /usr/share/icons/hicolor/64x64/apps(hicolor-icon-
     theme), /usr/share/icons/hicolor/96x96(hicolor-icon-theme, fedora-
     logos), /usr/share/icons/hicolor/scalable/apps(hicolor-icon-theme,
     fedora-logos), /usr/share/icons/hicolor/48x48(hicolor-icon-theme,
     fedora-logos), /usr/share/icons/hicolor/48x48/apps(hicolor-icon-theme,
     fedora-logos), /usr/share/icons/hicolor/64x64(hicolor-icon-theme),
     /usr/share/icons/hicolor/256x256(hicolor-icon-theme, fedora-logos),
     /usr/share/icons/hicolor(hicolor-icon-theme, fedora-logos),
     /usr/share/icons/hicolor/scalable(hicolor-icon-theme, fedora-logos)
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[x]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[!]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: gtk-update-icon-cache is invoked in %postun and %posttrans if package
     contains icons.
     Note: icons in coot
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 10240 bytes in 2 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: Package requires other packages for directories it uses.
[x]: Package must own all directories that it creates.
[x]: All build dependencies are listed in BuildRequires, except for any
     that are listed in the exceptions section of Packaging Guidelines.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Package contains desktop file if it is a GUI application.
[x]: Package installs a %{name}.desktop using desktop-file-install or
     desktop-file-validate if there is such a file.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

Python:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: A package which is used by another package via an egg interface should
     provide egg info.
[!]: Package meets the Packaging Guidelines::Python
[x]: Package contains BR: python2-devel or python3-devel
[x]: Binary eggs must be removed in %prep

===== SHOULD items =====

Generic:
[x]: Uses parallel make %{?_smp_mflags} macro.
[x]: Sources can be downloaded from URI in Source: tag
     Note: Could not download Source0: http://www2.mrc-
     lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.6.1.tar.gz
     See: http://fedoraproject.org/wiki/Packaging:Guidelines#Tags
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[!]: Final provides and requires are sane (see attachments).
[!]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in coot-
     devel , coot-doc , coot-debuginfo
[ ]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[!]: SourceX tarball generation or download is documented.
     Note: Package contains tarball without URL, check comments
[x]: Description and summary sections in the package spec file contains
     translations for supported Non-English languages, if available.
[?]: Package should compile and build into binary rpms on all supported
     architectures.
[x]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[!]: Spec use %global instead of %define unless justified.
     Note: %define requiring justification: %define refmac_dictionary %(rpm
     -q --queryformat '%%{name}-%%{version}' refmac-dictionary)
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: SourceX is a working URL.

===== EXTRA items =====

Generic:
[!]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
     Note: Arch-ed rpms have a total of 86138880 bytes in /usr/share
     coot-0.8.6.1-3.fc26.x86_64.rpm:86138880
     See:
     http://fedoraproject.org/wiki/Packaging:ReviewGuidelines#Package_Review_Guidelines
[!]: Package should not use obsolete m4 macros
     Note: Some obsoleted macros found, see the attachment.
     See: https://fedorahosted.org/FedoraReview/wiki/AutoTools
[x]: Rpmlint is run on debuginfo package(s).
     Note: No rpmlint messages.
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: coot-0.8.6.1-3.fc26.x86_64.rpm
          coot-devel-0.8.6.1-3.fc26.x86_64.rpm
          coot-doc-0.8.6.1-3.fc26.noarch.rpm
          coot-debuginfo-0.8.6.1-3.fc26.x86_64.rpm
          coot-0.8.6.1-3.fc26.src.rpm
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot-devel.x86_64: W: only-non-binary-in-usr-lib
coot-devel.x86_64: W: no-documentation
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot.src: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.src: W: strange-permission reference-structures.tar.gz 444
coot.src: W: strange-permission coot.in 755
coot.src:7: W: macro-in-comment %files
coot.src:128: W: macro-in-comment %{buildroot}
coot.src:128: W: macro-in-comment %{_includedir}
coot.src:129: W: macro-in-comment %{buildroot}
coot.src:129: W: macro-in-comment %{_includedir}
coot.src:129: W: macro-in-comment %{buildroot}
coot.src:129: W: macro-in-comment %{_includedir}
coot.src:130: W: macro-in-comment %{buildroot}
coot.src:130: W: macro-in-comment %{_includedir}
coot.src:130: W: macro-in-comment %{buildroot}
coot.src:130: W: macro-in-comment %{_includedir}
coot.src:133: W: macro-in-comment %{buildroot}
coot.src:133: W: macro-in-comment %{python_sitelib}
coot.src:134: W: macro-in-comment %{buildroot}
coot.src:134: W: macro-in-comment %{_datadir}
coot.src:134: W: macro-in-comment %{buildroot}
coot.src:134: W: macro-in-comment %{python_sitelib}
coot.src:151: W: macro-in-comment %{buildroot}
coot.src:151: W: macro-in-comment %{_bindir}
coot.src: W: invalid-url Source0: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.6.1.tar.gz HTTP Error 404: Not Found
5 packages and 0 specfiles checked; 0 errors, 29 warnings.




Rpmlint (debuginfo)
-------------------
Checking: coot-debuginfo-0.8.6.1-3.fc26.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.





Rpmlint (installed packages)
----------------------------
coot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot-devel.x86_64: W: only-non-binary-in-usr-lib
coot-devel.x86_64: W: no-documentation
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-ideal.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-map-heavy.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-db-main.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libccp4mg-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libpng16.so.16
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-lidia-core.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-coord-extras.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-analysis.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-high-res.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-protein-db.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-db-main.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coords.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-analysis.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libccp4mg-surface.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-shelx.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-geometry.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libcoot-map-heavy.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libpng16.so.16
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libcoot-lidia-core.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ligand.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libcoot-lidia-core.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libcoot-coord-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libclipper-core.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libmmdb2.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libgdk-x11-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libpangocairo-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libatk-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libcairo.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libgdk_pixbuf-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libgio-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libpangoft2-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libpango-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libglib-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libfontconfig.so.1
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-goograph.so.0.0.0 /lib64/libfreetype.so.6
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-mini-mol.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-heavy.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libcoot-map-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libcoot-lidia-core.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-ideal.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-cabuild.so.0.0.0 /lib64/libmmdb2.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libpangocairo-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libatk-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libcairo.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libgdk_pixbuf-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libgio-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libpangoft2-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libfontconfig.so.1
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-gtkgraph.so.0.0.0 /lib64/libfreetype.so.6
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libglut.so.3
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libXmu.so.6
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgtk-x11-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgdk-x11-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libpangocairo-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libatk-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libcairo.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgdk_pixbuf-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgio-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libpangoft2-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libpango-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libgobject-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libglib-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libfontconfig.so.1
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-surface.so.0.0.0 /lib64/libfreetype.so.6
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootaneer.so.0.0.0 /lib64/libmmdb2.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libcoot-coord-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia-core.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libcoot-lidia-core.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libcoot-coord-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-isosurface.so.0.0.0 /lib64/libmmdb2.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-tw.so.0.0.0 /lib64/libm.so.6
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-tw.so.0.0.0 /lib64/libgcc_s.so.1
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libpangocairo-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libatk-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libgdk_pixbuf-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libgio-2.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libpangoft2-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libpango-1.0.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libfontconfig.so.1
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libfreetype.so.6
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libpython2.7.so.1.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libdl.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-lidia.so.0.0.0 /lib64/libutil.so.1
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcootilus.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-mmdb.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libclipper-contrib.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-extras.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libcoot-shelx.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libcoot-lidia-core.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libcoot-coord-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libgsl.so.19
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libgslcblas.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libcoot-utils.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libclipper-ccp4.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-skeleton.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libcoot-geometry.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libcoot-mini-mol.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libclipper-fortran.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libclipper-cif.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libclipper-minimol.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libclipper-cns.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libclipper-phs.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libsrfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libsfftw.so.2
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libpthread.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libccp4c.so.0
coot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-map-utils.so.0.0.0 /lib64/libgslcblas.so.0
4 packages and 0 specfiles checked; 0 errors, 395 warnings.



Requires
--------
coot-debuginfo (rpmlib, GLIBC filtered):

coot-devel (rpmlib, GLIBC filtered):
    coot
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)

coot-doc (rpmlib, GLIBC filtered):
    coot

coot (rpmlib, GLIBC filtered):
    /bin/sh
    compat-guile18
    libGL.so.1()(64bit)
    libGLU.so.1()(64bit)
    libICE.so.6()(64bit)
    libSM.so.6()(64bit)
    libX11.so.6()(64bit)
    libXmu.so.6()(64bit)
    libXt.so.6()(64bit)
    libart_lgpl_2.so.2()(64bit)
    libatk-1.0.so.0()(64bit)
    libc.so.6()(64bit)
    libcairo.so.2()(64bit)
    libccp4c.so.0()(64bit)
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libclipper-ccp4.so.2()(64bit)
    libclipper-cif.so.2()(64bit)
    libclipper-cns.so.2()(64bit)
    libclipper-contrib.so.2()(64bit)
    libclipper-core.so.2()(64bit)
    libclipper-fortran.so.2()(64bit)
    libclipper-minimol.so.2()(64bit)
    libclipper-mmdb.so.2()(64bit)
    libclipper-phs.so.2()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)
    libcurl.so.4()(64bit)
    libdl.so.2()(64bit)
    libfontconfig.so.1()(64bit)
    libfreetype.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_4.0.0)(64bit)
    libgdk-x11-2.0.so.0()(64bit)
    libgdk_pixbuf-2.0.so.0()(64bit)
    libgdkglext-x11-1.0.so.0()(64bit)
    libgio-2.0.so.0()(64bit)
    libglib-2.0.so.0()(64bit)
    libglut.so.3()(64bit)
    libgmodule-2.0.so.0()(64bit)
    libgnomecanvas-2.so.0()(64bit)
    libgobject-2.0.so.0()(64bit)
    libgoocanvas.so.3()(64bit)
    libgsl.so.19()(64bit)
    libgslcblas.so.0()(64bit)
    libgtk-x11-2.0.so.0()(64bit)
    libgtkglext-x11-1.0.so.0()(64bit)
    libguile.so.17()(64bit)
    libm.so.6()(64bit)
    libmmdb2.so.0()(64bit)
    libpango-1.0.so.0()(64bit)
    libpangocairo-1.0.so.0()(64bit)
    libpangoft2-1.0.so.0()(64bit)
    libpangox-1.0.so.0()(64bit)
    libpng16.so.16()(64bit)
    libpng16.so.16(PNG16_0)(64bit)
    libpthread.so.0()(64bit)
    libpython2.7.so.1.0()(64bit)
    libsfftw.so.2()(64bit)
    libsrfftw.so.2()(64bit)
    libssm.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    libutil.so.1()(64bit)
    python(abi)
    refmac-dictionary
    rtld(GNU_HASH)



Provides
--------
coot-debuginfo:
    coot-debuginfo
    coot-debuginfo(x86-64)

coot-devel:
    coot-devel
    coot-devel(x86-64)

coot-doc:
    coot-doc

coot:
    appdata()
    appdata(coot.appdata.xml)
    application()
    application(coot.desktop)
    coot
    coot(x86-64)
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)



Source checksums
----------------
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz :
  CHECKSUM(SHA256) this package     : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a
  CHECKSUM(SHA256) upstream package : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a


AutoTools: Obsoleted m4s found
------------------------------
  AM_PROG_CC_STDC found in: coot-0.8.6.1/configure.ac:38


Generated by fedora-review 0.6.1 (f03e4e7) last change: 2016-05-02
Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1359402
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Generic, Shell-api, C/C++
Disabled plugins: Java, SugarActivity, fonts, Haskell, Ocaml, Perl, R, PHP
Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6

Comment 10 Tim Fenn 2016-10-30 18:01:57 UTC
(In reply to Antonio Trande from comment #9)
> 
> - hicolr-icon-theme should be a Requires package
> 

Done.

> - /usr/share/icons/hicolor/* directories are owned by hicolr-icon-theme.
>   You must list the coot.* image files only.
> 

Done.

> - All used licenses (GPLv2+ GPLv3+ LGPLv2+ LGPLv3+) are compatible among
> them.
>   I think you can indicate GPLv3+ only as resultant license.
> 

OK, so just switch this to GPLv3+ and delete all the other stuff?

> - Use %python2_sitelib instead of %python_sitelib
> 

Done.

> - I would split off libcoot-* libraries in a separated libcoot sub-package
>   in order to obtain
> 
>   coot
>   libcoot
>   libcoot-devel
>   coot-doc
> 

Done - I think I did this correctly - please check!

>   +
>   coot-data for all data files
> 
> - Please, leave a comment about additional SourceX
> 

Done.

> - Spec use %global instead of %define unless justified
> 

Done.

> - Package should not use obsolete m4 macros
>      Note: Some obsoleted macros found, see the attachment.
>      See: https://fedorahosted.org/FedoraReview/wiki/AutoTools
> 

Done.

> - Please, fix unused-direct-shlib-dependency warnings
> 

Done.

I also updated to 0.8.6.2, which fixes the broken link issue.  Also note I've included rdkit support now, as per a discussion with upstream and an additional patch.

https://timfenn.fedorapeople.org/coot.spec
https://timfenn.fedorapeople.org/coot-0.8.6.2-1.fc24.src.rpm

Comment 11 Antonio T. (sagitter) 2016-10-31 14:38:10 UTC
>OK, so just switch this to GPLv3+ and delete all the other stuff?
Yes.

Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======
- Package does not use a name that already exists.
  Note: A package with this name already exists. Please check
  https://admin.fedoraproject.org/pkgdb/package/coot
  See:
  https://fedoraproject.org/wiki/Packaging/NamingGuidelines#Conflicting_Package_Names

- Main package requires libcoot, not viceversa:

...
Requires: compat-guile18
Requires: hicolor-icon-theme
Requires: refmac-dictionary
Requires: lib%{name}%{?_isa} = %{version}-%{release}  <---
...
%package -n libcoot
Summary: Library files for coot
Group: Development/Libraries
...
%package -n libcoot-devel
Summary: Header files and library for developing programs with coot
Requires: lib%{name}%{?_isa} = %{version}-%{release}  <---
Group: Development/Libraries

- License and doc should be under '%files -n libcoot'

...
%files -n libcoot
# libccp4mg-utils.so* is LGPLv2+
# libcoot-surface.so* is a mix of LGPLv2+ and GPLv3+
# all others are GPLv3+
%doc AUTHORS README
%license COPYING
%{_libdir}/*.so.*
%{python2_sitearch}/*.so.*
...

- Python libraries should be packed separately in an arched
  'python2-libcoot' sub-package (sorry, i didn't seen it before).

  Main package should require it.

- doc subpackage provides PDF files only, it should not require
  the main one in my opinion.

- Useless ldconfig:

 %post
/sbin/ldconfig
/bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null || :

- coot-data ?

- I don't see any tests ran with 'make check'

- Please, remove commands and macros in the comments

- AutoTools: Obsoleted m4s found
  ------------------------------
    AM_PROG_CC_STDC found in: coot-0.8.6.2/configure.ac:38

===== MUST items =====

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig called in %post and %postun if required.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[x]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "LGPL (v2.1 or later) (with incorrect FSF address)", "LGPL",
     "GPL (v2 or later)", "GPL (v3 or later)", "Unknown or generated",
     "MIT/X11 (BSD like)", "LGPL (v3 or later)", "LGPL (v2.1 or later)".
     513 files have unknown license. Detailed output of licensecheck in
     /home/sagitter/1359402-coot/licensecheck.txt
[?]: License file installed when any subpackage combination is installed.
[x]: If the package is under multiple licenses, the licensing breakdown
     must be documented in the spec.
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[x]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: gtk-update-icon-cache is invoked in %postun and %posttrans if package
     contains icons.
     Note: icons in coot
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 10240 bytes in 2 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: Package requires other packages for directories it uses.
[x]: Package must own all directories that it creates.
[x]: Package does not own files or directories owned by other packages.
[x]: All build dependencies are listed in BuildRequires, except for any
     that are listed in the exceptions section of Packaging Guidelines.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Package contains desktop file if it is a GUI application.
[x]: Package installs a %{name}.desktop using desktop-file-install or
     desktop-file-validate if there is such a file.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

Python:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: A package which is used by another package via an egg interface should
     provide egg info.
[!]: Package meets the Packaging Guidelines::Python
[x]: Package contains BR: python2-devel or python3-devel
[x]: Binary eggs must be removed in %prep

===== SHOULD items =====

Generic:
[x]: Uses parallel make %{?_smp_mflags} macro.
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[!]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in libcoot
     , libcoot-devel , coot-doc , coot-debuginfo
[ ]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[!]: Scriptlets must be sane, if used.
[-]: Description and summary sections in the package spec file contains
     translations for supported Non-English languages, if available.
[?]: Package should compile and build into binary rpms on all supported
     architectures.
[?]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: Sources can be downloaded from URI in Source: tag
[x]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[!]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
     Note: Arch-ed rpms have a total of 86138880 bytes in /usr/share
     coot-0.8.6.2-1.fc26.x86_64.rpm:86138880
     See:
     http://fedoraproject.org/wiki/Packaging:ReviewGuidelines#Package_Review_Guidelines
[!]: Package should not use obsolete m4 macros
     Note: Some obsoleted macros found, see the attachment.
     See: https://fedorahosted.org/FedoraReview/wiki/AutoTools
[x]: Rpmlint is run on debuginfo package(s).
     Note: No rpmlint messages.
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: coot-0.8.6.2-1.fc26.x86_64.rpm
          libcoot-0.8.6.2-1.fc26.x86_64.rpm
          libcoot-devel-0.8.6.2-1.fc26.x86_64.rpm
          coot-doc-0.8.6.2-1.fc26.noarch.rpm
          coot-debuginfo-0.8.6.2-1.fc26.x86_64.rpm
          coot-0.8.6.2-1.fc26.src.rpm
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.x86_64: W: no-manual-page-for-binary pyrogen
libcoot.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot.x86_64: W: no-documentation
libcoot.x86_64: W: one-line-command-in-%post /sbin/ldconfig
libcoot.x86_64: W: one-line-command-in-%postun /sbin/ldconfig
libcoot-devel.x86_64: W: no-dependency-on libcoot/libcoot-libs/liblibcoot
libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
libcoot-devel.x86_64: W: no-documentation
libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/_pyrogen_swig.so _pyrogen_swig.so.0.0.0
libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/pyrogen_boost.so pyrogen_boost.so.0.0.0
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot.src: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.src: W: strange-permission reference-structures.tar.gz 444
coot.src: W: strange-permission coot.in 755
coot.src:7: W: macro-in-comment %files
coot.src:119: W: macro-in-comment %configure
coot.src:150: W: macro-in-comment %{buildroot}
coot.src:150: W: macro-in-comment %{_includedir}
coot.src:151: W: macro-in-comment %{buildroot}
coot.src:151: W: macro-in-comment %{_includedir}
coot.src:151: W: macro-in-comment %{buildroot}
coot.src:151: W: macro-in-comment %{_includedir}
coot.src:152: W: macro-in-comment %{buildroot}
coot.src:152: W: macro-in-comment %{_includedir}
coot.src:152: W: macro-in-comment %{buildroot}
coot.src:152: W: macro-in-comment %{_includedir}
coot.src:155: W: macro-in-comment %{buildroot}
coot.src:155: W: macro-in-comment %{python2_sitelib}
coot.src:156: W: macro-in-comment %{buildroot}
coot.src:156: W: macro-in-comment %{_datadir}
coot.src:156: W: macro-in-comment %{buildroot}
coot.src:156: W: macro-in-comment %{python2_sitelib}
coot.src:173: W: macro-in-comment %{buildroot}
coot.src:173: W: macro-in-comment %{_bindir}
6 packages and 0 specfiles checked; 0 errors, 37 warnings.




Rpmlint (debuginfo)
-------------------
Checking: coot-debuginfo-0.8.6.2-1.fc26.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.





Rpmlint (installed packages)
----------------------------
libcoot.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libgslcblas.so.0
libcoot.x86_64: W: no-documentation
libcoot.x86_64: W: one-line-command-in-%post /sbin/ldconfig
libcoot.x86_64: W: one-line-command-in-%postun /sbin/ldconfig
libcoot-devel.x86_64: W: no-dependency-on libcoot/libcoot-libs/liblibcoot
libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
libcoot-devel.x86_64: W: no-documentation
libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/pyrogen_boost.so pyrogen_boost.so.0.0.0
libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/_pyrogen_swig.so _pyrogen_swig.so.0.0.0
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.x86_64: W: no-manual-page-for-binary pyrogen
5 packages and 0 specfiles checked; 0 errors, 15 warnings.



Requires
--------
libcoot (rpmlib, GLIBC filtered):
    /bin/sh
    coot
    libDepictor.so.1()(64bit)
    libDescriptors.so.1()(64bit)
    libFileParsers.so.1()(64bit)
    libForceField.so.1()(64bit)
    libForceFieldHelpers.so.1()(64bit)
    libGL.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libMolChemicalFeatures.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libRDGeometryLib.so.1()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcairo.so.2()(64bit)
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libclipper-ccp4.so.2()(64bit)
    libclipper-contrib.so.2()(64bit)
    libclipper-core.so.2()(64bit)
    libclipper-minimol.so.2()(64bit)
    libclipper-mmdb.so.2()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_4.0.0)(64bit)
    libgdk-x11-2.0.so.0()(64bit)
    libglib-2.0.so.0()(64bit)
    libgobject-2.0.so.0()(64bit)
    libgoocanvas.so.3()(64bit)
    libgsl.so.19()(64bit)
    libgslcblas.so.0()(64bit)
    libgtk-x11-2.0.so.0()(64bit)
    libm.so.6()(64bit)
    libmmdb2.so.0()(64bit)
    libpango-1.0.so.0()(64bit)
    libpng16.so.16()(64bit)
    libpng16.so.16(PNG16_0)(64bit)
    libpython2.7.so.1.0()(64bit)
    libsrfftw.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    python(abi)
    rtld(GNU_HASH)

libcoot-devel (rpmlib, GLIBC filtered):
    coot
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)
    python(abi)

coot-debuginfo (rpmlib, GLIBC filtered):

coot-doc (rpmlib, GLIBC filtered):
    coot

coot (rpmlib, GLIBC filtered):
    /bin/sh
    compat-guile18
    hicolor-icon-theme
    libAlignment.so.1()(64bit)
    libDataStructs.so.1()(64bit)
    libDepictor.so.1()(64bit)
    libDescriptors.so.1()(64bit)
    libDistGeomHelpers.so.1()(64bit)
    libDistGeometry.so.1()(64bit)
    libEigenSolvers.so.1()(64bit)
    libFileParsers.so.1()(64bit)
    libForceField.so.1()(64bit)
    libForceFieldHelpers.so.1()(64bit)
    libGL.so.1()(64bit)
    libGLU.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libICE.so.6()(64bit)
    libMolChemicalFeatures.so.1()(64bit)
    libMolDraw2D.so.1()(64bit)
    libOptimizer.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libRDGeometryLib.so.1()(64bit)
    libSM.so.6()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libX11.so.6()(64bit)
    libXmu.so.6()(64bit)
    libXt.so.6()(64bit)
    libart_lgpl_2.so.2()(64bit)
    libatk-1.0.so.0()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcairo.so.2()(64bit)
    libccp4c.so.0()(64bit)
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libclipper-ccp4.so.2()(64bit)
    libclipper-cif.so.2()(64bit)
    libclipper-cns.so.2()(64bit)
    libclipper-contrib.so.2()(64bit)
    libclipper-core.so.2()(64bit)
    libclipper-fortran.so.2()(64bit)
    libclipper-minimol.so.2()(64bit)
    libclipper-mmdb.so.2()(64bit)
    libclipper-phs.so.2()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)
    libcurl.so.4()(64bit)
    libdl.so.2()(64bit)
    libfontconfig.so.1()(64bit)
    libfreetype.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgdk-x11-2.0.so.0()(64bit)
    libgdk_pixbuf-2.0.so.0()(64bit)
    libgdkglext-x11-1.0.so.0()(64bit)
    libgio-2.0.so.0()(64bit)
    libglib-2.0.so.0()(64bit)
    libglut.so.3()(64bit)
    libgmodule-2.0.so.0()(64bit)
    libgnomecanvas-2.so.0()(64bit)
    libgobject-2.0.so.0()(64bit)
    libgoocanvas.so.3()(64bit)
    libgsl.so.19()(64bit)
    libgslcblas.so.0()(64bit)
    libgtk-x11-2.0.so.0()(64bit)
    libgtkglext-x11-1.0.so.0()(64bit)
    libguile.so.17()(64bit)
    libm.so.6()(64bit)
    libmmdb2.so.0()(64bit)
    libpango-1.0.so.0()(64bit)
    libpangocairo-1.0.so.0()(64bit)
    libpangoft2-1.0.so.0()(64bit)
    libpangox-1.0.so.0()(64bit)
    libpng16.so.16()(64bit)
    libpthread.so.0()(64bit)
    libpython2.7.so.1.0()(64bit)
    libsfftw.so.2()(64bit)
    libsrfftw.so.2()(64bit)
    libssm.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    libutil.so.1()(64bit)
    python(abi)
    refmac-dictionary
    rtld(GNU_HASH)



Provides
--------
libcoot:
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libcoot
    libcoot(x86-64)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)

libcoot-devel:
    libcoot-devel
    libcoot-devel(x86-64)

coot-debuginfo:
    coot-debuginfo
    coot-debuginfo(x86-64)

coot-doc:
    coot-doc

coot:
    appdata()
    appdata(coot.appdata.xml)
    application()
    application(coot.desktop)
    coot
    coot(x86-64)



Source checksums
----------------
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.6.2.tar.gz :
  CHECKSUM(SHA256) this package     : 911eb76282c274e148d5351a689f428399c75f4cef7c121676a78b0a185f49c9
  CHECKSUM(SHA256) upstream package : 911eb76282c274e148d5351a689f428399c75f4cef7c121676a78b0a185f49c9
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz :
  CHECKSUM(SHA256) this package     : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a
  CHECKSUM(SHA256) upstream package : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a


AutoTools: Obsoleted m4s found
------------------------------
  AM_PROG_CC_STDC found in: coot-0.8.6.2/configure.ac:38


Generated by fedora-review 0.6.1 (f03e4e7) last change: 2016-05-02
Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1359402
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Generic, Shell-api, C/C++
Disabled plugins: Java, SugarActivity, fonts, Haskell, Ocaml, Perl, R, PHP
Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6

Comment 12 Tim Fenn 2016-11-04 12:52:49 UTC
(In reply to Antonio Trande from comment #11)
> >OK, so just switch this to GPLv3+ and delete all the other stuff?
> Yes.
> 

Done.

> Package Review
> ==============
> 
> Legend:
> [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
> [ ] = Manual review needed
> 
> 
> Issues:
> =======
> - Package does not use a name that already exists.
>   Note: A package with this name already exists. Please check
>   https://admin.fedoraproject.org/pkgdb/package/coot
>   See:
>  
> https://fedoraproject.org/wiki/Packaging/
> NamingGuidelines#Conflicting_Package_Names
> 
> - Main package requires libcoot, not viceversa:
> 

Fixed.

> 
> - License and doc should be under '%files -n libcoot'
> 

Done.

> 
> - Python libraries should be packed separately in an arched
>   'python2-libcoot' sub-package (sorry, i didn't seen it before).
> 
>   Main package should require it.
> 

Done.

> - doc subpackage provides PDF files only, it should not require
>   the main one in my opinion.
> 

OK, done.

> - Useless ldconfig:
> 
>  %post
> /sbin/ldconfig
> /bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null || :
> 

Oops, this was a result of moving things to libcoot. Fixed.

> - coot-data ?
> 

Done (oops missed this one before).

> - I don't see any tests ran with 'make check'
> 

There are checks compiled in several subdirectories - they're not defined as TESTS however. I could run them manually - I'll check with upstream.

> - Please, remove commands and macros in the comments
> 
> - AutoTools: Obsoleted m4s found
>   ------------------------------
>     AM_PROG_CC_STDC found in: coot-0.8.6.2/configure.ac:38
> 

This is commented out by Patch0, and autoconf is then re-run.  Acceptable?

https://timfenn.fedorapeople.org/coot.spec
https://timfenn.fedorapeople.org/coot-0.8.6.2-2.fc24.src.rpm

Comment 13 Antonio T. (sagitter) 2016-11-04 20:29:45 UTC
Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======
- Package does not use a name that already exists.
  Note: A package with this name already exists. Please check
  https://admin.fedoraproject.org/pkgdb/package/coot
  See:
  https://fedoraproject.org/wiki/Packaging/NamingGuidelines#Conflicting_Package_Names

- Add 'Requires: lib%{name}%{?_isa} = %{version}-%{release}' to libcoot-devel.

- Add 'Requires: python2-lib%{name}%{?_isa} = %{version}-%{release}' to python2-libcoot-devel.

- 'coot-data' must be a noarch package.
  Main package requires 'coot-data' as a noarch dependence.

  Requires: %{name}-data = %{version}-%{release}

- 'coot-doc' is a stand-alone package that must provide a license file.

- Following lines can be removed

%post -n python2-libcoot
/sbin/ldconfig

%postun -n python2-libcoot
/sbin/ldconfig

- ldconfig scriptlets can be written in this way

%post -n libcoot -p /sbin/ldconfig
%postun -n libcoot -p /sbin/ldconfig

- Please, remove those macros in the comments or silence them with %%.

- Fix strange-permission warnings (set them with 644)

coot.src: W: strange-permission reference-structures.tar.gz 444
coot.src: W: strange-permission coot.in 755

===== MUST items =====

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig called in %post and %postun if required.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[x]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "LGPL (v2.1 or later) (with incorrect FSF address)", "LGPL",
     "GPL (v2 or later)", "GPL (v3 or later)", "Unknown or generated",
     "MIT/X11 (BSD like)", "LGPL (v3 or later)", "LGPL (v2.1 or later)".
     513 files have unknown license. Detailed output of licensecheck in
     /home/sagitter/1359402-coot/licensecheck.txt
[!]: License file installed when any subpackage combination is installed.
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[x]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[!]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: gtk-update-icon-cache is invoked in %postun and %posttrans if package
     contains icons.
     Note: icons in coot
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 10240 bytes in 2 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: Package requires other packages for directories it uses.
[x]: Package must own all directories that it creates.
[x]: Package does not own files or directories owned by other packages.
[x]: All build dependencies are listed in BuildRequires, except for any
     that are listed in the exceptions section of Packaging Guidelines.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Package contains desktop file if it is a GUI application.
[x]: Package installs a %{name}.desktop using desktop-file-install or
     desktop-file-validate if there is such a file.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

Python:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: A package which is used by another package via an egg interface should
     provide egg info.
[x]: Package meets the Packaging Guidelines::Python
[x]: Package contains BR: python2-devel or python3-devel
[x]: Binary eggs must be removed in %prep

===== SHOULD items =====

Generic:
[x]: Uses parallel make %{?_smp_mflags} macro.
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[!]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in coot-
     data , libcoot , libcoot-devel , python2-libcoot , python2-libcoot-
     devel , coot-doc , coot-debuginfo
[ ]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[!]: Scriptlets must be sane, if used.
[-]: Description and summary sections in the package spec file contains
     translations for supported Non-English languages, if available.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[?]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: Sources can be downloaded from URI in Source: tag
[x]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[x]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
     Note: Arch-ed rpms have a total of 86159360 bytes in /usr/share coot-
     data-0.8.6.2-2.fc26.x86_64.rpm:85975040
     See:
     http://fedoraproject.org/wiki/Packaging:ReviewGuidelines#Package_Review_Guidelines
[!]: Package should not use obsolete m4 macros
     Note: Some obsoleted macros found, see the attachment.
     See: https://fedorahosted.org/FedoraReview/wiki/AutoTools
[x]: Rpmlint is run on debuginfo package(s).
     Note: No rpmlint messages.
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: coot-0.8.6.2-2.fc26.x86_64.rpm
          coot-data-0.8.6.2-2.fc26.x86_64.rpm
          libcoot-0.8.6.2-2.fc26.x86_64.rpm
          libcoot-devel-0.8.6.2-2.fc26.x86_64.rpm
          python2-libcoot-0.8.6.2-2.fc26.x86_64.rpm
          python2-libcoot-devel-0.8.6.2-2.fc26.x86_64.rpm
          coot-doc-0.8.6.2-2.fc26.noarch.rpm
          coot-debuginfo-0.8.6.2-2.fc26.x86_64.rpm
          coot-0.8.6.2-2.fc26.src.rpm
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.x86_64: W: no-manual-page-for-binary pyrogen
coot-data.x86_64: W: spelling-error %description -l en_US rotamer -> roamer, Rotterdam, Tamera
coot-data.x86_64: W: no-documentation
libcoot.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot.x86_64: W: one-line-command-in-%post /sbin/ldconfig
libcoot.x86_64: W: one-line-command-in-%postun /sbin/ldconfig
libcoot-devel.x86_64: W: no-dependency-on libcoot/libcoot-libs/liblibcoot
libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
libcoot-devel.x86_64: W: no-documentation
python2-libcoot.x86_64: W: no-documentation
python2-libcoot.x86_64: W: one-line-command-in-%post /sbin/ldconfig
python2-libcoot.x86_64: W: one-line-command-in-%postun /sbin/ldconfig
python2-libcoot-devel.x86_64: W: no-dependency-on python2-libcoot/python2-libcoot-libs/libpython2-libcoot
python2-libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
python2-libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
python2-libcoot-devel.x86_64: W: no-documentation
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/_pyrogen_swig.so _pyrogen_swig.so.0.0.0
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/pyrogen_boost.so pyrogen_boost.so.0.0.0
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot.src: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.src: W: strange-permission reference-structures.tar.gz 444
coot.src: W: strange-permission coot.in 755
coot.src:7: W: macro-in-comment %files
coot.src:146: W: macro-in-comment %configure
coot.src:177: W: macro-in-comment %{buildroot}
coot.src:177: W: macro-in-comment %{_includedir}
coot.src:178: W: macro-in-comment %{buildroot}
coot.src:178: W: macro-in-comment %{_includedir}
coot.src:178: W: macro-in-comment %{buildroot}
coot.src:178: W: macro-in-comment %{_includedir}
coot.src:179: W: macro-in-comment %{buildroot}
coot.src:179: W: macro-in-comment %{_includedir}
coot.src:179: W: macro-in-comment %{buildroot}
coot.src:179: W: macro-in-comment %{_includedir}
coot.src:182: W: macro-in-comment %{buildroot}
coot.src:182: W: macro-in-comment %{python2_sitelib}
coot.src:183: W: macro-in-comment %{buildroot}
coot.src:183: W: macro-in-comment %{_datadir}
coot.src:183: W: macro-in-comment %{buildroot}
coot.src:183: W: macro-in-comment %{python2_sitelib}
coot.src:200: W: macro-in-comment %{buildroot}
coot.src:200: W: macro-in-comment %{_bindir}
9 packages and 0 specfiles checked; 0 errors, 45 warnings.




Rpmlint (debuginfo)
-------------------
Checking: coot-debuginfo-0.8.6.2-2.fc26.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.





Rpmlint (installed packages)
----------------------------
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.x86_64: W: no-manual-page-for-binary pyrogen
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot-data.x86_64: W: spelling-error %description -l en_US rotamer -> roamer, Rotterdam, Tamera
coot-data.x86_64: W: no-documentation
python2-libcoot.x86_64: W: no-documentation
python2-libcoot.x86_64: W: one-line-command-in-%post /sbin/ldconfig
python2-libcoot.x86_64: W: one-line-command-in-%postun /sbin/ldconfig
libcoot.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libgslcblas.so.0
libcoot.x86_64: W: one-line-command-in-%post /sbin/ldconfig
libcoot.x86_64: W: one-line-command-in-%postun /sbin/ldconfig
libcoot-devel.x86_64: W: no-dependency-on libcoot/libcoot-libs/liblibcoot
libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
libcoot-devel.x86_64: W: no-documentation
python2-libcoot-devel.x86_64: W: no-dependency-on python2-libcoot/python2-libcoot-libs/libpython2-libcoot
python2-libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
python2-libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
python2-libcoot-devel.x86_64: W: no-documentation
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/_pyrogen_swig.so _pyrogen_swig.so.0.0.0
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/pyrogen_boost.so pyrogen_boost.so.0.0.0
8 packages and 0 specfiles checked; 0 errors, 23 warnings.



Requires
--------
coot (rpmlib, GLIBC filtered):
    /bin/sh
    compat-guile18
    coot-data(x86-64)
    hicolor-icon-theme
    libAlignment.so.1()(64bit)
    libDataStructs.so.1()(64bit)
    libDepictor.so.1()(64bit)
    libDescriptors.so.1()(64bit)
    libDistGeomHelpers.so.1()(64bit)
    libDistGeometry.so.1()(64bit)
    libEigenSolvers.so.1()(64bit)
    libFileParsers.so.1()(64bit)
    libForceField.so.1()(64bit)
    libForceFieldHelpers.so.1()(64bit)
    libGL.so.1()(64bit)
    libGLU.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libICE.so.6()(64bit)
    libMolChemicalFeatures.so.1()(64bit)
    libMolDraw2D.so.1()(64bit)
    libOptimizer.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libRDGeometryLib.so.1()(64bit)
    libSM.so.6()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libX11.so.6()(64bit)
    libXmu.so.6()(64bit)
    libXt.so.6()(64bit)
    libart_lgpl_2.so.2()(64bit)
    libatk-1.0.so.0()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcairo.so.2()(64bit)
    libccp4c.so.0()(64bit)
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libclipper-ccp4.so.2()(64bit)
    libclipper-cif.so.2()(64bit)
    libclipper-cns.so.2()(64bit)
    libclipper-contrib.so.2()(64bit)
    libclipper-core.so.2()(64bit)
    libclipper-fortran.so.2()(64bit)
    libclipper-minimol.so.2()(64bit)
    libclipper-mmdb.so.2()(64bit)
    libclipper-phs.so.2()(64bit)
    libcoot(x86-64)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)
    libcurl.so.4()(64bit)
    libdl.so.2()(64bit)
    libfontconfig.so.1()(64bit)
    libfreetype.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgdk-x11-2.0.so.0()(64bit)
    libgdk_pixbuf-2.0.so.0()(64bit)
    libgdkglext-x11-1.0.so.0()(64bit)
    libgio-2.0.so.0()(64bit)
    libglib-2.0.so.0()(64bit)
    libglut.so.3()(64bit)
    libgmodule-2.0.so.0()(64bit)
    libgnomecanvas-2.so.0()(64bit)
    libgobject-2.0.so.0()(64bit)
    libgoocanvas.so.3()(64bit)
    libgsl.so.19()(64bit)
    libgslcblas.so.0()(64bit)
    libgtk-x11-2.0.so.0()(64bit)
    libgtkglext-x11-1.0.so.0()(64bit)
    libguile.so.17()(64bit)
    libm.so.6()(64bit)
    libmmdb2.so.0()(64bit)
    libpango-1.0.so.0()(64bit)
    libpangocairo-1.0.so.0()(64bit)
    libpangoft2-1.0.so.0()(64bit)
    libpangox-1.0.so.0()(64bit)
    libpng16.so.16()(64bit)
    libpthread.so.0()(64bit)
    libpython2.7.so.1.0()(64bit)
    libsfftw.so.2()(64bit)
    libsrfftw.so.2()(64bit)
    libssm.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    libutil.so.1()(64bit)
    python2-libcoot(x86-64)
    refmac-dictionary
    rtld(GNU_HASH)

coot-doc (rpmlib, GLIBC filtered):

coot-data (rpmlib, GLIBC filtered):

python2-libcoot (rpmlib, GLIBC filtered):
    /bin/sh
    libDepictor.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libmmdb2.so.0()(64bit)
    libpython2.7.so.1.0()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    python(abi)
    rtld(GNU_HASH)

libcoot (rpmlib, GLIBC filtered):
    /bin/sh
    libDepictor.so.1()(64bit)
    libDescriptors.so.1()(64bit)
    libFileParsers.so.1()(64bit)
    libForceField.so.1()(64bit)
    libForceFieldHelpers.so.1()(64bit)
    libGL.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libMolChemicalFeatures.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libRDGeometryLib.so.1()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcairo.so.2()(64bit)
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libclipper-ccp4.so.2()(64bit)
    libclipper-contrib.so.2()(64bit)
    libclipper-core.so.2()(64bit)
    libclipper-minimol.so.2()(64bit)
    libclipper-mmdb.so.2()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_4.0.0)(64bit)
    libgdk-x11-2.0.so.0()(64bit)
    libglib-2.0.so.0()(64bit)
    libgobject-2.0.so.0()(64bit)
    libgoocanvas.so.3()(64bit)
    libgsl.so.19()(64bit)
    libgslcblas.so.0()(64bit)
    libgtk-x11-2.0.so.0()(64bit)
    libm.so.6()(64bit)
    libmmdb2.so.0()(64bit)
    libpango-1.0.so.0()(64bit)
    libpng16.so.16()(64bit)
    libpng16.so.16(PNG16_0)(64bit)
    libpython2.7.so.1.0()(64bit)
    libsrfftw.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    rtld(GNU_HASH)

libcoot-devel (rpmlib, GLIBC filtered):
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)

coot-debuginfo (rpmlib, GLIBC filtered):

python2-libcoot-devel (rpmlib, GLIBC filtered):
    python(abi)



Provides
--------
coot:
    appdata()
    appdata(coot.appdata.xml)
    application()
    application(coot.desktop)
    coot
    coot(x86-64)

coot-doc:
    coot-doc

coot-data:
    coot-data
    coot-data(x86-64)

python2-libcoot:
    python2-libcoot
    python2-libcoot(x86-64)

libcoot:
    libccp4mg-surface.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libcoot
    libcoot(x86-64)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)

libcoot-devel:
    libcoot-devel
    libcoot-devel(x86-64)

coot-debuginfo:
    coot-debuginfo
    coot-debuginfo(x86-64)

python2-libcoot-devel:
    python2-libcoot-devel
    python2-libcoot-devel(x86-64)



Source checksums
----------------
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.6.2.tar.gz :
  CHECKSUM(SHA256) this package     : 911eb76282c274e148d5351a689f428399c75f4cef7c121676a78b0a185f49c9
  CHECKSUM(SHA256) upstream package : 911eb76282c274e148d5351a689f428399c75f4cef7c121676a78b0a185f49c9
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz :
  CHECKSUM(SHA256) this package     : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a
  CHECKSUM(SHA256) upstream package : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a


AutoTools: Obsoleted m4s found
------------------------------
  AM_PROG_CC_STDC found in: coot-0.8.6.2/configure.ac:38


Generated by fedora-review 0.6.1 (f03e4e7) last change: 2016-05-02
Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1359402
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Generic, Shell-api, C/C++
Disabled plugins: Java, SugarActivity, fonts, Haskell, Ocaml, Perl, R, PHP
Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6

Comment 14 Tim Fenn 2016-11-11 15:23:31 UTC
(In reply to Antonio Trande from comment #13)
> Package Review
> ==============
> 
> Legend:
> [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
> [ ] = Manual review needed
> 
> 
> Issues:
> =======
> - Package does not use a name that already exists.
>   Note: A package with this name already exists. Please check
>   https://admin.fedoraproject.org/pkgdb/package/coot
>   See:
>  
> https://fedoraproject.org/wiki/Packaging/
> NamingGuidelines#Conflicting_Package_Names
> 
> - Add 'Requires: lib%{name}%{?_isa} = %{version}-%{release}' to
> libcoot-devel.
> 

Done.

> - Add 'Requires: python2-lib%{name}%{?_isa} = %{version}-%{release}' to
> python2-libcoot-devel.
> 

Done.

> - 'coot-data' must be a noarch package.
>   Main package requires 'coot-data' as a noarch dependence.
> 
>   Requires: %{name}-data = %{version}-%{release}
> 


Done.

> - 'coot-doc' is a stand-alone package that must provide a license file.
> 

Done.

> - Following lines can be removed
> 
> %post -n python2-libcoot
> /sbin/ldconfig
> 
> %postun -n python2-libcoot
> /sbin/ldconfig
> 
> - ldconfig scriptlets can be written in this way
> 
> %post -n libcoot -p /sbin/ldconfig
> %postun -n libcoot -p /sbin/ldconfig
> 

Done.

> - Please, remove those macros in the comments or silence them with %%.
> 

Done.

> - Fix strange-permission warnings (set them with 644)
> 
> coot.src: W: strange-permission reference-structures.tar.gz 444

Fixed.

> coot.src: W: strange-permission coot.in 755
> 

This is set to 755 as its processed by autoconf to generate the coot script that starts the main program.

I've also discussed the testing of the build with upstream, and there are several files/custom scripts required to run the tests. I've asked upstream to consider streamlining this in some way, but for now I've disabled the "make check", since by itself it does nothing.

Also, the package was updated to version 0.8.7 (which fixes some of the smaller issues, such as removing AM_PROG_CC_STDC).

https://timfenn.fedorapeople.org/coot.spec
https://timfenn.fedorapeople.org/coot-0.8.7-1.fc24.src.rpm

Comment 15 Antonio T. (sagitter) 2016-11-11 17:06:37 UTC
coot does not compile on rawhide:

libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.7\" "-DPACKAGE_STRING=\"coot 0.8.7\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/libpng16 -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c lbg-search.cc  -fPIC -DPIC -o .libs/lbg-search.o
lbg-search.cc:37:47: fatal error: GraphMol/MolDraw2D/MolDraw2DCairo.h: No such file or directory
 #include <GraphMol/MolDraw2D/MolDraw2DCairo.h>
                                               ^

Wrong path of header file.

Comment 16 Tim Fenn 2016-11-12 16:44:01 UTC
(In reply to Antonio Trande from comment #15)
> coot does not compile on rawhide:
> 
> libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\"
> -DPACKAGE_VERSION=\"0.8.7\" "-DPACKAGE_STRING=\"coot 0.8.7\""
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\"
> -DVERSION=\"0.8.7\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
> -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1
> "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I.
> -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -pthread
> -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0
> -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1
> -I/usr/include/libdrm -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16
> -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
> -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include
> -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2
> -I/usr/include/libpng16 -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit
> -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7
> -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g
> -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
> -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic
> -fno-strict-aliasing -Wall -Wno-unused -c lbg-search.cc  -fPIC -DPIC -o
> .libs/lbg-search.o
> lbg-search.cc:37:47: fatal error: GraphMol/MolDraw2D/MolDraw2DCairo.h: No
> such file or directory
>  #include <GraphMol/MolDraw2D/MolDraw2DCairo.h>
>                                                ^
> 
> Wrong path of header file.

Hrm, there seems to be an issue with the rdkit package in rawhide  - I know its changed recently to try to fix this issue:

https://sourceforge.net/p/rdkit/mailman/message/35461353/

But it doesn't seem to be working properly just yet - here's the rawhide build without the rdkit patch:

https://kojipkgs.fedoraproject.org//work/tasks/2472/16422472/build.log

In file included from lbg-search.cc:37:0:
/usr/include/rdkit/MolDraw2DCairo.h:18:42: fatal error: GraphMol/MolDraw2D/MolDraw2D.h: No such file or directory
 #include <GraphMol/MolDraw2D/MolDraw2D.h>

Unless I'm missing something - any suggestions?

Comment 17 Antonio T. (sagitter) 2016-11-12 17:16:38 UTC
Why are you using coot-rdkit.patch ?

--- lbg/lbg-search.cc_orig	2016-11-09 18:29:44.870809951 -0500
+++ lbg/lbg-search.cc	2016-11-09 18:42:43.549933656 -0500
@@ -34,7 +34,7 @@
 #include "geometry/srs-interface.hh"
 #ifdef RDKIT_HAS_CAIRO_SUPPORT
 #include <cairo.h>
-#include <MolDraw2DCairo.h>
+#include <GraphMol/MolDraw2D/MolDraw2DCairo.h>
 #include "lidia-core/rdkit-interface.hh"
 #else
 #include "lidia-core/rdkit-interface.hh"

Error reported on comment#15 comes out because of it.

Comment 18 Tim Fenn 2016-11-13 17:31:07 UTC
(In reply to Antonio Trande from comment #17)
> Why are you using coot-rdkit.patch ?
> 

It doesn't compile on F24 without it. However on rawhide it doesn't compile with or without the patch, as it seems the latest rdkit that includes

GraphMol/MolDraw2D/MolDraw2D.h

From

/usr/include/rdkit/MolDraw2DCairo.h

Isn't working as it should-I'll try to dig more in to this.

Comment 19 Antonio T. (sagitter) 2016-11-13 17:50:02 UTC
(In reply to Tim Fenn from comment #18)
> (In reply to Antonio Trande from comment #17)
> > Why are you using coot-rdkit.patch ?
> > 
> 
> It doesn't compile on F24 without it.

> However on rawhide it doesn't compile
> with or without the patch, as it seems the latest rdkit that includes
> 
> GraphMol/MolDraw2D/MolDraw2D.h
> 
> From
> 
> /usr/include/rdkit/MolDraw2DCairo.h
> 
> Isn't working as it should-I'll try to dig more in to this.

Looks like f24-rdkit version is highter than rawhide-rdkit version:

>
repoquery -l rdkit-devel --releasever=rawhide --disablerepo=rpmfusion* |grep MolDraw2D.h

/usr/include/rdkit/MolDraw2D.h
/usr/include/rdkit/MolDraw2D.h
>

>
rpm -q --list rdkit-devel |grep MolDraw2D.h
/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h
>

Your patch will work on f24 only; you need to use a conditional macro in this case.

Comment 20 Antonio T. (sagitter) 2016-11-13 17:54:33 UTC
(In reply to Antonio Trande from comment #19)
> (In reply to Tim Fenn from comment #18)
> > (In reply to Antonio Trande from comment #17)
> > > Why are you using coot-rdkit.patch ?
> > > 
> > 
> > It doesn't compile on F24 without it.
> 
> > However on rawhide it doesn't compile
> > with or without the patch, as it seems the latest rdkit that includes
> > 
> > GraphMol/MolDraw2D/MolDraw2D.h
> > 
> > From
> > 
> > /usr/include/rdkit/MolDraw2DCairo.h
> > 
> > Isn't working as it should-I'll try to dig more in to this.
> 
> Looks like f24-rdkit version is highter than rawhide-rdkit version:
> 
> >
> repoquery -l rdkit-devel --releasever=rawhide --disablerepo=rpmfusion* |grep
> MolDraw2D.h
> 
> /usr/include/rdkit/MolDraw2D.h
> /usr/include/rdkit/MolDraw2D.h
> >
> 
> >
> rpm -q --list rdkit-devel |grep MolDraw2D.h
> /usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h
> >
> 
> Your patch will work on f24 only; you need to use a conditional macro in
> this case.

Sorry, i chose wrong file.

$ repoquery -l rdkit-devel --releasever=rawhide |grep MolDraw2DCairo.h

/usr/include/rdkit/MolDraw2DCairo.h
/usr/include/rdkit/MolDraw2DCairo.h

$ rpm -q --list rdkit-devel |grep MolDraw2DCairo.h
/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h

Comment 21 Tim Fenn 2016-11-16 12:56:17 UTC
(In reply to Antonio Trande from comment #20)
> (In reply to Antonio Trande from comment #19)
> > (In reply to Tim Fenn from comment #18)
> > > (In reply to Antonio Trande from comment #17)
> > > > Why are you using coot-rdkit.patch ?
> > > > 
> > > 
> > > It doesn't compile on F24 without it.
> > 
> > > However on rawhide it doesn't compile
> > > with or without the patch, as it seems the latest rdkit that includes
> > > 
> > > GraphMol/MolDraw2D/MolDraw2D.h
> > > 
> > > From
> > > 
> > > /usr/include/rdkit/MolDraw2DCairo.h
> > > 
> > > Isn't working as it should-I'll try to dig more in to this.
> > 
> > Looks like f24-rdkit version is highter than rawhide-rdkit version:
> > 
> > >
> > repoquery -l rdkit-devel --releasever=rawhide --disablerepo=rpmfusion* |grep
> > MolDraw2D.h
> > 
> > /usr/include/rdkit/MolDraw2D.h
> > /usr/include/rdkit/MolDraw2D.h
> > >
> > 
> > >
> > rpm -q --list rdkit-devel |grep MolDraw2D.h
> > /usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h
> > >
> > 
> > Your patch will work on f24 only; you need to use a conditional macro in
> > this case.
> 
> Sorry, i chose wrong file.
> 
> $ repoquery -l rdkit-devel --releasever=rawhide |grep MolDraw2DCairo.h
> 
> /usr/include/rdkit/MolDraw2DCairo.h
> /usr/include/rdkit/MolDraw2DCairo.h
> 
> $ rpm -q --list rdkit-devel |grep MolDraw2DCairo.h
> /usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h

I'd be happy to do that, but I've been unable to get the rawhide builds to complete successfully - the MolDraw2DCairo.h in rawhide isn't successfully bringing in MolDraw2D.h.

Comment 22 Gianluca Sforna 2016-11-17 07:27:13 UTC
Sorry guys for the rdkit related issues.

Yes, right now I pushed the patch for the missing headers only in F24/F25

rdkit in rawhide had several setbacks (new archs added with missing deps, a pre-release Inchi library that looks like it's breaking rdkit tests, incompatible commonmark vs recommonmark python libraries, to mention a few) so I am still not able to build it correctly.

So, for now I'd suggest you stick with F24/F25 packages to complete the review, and do not bother complicating your package to build against rdkit rawhide; as soon as I fix rdkit you will be able to build on all dist targets with no changes.

Comment 23 Tim Fenn 2016-11-17 18:21:34 UTC
(In reply to Gianluca Sforna from comment #22)
> Sorry guys for the rdkit related issues.
> 
> Yes, right now I pushed the patch for the missing headers only in F24/F25
> 
> rdkit in rawhide had several setbacks (new archs added with missing deps, a
> pre-release Inchi library that looks like it's breaking rdkit tests,
> incompatible commonmark vs recommonmark python libraries, to mention a few)
> so I am still not able to build it correctly.
> 
> So, for now I'd suggest you stick with F24/F25 packages to complete the
> review, and do not bother complicating your package to build against rdkit
> rawhide; as soon as I fix rdkit you will be able to build on all dist
> targets with no changes.

Ah, thanks for the info Gianluca.  Antonio: the package as-is then should work on F24/F25, but I'll try to keep a close eye on the rdkit updates (or Gianluca can just update this request when its fixed?) and fix things as need be.  Sound good?

Comment 24 Antonio T. (sagitter) 2016-11-17 18:38:12 UTC
(In reply to Tim Fenn from comment #23)
> (In reply to Gianluca Sforna from comment #22)
> > Sorry guys for the rdkit related issues.
> > 
> > Yes, right now I pushed the patch for the missing headers only in F24/F25
> > 
> > rdkit in rawhide had several setbacks (new archs added with missing deps, a
> > pre-release Inchi library that looks like it's breaking rdkit tests,
> > incompatible commonmark vs recommonmark python libraries, to mention a few)
> > so I am still not able to build it correctly.
> > 
> > So, for now I'd suggest you stick with F24/F25 packages to complete the
> > review, and do not bother complicating your package to build against rdkit
> > rawhide; as soon as I fix rdkit you will be able to build on all dist
> > targets with no changes.
> 
> Ah, thanks for the info Gianluca.  Antonio: the package as-is then should
> work on F24/F25, but I'll try to keep a close eye on the rdkit updates (or
> Gianluca can just update this request when its fixed?) and fix things as
> need be.  Sound good?

We have to wait then; there is no hurry.
You could open a Copr project for coot in the meantime.

Comment 25 Gianluca Sforna 2016-11-17 19:05:50 UTC
I just managed to build rdkit in rawhide (no docs, no tests, but at least we're there) so now you should be able to compile against it.

Comment 26 Tim Fenn 2016-11-18 01:37:09 UTC
(In reply to Gianluca Sforna from comment #25)
> I just managed to build rdkit in rawhide (no docs, no tests, but at least
> we're there) so now you should be able to compile against it.

Ah great, yes - this works now:

http://koji.fedoraproject.org/koji/taskinfo?taskID=16502991

Comment 27 Antonio T. (sagitter) 2016-11-18 18:49:55 UTC
Created attachment 1221971 [details]
review log

Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======

- ----> sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool <-----

This commands does not work.
Try to set LDFLAGS="$RPM_LD_FLAGS -Wl,--as-needed"

- undefined-non-weak-symbol warnings appears on rawhide only; something is changed in new release
(see rpmlint output). Please ask to upstream.

Review log attached because too long.

Comment 28 Tim Fenn 2016-12-07 01:45:44 UTC
(In reply to Antonio Trande from comment #27)
> Created attachment 1221971 [details]
> review log
> 
> Package Review
> ==============
> 
> Legend:
> [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
> [ ] = Manual review needed
> 
> 
> Issues:
> =======
> 
> - ----> sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool <-----
> 
> This commands does not work.
> Try to set LDFLAGS="$RPM_LD_FLAGS -Wl,--as-needed"
> 

Can't get this to work - part of the problem is many of these dependencies are pulled in using pkg-config, so there isn't a simple solution that I can think of/come up with.  Any suggestions?

> - undefined-non-weak-symbol warnings appears on rawhide only; something is
> changed in new release
> (see rpmlint output). Please ask to upstream.
> 

This is straightforward to fix, but I'm more concerned about how to handle the shlib issue?

Comment 29 Antonio T. (sagitter) 2016-12-07 18:52:12 UTC
(In reply to Tim Fenn from comment #28)
> (In reply to Antonio Trande from comment #27)
> > Created attachment 1221971 [details]
> > review log
> > 
> > Package Review
> > ==============
> > 
> > Legend:
> > [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
> > [ ] = Manual review needed
> > 
> > 
> > Issues:
> > =======
> > 
> > - ----> sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool <-----
> > 
> > This commands does not work.
> > Try to set LDFLAGS="$RPM_LD_FLAGS -Wl,--as-needed"
> > 
> 
> Can't get this to work - part of the problem is many of these dependencies
> are pulled in using pkg-config, so there isn't a simple solution that I can
> think of/come up with.  Any suggestions?
> 

Talking with upstream folks?

Comment 30 Tim Fenn 2016-12-12 00:50:41 UTC
(In reply to Antonio Trande from comment #29)
> (In reply to Tim Fenn from comment #28)
> > (In reply to Antonio Trande from comment #27)
> > > Created attachment 1221971 [details]
> > > review log
> > > 
> > > Package Review
> > > ==============
> > > 
> > > Legend:
> > > [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
> > > [ ] = Manual review needed
> > > 
> > > 
> > > Issues:
> > > =======
> > > 
> > > - ----> sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool <-----
> > > 
> > > This commands does not work.
> > > Try to set LDFLAGS="$RPM_LD_FLAGS -Wl,--as-needed"
> > > 
> > 
> > Can't get this to work - part of the problem is many of these dependencies
> > are pulled in using pkg-config, so there isn't a simple solution that I can
> > think of/come up with.  Any suggestions?
> > 
> 
> Talking with upstream folks?

Yes - they are aware of the issue and working on it (although given the way pkgconfig works, it may not be a straightforward fix?).
I would imagine other fedora packages use this mechanism to remove unused-direct-shlib issues - is there a more general way to resolve this?

Comment 31 Tim Fenn 2017-01-15 18:46:25 UTC
Finally found enough time to fix the majority (if not all) the unused-direct-shlib issues:

https://timfenn.fedorapeople.org/coot.spec
https://timfenn.fedorapeople.org/coot-0.8.7-2.fc24.src.rpm

Comment 32 Antonio T. (sagitter) 2017-01-18 12:23:14 UTC
Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======
- Please, remove empty sections (%check, %clean)

- Since Python sub-directory is named 'coot', i think it's better naming the related packages as python2-coot.
 
  I guess, it's a nonsense packaging two symlinks, so please erase python2-coot-devel. Sorry, i had not realized this before.

 Also, add the 'python-provide' macro to python2-coot
 %{?python_provide:%python_provide python2-%{name}}

- Please, don't use hardcoded-library-path:

RDKIT_CXXFLAGS="-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT" -->
RDKIT_CXXFLAGS="-I%{_includedir}/rdkit -DRDKIT_HAS_CAIRO_SUPPORT"

  
===== MUST items =====

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig called in %post and %postun if required.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[x]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "LGPL (v2.1 or later) (with incorrect FSF address)", "LGPL",
     "GPL (v2 or later)", "GPL (v3 or later)", "Unknown or generated",
     "MIT/X11 (BSD like)", "*No copyright* GPL (v3 or later)", "GPL (v2 or
     later) GPL (v2 or later)", "LGPL (v3 or later)", "GPL (v3 or later)
     GPL (v3 or later)", "GPL (v2 or later) (with incorrect FSF address)",
     "LGPL (v2.1 or later)", "FSF All Permissive", "FSF Unlimited". 902
     files have unknown license. Detailed output of licensecheck in
     /home/sagitter/1359402-coot/licensecheck.txt
[!]: License file installed when any subpackage combination is installed.
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[x]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: gtk-update-icon-cache is invoked in %postun and %posttrans if package
     contains icons.
     Note: icons in coot
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 10240 bytes in 2 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: Package requires other packages for directories it uses.
[x]: Package must own all directories that it creates.
[x]: Package does not own files or directories owned by other packages.
[x]: All build dependencies are listed in BuildRequires, except for any
     that are listed in the exceptions section of Packaging Guidelines.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Package contains desktop file if it is a GUI application.
[x]: Package installs a %{name}.desktop using desktop-file-install or
     desktop-file-validate if there is such a file.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

Python:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: A package which is used by another package via an egg interface should
     provide egg info.
[!]: Package meets the Packaging Guidelines::Python
[x]: Package contains BR: python2-devel or python3-devel
[x]: Binary eggs must be removed in %prep

===== SHOULD items =====

Generic:
[x]: Uses parallel make %{?_smp_mflags} macro.
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[x]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in coot-
     data , libcoot , python2-libcoot , coot-doc , coot-debuginfo
[x]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[x]: Scriptlets must be sane, if used.
[-]: Description and summary sections in the package spec file contains
     translations for supported Non-English languages, if available.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[-]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: Sources can be downloaded from URI in Source: tag
[x]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[x]: Rpmlint is run on debuginfo package(s).
     Note: No rpmlint messages.
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
[x]: Package should not use obsolete m4 macros
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: coot-0.8.7-2.fc26.x86_64.rpm
          coot-data-0.8.7-2.fc26.noarch.rpm
          libcoot-0.8.7-2.fc26.x86_64.rpm
          libcoot-devel-0.8.7-2.fc26.x86_64.rpm
          python2-libcoot-0.8.7-2.fc26.x86_64.rpm
          python2-libcoot-devel-0.8.7-2.fc26.x86_64.rpm
          coot-doc-0.8.7-2.fc26.noarch.rpm
          coot-debuginfo-0.8.7-2.fc26.x86_64.rpm
          coot-0.8.7-2.fc26.src.rpm
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.x86_64: W: no-manual-page-for-binary pyrogen
coot-data.noarch: W: spelling-error %description -l en_US rotamer -> roamer, Rotterdam, Tamera
coot-data.noarch: W: no-documentation
libcoot.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
libcoot-devel.x86_64: W: no-documentation
python2-libcoot.x86_64: W: no-documentation
python2-libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
python2-libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
python2-libcoot-devel.x86_64: W: no-documentation
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/pyrogen_boost.so pyrogen_boost.so.0.0.0
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/_pyrogen_swig.so _pyrogen_swig.so.0.0.0
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot.src: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.src: W: strange-permission coot.in 755
9 packages and 0 specfiles checked; 0 errors, 18 warnings.




Rpmlint (debuginfo)
-------------------
Checking: coot-debuginfo-0.8.7-2.fc26.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.





Rpmlint (installed packages)
----------------------------
sh: /usr/bin/python: No such file or directory
coot.x86_64: W: spelling-error %description -l en_US mmdb -> mm db, mm-db, DBMS
coot.x86_64: W: no-manual-page-for-binary pyrogen
coot-doc.noarch: W: summary-not-capitalized C documentation PDF files for coot
coot-doc.noarch: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
coot-data.noarch: W: spelling-error %description -l en_US rotamer -> roamer, Rotterdam, Tamera
coot-data.noarch: W: no-documentation
python2-libcoot.x86_64: W: no-documentation
libcoot.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot.x86_64: W: unused-direct-shlib-dependency /usr/lib64/libcoot-coord-utils.so.0.0.0 /lib64/libgslcblas.so.0
libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
libcoot-devel.x86_64: W: no-documentation
python2-libcoot-devel.x86_64: W: spelling-error %description -l en_US macromolecular -> macro molecular, macro-molecular, molecular
python2-libcoot-devel.x86_64: W: only-non-binary-in-usr-lib
python2-libcoot-devel.x86_64: W: no-documentation
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/_pyrogen_swig.so _pyrogen_swig.so.0.0.0
python2-libcoot-devel.x86_64: W: dangling-relative-symlink /usr/lib64/python2.7/site-packages/pyrogen_boost.so pyrogen_boost.so.0.0.0
8 packages and 0 specfiles checked; 0 errors, 17 warnings.



Requires
--------
coot (rpmlib, GLIBC filtered):
    /bin/sh
    compat-guile18
    coot-data
    hicolor-icon-theme
    libAlignment.so.1()(64bit)
    libDataStructs.so.1()(64bit)
    libDepictor.so.1()(64bit)
    libDescriptors.so.1()(64bit)
    libDistGeomHelpers.so.1()(64bit)
    libDistGeometry.so.1()(64bit)
    libEigenSolvers.so.1()(64bit)
    libFileParsers.so.1()(64bit)
    libForceField.so.1()(64bit)
    libForceFieldHelpers.so.1()(64bit)
    libGL.so.1()(64bit)
    libGLU.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libICE.so.6()(64bit)
    libMolChemicalFeatures.so.1()(64bit)
    libMolDraw2D.so.1()(64bit)
    libOptimizer.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libRDGeometryLib.so.1()(64bit)
    libSM.so.6()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libX11.so.6()(64bit)
    libXmu.so.6()(64bit)
    libXt.so.6()(64bit)
    libart_lgpl_2.so.2()(64bit)
    libatk-1.0.so.0()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcairo.so.2()(64bit)
    libccp4c.so.0()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libclipper-ccp4.so.2()(64bit)
    libclipper-cif.so.2()(64bit)
    libclipper-cns.so.2()(64bit)
    libclipper-contrib.so.2()(64bit)
    libclipper-core.so.2()(64bit)
    libclipper-fortran.so.2()(64bit)
    libclipper-minimol.so.2()(64bit)
    libclipper-mmdb.so.2()(64bit)
    libclipper-phs.so.2()(64bit)
    libcoot(x86-64)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-electrostatics.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)
    libcurl.so.4()(64bit)
    libdl.so.2()(64bit)
    libfontconfig.so.1()(64bit)
    libfreetype.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgdk-x11-2.0.so.0()(64bit)
    libgdk_pixbuf-2.0.so.0()(64bit)
    libgdkglext-x11-1.0.so.0()(64bit)
    libgio-2.0.so.0()(64bit)
    libglib-2.0.so.0()(64bit)
    libglut.so.3()(64bit)
    libgmodule-2.0.so.0()(64bit)
    libgnomecanvas-2.so.0()(64bit)
    libgobject-2.0.so.0()(64bit)
    libgoocanvas.so.3()(64bit)
    libgsl.so.19()(64bit)
    libgslcblas.so.0()(64bit)
    libgtk-x11-2.0.so.0()(64bit)
    libgtkglext-x11-1.0.so.0()(64bit)
    libguile.so.17()(64bit)
    libm.so.6()(64bit)
    libmmdb2.so.0()(64bit)
    libpango-1.0.so.0()(64bit)
    libpangocairo-1.0.so.0()(64bit)
    libpangoft2-1.0.so.0()(64bit)
    libpangox-1.0.so.0()(64bit)
    libpng16.so.16()(64bit)
    libpthread.so.0()(64bit)
    libpython2.7.so.1.0()(64bit)
    libsfftw.so.2()(64bit)
    libsrfftw.so.2()(64bit)
    libssm.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    libutil.so.1()(64bit)
    python2-libcoot(x86-64)
    refmac-dictionary
    rtld(GNU_HASH)

coot-doc (rpmlib, GLIBC filtered):

coot-data (rpmlib, GLIBC filtered):

python2-libcoot (rpmlib, GLIBC filtered):
    libDepictor.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libmmdb2.so.0()(64bit)
    libpython2.7.so.1.0()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    python(abi)
    rtld(GNU_HASH)

libcoot (rpmlib, GLIBC filtered):
    /sbin/ldconfig
    libDepictor.so.1()(64bit)
    libDescriptors.so.1()(64bit)
    libFileParsers.so.1()(64bit)
    libForceField.so.1()(64bit)
    libForceFieldHelpers.so.1()(64bit)
    libGL.so.1()(64bit)
    libGraphMol.so.1()(64bit)
    libMolChemicalFeatures.so.1()(64bit)
    libRDGeneral.so.1()(64bit)
    libRDGeometryLib.so.1()(64bit)
    libSmilesParse.so.1()(64bit)
    libSubstructMatch.so.1()(64bit)
    libboost_python.so.1.60.0()(64bit)
    libc.so.6()(64bit)
    libcairo.so.2()(64bit)
    libccp4mg-utils.so.0()(64bit)
    libclipper-ccp4.so.2()(64bit)
    libclipper-contrib.so.2()(64bit)
    libclipper-core.so.2()(64bit)
    libclipper-minimol.so.2()(64bit)
    libclipper-mmdb.so.2()(64bit)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-electrostatics.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_4.0.0)(64bit)
    libgdk-x11-2.0.so.0()(64bit)
    libglib-2.0.so.0()(64bit)
    libgobject-2.0.so.0()(64bit)
    libgoocanvas.so.3()(64bit)
    libgsl.so.19()(64bit)
    libgslcblas.so.0()(64bit)
    libgtk-x11-2.0.so.0()(64bit)
    libm.so.6()(64bit)
    libmmdb2.so.0()(64bit)
    libpango-1.0.so.0()(64bit)
    libpng16.so.16()(64bit)
    libpng16.so.16(PNG16_0)(64bit)
    libpython2.7.so.1.0()(64bit)
    libsrfftw.so.2()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.1)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    rtld(GNU_HASH)

libcoot-devel (rpmlib, GLIBC filtered):
    libccp4mg-utils.so.0()(64bit)
    libcoot(x86-64)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-electrostatics.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)

coot-debuginfo (rpmlib, GLIBC filtered):

python2-libcoot-devel (rpmlib, GLIBC filtered):
    python(abi)
    python2-libcoot(x86-64)



Provides
--------
coot:
    appdata()
    appdata(coot.appdata.xml)
    application()
    application(coot.desktop)
    coot
    coot(x86-64)

coot-doc:
    coot-doc

coot-data:
    coot-data

python2-libcoot:
    python2-libcoot
    python2-libcoot(x86-64)

libcoot:
    libccp4mg-utils.so.0()(64bit)
    libcoot
    libcoot(x86-64)
    libcoot-AngleInfo.so.0()(64bit)
    libcoot-analysis.so.0()(64bit)
    libcoot-cabuild.so.0()(64bit)
    libcoot-compat.so.0()(64bit)
    libcoot-coord-extras.so.0()(64bit)
    libcoot-coord-utils.so.0()(64bit)
    libcoot-coords.so.0()(64bit)
    libcoot-db-main.so.0()(64bit)
    libcoot-electrostatics.so.0()(64bit)
    libcoot-geometry.so.0()(64bit)
    libcoot-goograph.so.0()(64bit)
    libcoot-gtkgraph.so.0()(64bit)
    libcoot-high-res.so.0()(64bit)
    libcoot-ideal.so.0()(64bit)
    libcoot-isosurface.so.0()(64bit)
    libcoot-lidia-core.so.0()(64bit)
    libcoot-lidia.so.0()(64bit)
    libcoot-ligand.so.0()(64bit)
    libcoot-map-heavy.so.0()(64bit)
    libcoot-map-utils.so.0()(64bit)
    libcoot-mini-mol.so.0()(64bit)
    libcoot-protein-db.so.0()(64bit)
    libcoot-shelx.so.0()(64bit)
    libcoot-skeleton.so.0()(64bit)
    libcoot-surface.so.0()(64bit)
    libcoot-tw.so.0()(64bit)
    libcoot-utils.so.0()(64bit)
    libcoot_py_restraints.so.0()(64bit)
    libcootaneer.so.0()(64bit)
    libcootilus.so.0()(64bit)

libcoot-devel:
    libcoot-devel
    libcoot-devel(x86-64)

coot-debuginfo:
    coot-debuginfo
    coot-debuginfo(x86-64)

python2-libcoot-devel:
    python2-libcoot-devel
    python2-libcoot-devel(x86-64)



Source checksums
----------------
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.7.tar.gz :
  CHECKSUM(SHA256) this package     : 2ec33d2b13865cb0524167b6e36f5d9e0f9a9cf90cd61d8e0bb52e1bbf834a59
  CHECKSUM(SHA256) upstream package : 2ec33d2b13865cb0524167b6e36f5d9e0f9a9cf90cd61d8e0bb52e1bbf834a59
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz :
  CHECKSUM(SHA256) this package     : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a
  CHECKSUM(SHA256) upstream package : 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a


Generated by fedora-review 0.6.1 (f03e4e7) last change: 2016-05-02
Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1359402
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Generic, Shell-api, C/C++
Disabled plugins: Java, SugarActivity, fonts, Haskell, Ocaml, Perl, R, PHP
Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6

Comment 33 Tim Fenn 2017-01-27 01:37:18 UTC
(In reply to Antonio Trande from comment #32)
> - Please, remove empty sections (%check, %clean)
> 

Done.

> - Since Python sub-directory is named 'coot', i think it's better naming the
> related packages as python2-coot.
>  

Done.

>   I guess, it's a nonsense packaging two symlinks, so please erase
> python2-coot-devel. Sorry, i had not realized this before.
> 

No worries, fixed.

>  Also, add the 'python-provide' macro to python2-coot
>  %{?python_provide:%python_provide python2-%{name}}
> 

Done.

> - Please, don't use hardcoded-library-path:
> 
> RDKIT_CXXFLAGS="-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT" -->
> RDKIT_CXXFLAGS="-I%{_includedir}/rdkit -DRDKIT_HAS_CAIRO_SUPPORT"
> 

Fixed.

https://timfenn.fedorapeople.org/coot.spec
https://timfenn.fedorapeople.org/coot-0.8.7-3.fc24.src.rpm

Comment 34 Antonio T. (sagitter) 2017-01-27 11:32:57 UTC
Package approved.

Comment 35 Tim Fenn 2017-02-01 17:09:03 UTC
my fedora account doesn't have TICKET_CREATE privileges on rel-eng trac to make the unretire request. How should I proceed?

Comment 36 Antonio T. (sagitter) 2017-02-02 11:45:55 UTC
Ask on 'devel' mailing list.

Comment 37 Package Review 2021-04-28 00:45:15 UTC
This is an automatic check from review-stats script.

This review request ticket hasn't been updated for some time, but it seems
that the review is still being working out by you. If this is right, please
respond to this comment clearing the NEEDINFO flag and try to reach out the
submitter to proceed with the review.

If you're not interested in reviewing this ticket anymore, please clear the
fedora-review flag and reset the assignee, so that a new reviewer can take
this ticket.

Without any reply, this request will shortly be resetted.

Comment 38 Antonio T. sagitter 2021-04-28 10:52:27 UTC
This package was reviewed and approved. Now, it's unmaintained.
I'm closing this ticket.


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