[Bug 1878903] Review Request: jmol - Java viewer for chemical structures in 3D

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https://bugzilla.redhat.com/show_bug.cgi?id=1878903



--- Comment #4 from Andy Mender <andymenderunix@xxxxxxxxx> ---
Thanks a lot for packaging Jmol! I remember using it quite a bit during my PhD
studies. 

COPR project with jmol and its dependency naga:
https://copr.fedorainfracloud.org/coprs/andymenderunix/jmol/
If you'd like to get write access to it, please request permissions via COPR
:).

> Name:           jmol
> Version:        14.31.4
> Release:        1%{?dist}
> Summary:        Java viewer for chemical structures in 3D

A couple of new versions were recently released, newest being 14.31.8:
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.31/Jmol%2014.31.8/

> Requires:       apache-commons-cli
> Requires:       hicolor-icon-theme
> Requires:       java
> Requires:       javapackages-tools
> Requires:       naga
The Java Packaging Guidelines mention also that a Requires on
javapackages-filesystem and java-headless should be added as well:
https://docs.fedoraproject.org/en-US/packaging-guidelines/Java/#_buildrequires_and_requires
> Requires:       java-headless
> Requires:       javapackages-filesystem

> %files -n jsmol
> %doc appletweb/jsmol/README.TXT
> %{_jsdir}/jsmol/

If jsmol is an independent package, it needs to provide its own license file
with the %license macro. If it's not independent, it needs to explicitly
Requires the main jmol package:
> Requires: %{name} = %{version}-%{release}

> # Icons from Nuvola are included, but at different sizes than Fedora provides
> Provides:       bundled(nuvola-icon-theme)

Is the license on this icon set compatible with the other licenses?

Full review below:

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

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


Issues:
=======
- Package installs properly.
  Note: Installation errors (see attachment)
  See: https://docs.fedoraproject.org/en-US/packaging-guidelines/
- This seems like a Java package, please install fedora-review-plugin-java
  to get additional checks
  Review: not maintained anymore.
- Package does not use a name that already exists.
  Note: A package with this name already exists. Please check
  https://src.fedoraproject.org/rpms/jmol
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/Naming/#_conflicting_package_names
  Review: It's fine, since it's a re-review of a retired package.


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

Generic:
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
     Note: Using prebuilt packages
     Review: Tested in COPR. 
[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: "Unknown or generated", "GNU Lesser General Public License
     (v2.1 or later)", "*No copyright* IBM Public License 1.0", "BSD
     2-clause "Simplified" License", "GPL (v2 or later) (with incorrect FSF
     address)", "BSD 2-clause "Simplified" License GNU Lesser General
     Public License (v2.1 or later)", "GPL (v2)", "*No copyright* GNU
     Lesser General Public License (v2.1 or later)", "GNU Lesser General
     Public License", "BSD 3-clause "New" or "Revised" License", "*No
     copyright* Apache License 2.0", "*No copyright* Creative Commons
     Attribution-ShareAlike 3.0 Unported License". 840 files have unknown
     license. Detailed output of licensecheck in
     /home/amender/rpmbuild/SPECS/jmol/jmol/licensecheck.txt
[!]: License file installed when any subpackage combination is installed.
     Review: missing in jsmol.
[x]: If the package is under multiple licenses, the licensing breakdown
     must be documented in the spec.
[ ]: Package contains no bundled libraries without FPC exception.
     Review: contains 3 bundled libraries. Were FPC exceptions granted for
these?
[x]: Changelog in prescribed format.
     Review: Yes, but should include past entries as suggested by Susi Lehtola.
[x]: Sources contain only permissible code or content.
[-]: Development files must be in a -devel package
[?]: 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.
[x]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
     Review: Obsoletes for jspecview properly indicated.
[x]: Requires correct, justified where necessary.
     Review: yes, but see earlier comments.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[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 593920 bytes in 4 files.
[x]: Package complies to the Packaging Guidelines
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: If (and only if) the source package includes the text of the
     license(s) in its own file, then that file, containing the text of the
     license(s) for the package is included in %license.
[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]: 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 must not depend on deprecated() packages.
[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

Java:
[x]: Bundled jar/class files should be removed before build

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

Generic:
[x]: Reviewer should test that the package builds in mock.
[-]: 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 jsmol
     Review: mentioned in earlier comment.
[?]: Package functions as described.
[!]: Latest version is packaged.
     Review: No, see earlier comments.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[-]: Sources are verified with gpgverify first in %prep if upstream
     publishes signatures.
     Note: gpgverify is not 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.
     Review: verified in COPR.
[-]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[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:
[!]: Rpmlint is run on all installed packages.
     Note: Mock build failed
     See: https://docs.fedoraproject.org/en-US/packaging-
     guidelines/#_use_rpmlint


Installation errors
-------------------
INFO: mock.py version 2.6 starting (python version = 3.8.5)...
Start: init plugins
INFO: selinux enabled
Finish: init plugins
INFO: Signal handler active
Start: run
Start: chroot init
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 2.6
INFO: Mock Version: 2.6
Finish: chroot init
INFO: installing package(s):
/home/amender/rpmbuild/SPECS/jmol/jmol-javadoc-14.31.4-1.fc34.noarch.rpm
/home/amender/rpmbuild/SPECS/jmol/jsmol-14.31.4-1.fc34.noarch.rpm
/home/amender/rpmbuild/SPECS/jmol/jmol-doc-14.31.4-1.fc34.noarch.rpm
/home/amender/rpmbuild/SPECS/jmol/jmol-14.31.4-1.fc34.noarch.rpm
ERROR: Command failed: 
 # /usr/bin/dnf --installroot /var/lib/mock/fedora-rawhide-x86_64/root/
--releasever 34 --setopt=deltarpm=False --allowerasing --disableplugin=local
--disableplugin=spacewalk install
/home/amender/rpmbuild/SPECS/jmol/jmol-javadoc-14.31.4-1.fc34.noarch.rpm
/home/amender/rpmbuild/SPECS/jmol/jsmol-14.31.4-1.fc34.noarch.rpm
/home/amender/rpmbuild/SPECS/jmol/jmol-doc-14.31.4-1.fc34.noarch.rpm
/home/amender/rpmbuild/SPECS/jmol/jmol-14.31.4-1.fc34.noarch.rpm
--setopt=tsflags=nocontexts



Rpmlint
-------
Checking: jmol-14.31.4-1.fc34.noarch.rpm
          jsmol-14.31.4-1.fc34.noarch.rpm
          jmol-javadoc-14.31.4-1.fc34.noarch.rpm
          jmol-doc-14.31.4-1.fc34.noarch.rpm
          jmol-14.31.4-1.fc34.src.rpm
jmol.noarch: W: obsolete-not-provided jspecview
jmol.noarch: E: incorrect-fsf-address /usr/share/licenses/jmol/COPYRIGHT.txt
jmol.noarch: W: no-manual-page-for-binary jmol
jsmol.noarch: W: spelling-error %description -l en_US jmol -> moll
jsmol.noarch: W: spelling-error %description -l en_US sourceforge ->
Sourceforge, source forge, source-forge
jmol-javadoc.noarch: W: obsolete-not-provided jspecview-javadoc
jmol-javadoc.noarch: E: incorrect-fsf-address
/usr/share/licenses/jmol-javadoc/COPYRIGHT.txt
jmol-doc.noarch: E: incorrect-fsf-address
/usr/share/licenses/jmol-doc/COPYRIGHT.txt
jmol.src:56: W: unversioned-explicit-provides bundled(jspecview)
jmol.src:59: W: unversioned-explicit-provides bundled(sparshui)
jmol.src:62: W: unversioned-explicit-provides bundled(nuvola-icon-theme)
5 packages and 0 specfiles checked; 3 errors, 8 warnings.




Source checksums
----------------
http://biomodel.uah.es/Jmol/logos/Jmol_icon13.svg :
  CHECKSUM(SHA256) this package     :
247d373230b127826809480183b624d0ceff3b22a49ac1626ff31aa526af0b5a
  CHECKSUM(SHA256) upstream package :
247d373230b127826809480183b624d0ceff3b22a49ac1626ff31aa526af0b5a
http://downloads.sourceforge.net/jmol/Jmol-14.31.4-full.tar.gz :
  CHECKSUM(SHA256) this package     :
3700a7a684a0ff20decee2817f1ea3ffa1d09effbba534ee116dca9ec9ac8670
  CHECKSUM(SHA256) upstream package :
3700a7a684a0ff20decee2817f1ea3ffa1d09effbba534ee116dca9ec9ac8670


Requires
--------
jmol (rpmlib, GLIBC filtered):
    /usr/bin/bash
    apache-commons-cli
    hicolor-icon-theme
    java
    javapackages-tools
    naga

jsmol (rpmlib, GLIBC filtered):
    web-assets-filesystem

jmol-javadoc (rpmlib, GLIBC filtered):
    javapackages-tools

jmol-doc (rpmlib, GLIBC filtered):



Provides
--------
jmol:
    application()
    application(jmol.desktop)
    bundled(jspecview)
    bundled(nuvola-icon-theme)
    bundled(sparshui)
    jmol

jsmol:
    jsmol

jmol-javadoc:
    jmol-javadoc

jmol-doc:
    jmol-doc


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