[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry

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https://bugzilla.redhat.com/show_bug.cgi?id=984605



--- Comment #26 from marcindulak <Marcin.Dulak@xxxxxxxxx> ---
(In reply to Antonio Trande from comment #24)
> - 'common' subpackage contains data files and should be a 'noarch' package

OK now

> -  License file is missing if you don't install basic package (nwchem).
>    Add '%doc LICENSE.txt' to %files in nwchem-common

OK now

> - '/etc/profile.d' directory is owned by 'setup' package. Please, list all
> files
>   installed within it explicitely

i think this request is just for readability - nwchem does not own
/etc/profile.d, so i changed the * glob to a more readable one.
/etc/profile.d files are now %config(noreplace) - just in case someone
edits the files to set some additional nwchem variables

> - ExcludeArch tag issue: the ARM package is not built (see comment#22)

OK now

> - Many tests are not passed. Decide if it's convenient for you to execute
> them or not.

i keep the tests as is. Failed tests is clearly an indication that something is
wrong, and i see more of failed tests on i686. For example
tests/h2o_opt/h2o_opt fails on Rawhide i686 at so called "geometry
optimization" - looks like some numerical problems. The same test passes on
EPEL6 i686, or on Fedora 20 x86_64.

> - Please, fix the 'summary-too-long' errors.

OK now

> 
> Additional notes:
> 
> - newchem building does not use all OPTFLAGS requested by Fedora Packaging
> Guidelines because 
> they seem compromise the software functionalities; upstream maintainers said
> in 
> INSTALL file:
> 
>    "The basic build tries to optimize NWChem for most systems and
>    most operating systems.  Therefore, possible optimizations have
>    been excluded." 
>  
> - nwchem compiles/uses but does not distribute managed/optimized versions of
> GA package.
> 
> Package Review
> ==============
> 
> Legend:
> [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
> [ ] = Manual review needed
> 
> 
> 
> ===== MUST items =====
> 
> C/C++:
> [x]: Package does not contain kernel modules.
> [x]: Package contains no static executables.
> [x]: Package does not contain any libtool archives (.la)
> [x]: Rpath absent or only used for internal libs.
> 
> 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:
>      "GPL (v2 or later)", "Unknown or generated", "BSD (4 clause)", "LGPL (v2
>      or later) (with incorrect FSF address)", "*No copyright* Public domain",
>      "BSD (3 clause)", "BSD (2 clause)". 4064 files have unknown license.
>      Detailed output of licensecheck in
> /home/sagitter/nwchem/licensecheck.txt
> [!]: License file installed when any subpackage combination is installed.
> [!]: Package must own all directories that it creates.
>      Note: Directories without known owners: /etc/profile.d
> [?]: %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.
> [-]: Package contains desktop file if it is a GUI application.
> [-]: 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]: Useful -debuginfo package or justification otherwise.
> [!]: 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 1 files.
> [!]: 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]: 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 %doc.
> [x]: Package requires other packages for directories it uses.
> [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 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 do not use a name that already exist
> [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
> 
> ===== SHOULD items =====
> 
> Generic:
> [x]: 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 nwchem-
>      openmpi , nwchem-mpich , nwchem-common
> [ ]: Package functions as described.
> [x]: Latest version is packaged.
> [x]: Package does not include license text files separate from upstream.
> [-]: 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]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
> [x]: Sources can be downloaded from URI in Source: tag
> [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]: Dist tag is present (not strictly required in GL).
> [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
> [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 40038400 bytes in /usr/share nwchem-
>      common-6.3.2-4.fc21.i686.rpm:40028160
>      See:
>     
> http://fedoraproject.org/wiki/Packaging:
> ReviewGuidelines#Package_Review_Guidelines
> [x]: Rpmlint is run on all installed packages.
>      Note: There are rpmlint messages (see attachment).
> 
> 
> Rpmlint
> -------
> Checking: nwchem-6.3.2-4.fc21.i686.rpm
>           nwchem-openmpi-6.3.2-4.fc21.i686.rpm
>           nwchem-mpich-6.3.2-4.fc21.i686.rpm
>           nwchem-common-6.3.2-4.fc21.i686.rpm
>           nwchem-6.3.2-4.fc21.src.rpm
> nwchem.i686: W: spelling-error %description -l en_US scalable -> salable,
> callable, calculable
> nwchem.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem.i686: W: spelling-error %description -l en_US Bylaska -> Alaska
> nwchem.i686: W: spelling-error %description -l en_US Govind -> Gov ind,
> Gov-ind, Indigo
> nwchem.i686: W: spelling-error %description -l en_US Kowalski -> Malinowski
> nwchem.i686: W: spelling-error %description -l en_US Straatsma -> Stratum
> nwchem.i686: W: spelling-error %description -l en_US Nieplocha -> Epochal
> nwchem.i686: W: spelling-error %description -l en_US Apra -> Apr, Ara, Apia
> nwchem.i686: W: spelling-error %description -l en_US Windus -> Hindus,
> Winds, Windups
> nwchem.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem.i686: W: spelling-error %description -l en_US Commun -> Com mun,
> Com-mun, Commune
> nwchem.i686: W: no-manual-page-for-binary nwchem
> nwchem-openmpi.i686: W: spelling-error %description -l en_US scalable ->
> salable, callable, calculable
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Bylaska ->
> Alaska
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Govind -> Gov
> ind, Gov-ind, Indigo
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Kowalski ->
> Malinowski
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Straatsma ->
> Stratum
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Nieplocha ->
> Epochal
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Apra -> Apr,
> Ara, Apia
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Windus ->
> Hindus, Winds, Windups
> nwchem-openmpi.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Commun -> Com
> mun, Com-mun, Commune
> nwchem-openmpi.i686: W: no-documentation
> nwchem-mpich.i686: W: spelling-error Summary(en_US) openmpi -> opening
> nwchem-mpich.i686: E: summary-too-long C Delivering High-Performance
> Computational Chemistry to Science - openmpi version - mpich version
> nwchem-mpich.i686: W: spelling-error %description -l en_US scalable ->
> salable, callable, calculable
> nwchem-mpich.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem-mpich.i686: W: spelling-error %description -l en_US Bylaska -> Alaska
> nwchem-mpich.i686: W: spelling-error %description -l en_US Govind -> Gov
> ind, Gov-ind, Indigo
> nwchem-mpich.i686: W: spelling-error %description -l en_US Kowalski ->
> Malinowski
> nwchem-mpich.i686: W: spelling-error %description -l en_US Straatsma ->
> Stratum
> nwchem-mpich.i686: W: spelling-error %description -l en_US Nieplocha ->
> Epochal
> nwchem-mpich.i686: W: spelling-error %description -l en_US Apra -> Apr, Ara,
> Apia
> nwchem-mpich.i686: W: spelling-error %description -l en_US Windus -> Hindus,
> Winds, Windups
> nwchem-mpich.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem-mpich.i686: W: spelling-error %description -l en_US Commun -> Com
> mun, Com-mun, Commune
> nwchem-mpich.i686: W: no-documentation
> nwchem-common.i686: W: spelling-error Summary(en_US) openmpi -> opening
> nwchem-common.i686: W: spelling-error Summary(en_US) mpich -> chimp
> nwchem-common.i686: E: summary-too-long C Delivering High-Performance
> Computational Chemistry to Science - openmpi version - mpich version -
> common files
> nwchem-common.i686: W: spelling-error %description -l en_US scalable ->
> salable, callable, calculable
> nwchem-common.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem-common.i686: W: spelling-error %description -l en_US Bylaska -> Alaska
> nwchem-common.i686: W: spelling-error %description -l en_US Govind -> Gov
> ind, Gov-ind, Indigo
> nwchem-common.i686: W: spelling-error %description -l en_US Kowalski ->
> Malinowski
> nwchem-common.i686: W: spelling-error %description -l en_US Straatsma ->
> Stratum
> nwchem-common.i686: W: spelling-error %description -l en_US Nieplocha ->
> Epochal
> nwchem-common.i686: W: spelling-error %description -l en_US Apra -> Apr,
> Ara, Apia
> nwchem-common.i686: W: spelling-error %description -l en_US Windus ->
> Hindus, Winds, Windups
> nwchem-common.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem-common.i686: W: spelling-error %description -l en_US Commun -> Com
> mun, Com-mun, Commune
> nwchem-common.i686: W: no-documentation
> nwchem-common.i686: W: non-conffile-in-etc /etc/profile.d/nwchem.sh
> nwchem-common.i686: W: non-conffile-in-etc /etc/profile.d/nwchem.csh
> nwchem.src: W: spelling-error %description -l en_US scalable -> salable,
> callable, calculable
> nwchem.src: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem.src: W: spelling-error %description -l en_US Bylaska -> Alaska
> nwchem.src: W: spelling-error %description -l en_US Govind -> Gov ind,
> Gov-ind, Indigo
> nwchem.src: W: spelling-error %description -l en_US Kowalski -> Malinowski
> nwchem.src: W: spelling-error %description -l en_US Straatsma -> Stratum
> nwchem.src: W: spelling-error %description -l en_US Nieplocha -> Epochal
> nwchem.src: W: spelling-error %description -l en_US Apra -> Apr, Ara, Apia
> nwchem.src: W: spelling-error %description -l en_US Windus -> Hindus, Winds,
> Windups
> nwchem.src: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem.src: W: spelling-error %description -l en_US Commun -> Com mun,
> Com-mun, Commune
> 5 packages and 0 specfiles checked; 2 errors, 64 warnings.
> 
> 
> 
> 
> Rpmlint (installed packages)
> ----------------------------
> # rpmlint nwchem nwchem-common nwchem-openmpi nwchem-mpich
> nwchem.i686: W: spelling-error %description -l en_US scalable -> salable,
> callable, calculable
> nwchem.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem.i686: W: spelling-error %description -l en_US Bylaska -> Alaska
> nwchem.i686: W: spelling-error %description -l en_US Govind -> Gov ind,
> Gov-ind, Indigo
> nwchem.i686: W: spelling-error %description -l en_US Kowalski -> Malinowski
> nwchem.i686: W: spelling-error %description -l en_US Straatsma -> Stratagem
> nwchem.i686: W: spelling-error %description -l en_US Nieplocha -> Epochal
> nwchem.i686: W: spelling-error %description -l en_US Apra -> Apr, Ara, Apia
> nwchem.i686: W: spelling-error %description -l en_US Windus -> Hindus,
> Winds, Windups
> nwchem.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem.i686: W: spelling-error %description -l en_US Commun -> Com mun,
> Com-mun, Commune
> nwchem.i686: W: no-manual-page-for-binary nwchem
> nwchem-common.i686: W: spelling-error Summary(en_US) openmpi -> opening
> nwchem-common.i686: W: spelling-error Summary(en_US) mpich -> chimp
> nwchem-common.i686: E: summary-too-long C Delivering High-Performance
> Computational Chemistry to Science - openmpi version - mpich version -
> common files
> nwchem-common.i686: W: spelling-error %description -l en_US scalable ->
> salable, callable, calculable
> nwchem-common.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem-common.i686: W: spelling-error %description -l en_US Bylaska -> Alaska
> nwchem-common.i686: W: spelling-error %description -l en_US Govind -> Gov
> ind, Gov-ind, Indigo
> nwchem-common.i686: W: spelling-error %description -l en_US Kowalski ->
> Malinowski
> nwchem-common.i686: W: spelling-error %description -l en_US Straatsma ->
> Stratagem
> nwchem-common.i686: W: spelling-error %description -l en_US Nieplocha ->
> Epochal
> nwchem-common.i686: W: spelling-error %description -l en_US Apra -> Apr,
> Ara, Apia
> nwchem-common.i686: W: spelling-error %description -l en_US Windus ->
> Hindus, Winds, Windups
> nwchem-common.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem-common.i686: W: spelling-error %description -l en_US Commun -> Com
> mun, Com-mun, Commune
> nwchem-common.i686: W: no-documentation
> nwchem-common.i686: W: non-conffile-in-etc /etc/profile.d/nwchem.sh
> nwchem-common.i686: W: non-conffile-in-etc /etc/profile.d/nwchem.csh
> nwchem-openmpi.i686: W: spelling-error %description -l en_US scalable ->
> salable, callable, calculable
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Bylaska ->
> Alaska
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Govind -> Gov
> ind, Gov-ind, Indigo
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Kowalski ->
> Malinowski
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Straatsma ->
> Stratagem
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Nieplocha ->
> Epochal
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Apra -> Apr,
> Ara, Apia
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Windus ->
> Hindus, Winds, Windups
> nwchem-openmpi.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem-openmpi.i686: W: spelling-error %description -l en_US Commun -> Com
> mun, Com-mun, Commune
> nwchem-openmpi.i686: W: no-documentation
> nwchem-mpich.i686: W: spelling-error Summary(en_US) openmpi -> opening
> nwchem-mpich.i686: E: summary-too-long C Delivering High-Performance
> Computational Chemistry to Science - openmpi version - mpich version
> nwchem-mpich.i686: W: spelling-error %description -l en_US scalable ->
> salable, callable, calculable
> nwchem-mpich.i686: W: spelling-error %description -l en_US Valiev -> Valise
> nwchem-mpich.i686: W: spelling-error %description -l en_US Bylaska -> Alaska
> nwchem-mpich.i686: W: spelling-error %description -l en_US Govind -> Gov
> ind, Gov-ind, Indigo
> nwchem-mpich.i686: W: spelling-error %description -l en_US Kowalski ->
> Malinowski
> nwchem-mpich.i686: W: spelling-error %description -l en_US Straatsma ->
> Stratagem
> nwchem-mpich.i686: W: spelling-error %description -l en_US Nieplocha ->
> Epochal
> nwchem-mpich.i686: W: spelling-error %description -l en_US Apra -> Apr, Ara,
> Apia
> nwchem-mpich.i686: W: spelling-error %description -l en_US Windus -> Hindus,
> Winds, Windups
> nwchem-mpich.i686: W: spelling-error %description -l en_US de -> DE, ed, d
> nwchem-mpich.i686: W: spelling-error %description -l en_US Commun -> Com
> mun, Com-mun, Commune
> nwchem-mpich.i686: W: no-documentation
> 4 packages and 0 specfiles checked; 2 errors, 53 warnings.
> # echo 'rpmlint-done:'
> 
> 
> 
> Requires
> --------
> nwchem (rpmlib, GLIBC filtered):
>     libc.so.6
>     libdl.so.2
>     libgcc_s.so.1
>     libgcc_s.so.1(GCC_4.0.0)
>     libgfortran.so.3
>     libgfortran.so.3(GFORTRAN_1.0)
>     libgfortran.so.3(GFORTRAN_1.4)
>     libm.so.6
>     libncurses.so.5
>     libpthread.so.0
>     libpython2.7.so.1.0
>     libquadmath.so.0
>     libreadline.so.6
>     libsysfs.so.2
>     libtatlas.so.3
>     libtinfo.so.5
>     libutil.so.1
>     libz.so.1
>     nwchem-common
>     openssh-clients
>     rtld(GNU_HASH)
> 
> nwchem-common (rpmlib, GLIBC filtered):
> 
> nwchem-openmpi (rpmlib, GLIBC filtered):
>     libc.so.6
>     libdl.so.2
>     libgcc_s.so.1
>     libgcc_s.so.1(GCC_4.0.0)
>     libgfortran.so.3
>     libgfortran.so.3(GFORTRAN_1.0)
>     libgfortran.so.3(GFORTRAN_1.4)
>     libm.so.6
>     libmpi.so.1
>     libmpi_mpifh.so.2
>     libmpi_usempi.so.1
>     libncurses.so.5
>     libpthread.so.0
>     libpython2.7.so.1.0
>     libquadmath.so.0
>     libreadline.so.6
>     libsysfs.so.2
>     libtatlas.so.3
>     libtinfo.so.5
>     libutil.so.1
>     libz.so.1
>     nwchem-common
>     openmpi
>     rtld(GNU_HASH)
> 
> nwchem-mpich (rpmlib, GLIBC filtered):
>     libc.so.6
>     libdl.so.2
>     libgcc_s.so.1
>     libgcc_s.so.1(GCC_4.0.0)
>     libgfortran.so.3
>     libgfortran.so.3(GFORTRAN_1.0)
>     libgfortran.so.3(GFORTRAN_1.4)
>     libm.so.6
>     libmpich.so.10
>     libncurses.so.5
>     libpthread.so.0
>     libpython2.7.so.1.0
>     libquadmath.so.0
>     libreadline.so.6
>     libsysfs.so.2
>     libtatlas.so.3
>     libtinfo.so.5
>     libutil.so.1
>     libz.so.1
>     mpich
>     nwchem-common
>     rtld(GNU_HASH)
> 
> 
> 
> Provides
> --------
> nwchem:
>     nwchem
>     nwchem(x86-32)
> 
> nwchem-common:
>     nwchem-common
>     nwchem-common(x86-32)
> 
> nwchem-openmpi:
>     nwchem-openmpi
>     nwchem-openmpi(x86-32)
> 
> nwchem-mpich:
>     nwchem-mpich
>     nwchem-mpich(x86-32)
> 
> 
> 
> Source checksums
> ----------------
> http://www.nwchem-sw.org/images/Nwchem-6.3.revision2-src.2013-10-17.tar.gz :
>   CHECKSUM(SHA256) this package     :
> 6a6adf068d559be1ab1bf0addc6b8aa65dbb746b8716a913f5f1bb2eb16f1718
>   CHECKSUM(SHA256) upstream package :
> 6a6adf068d559be1ab1bf0addc6b8aa65dbb746b8716a913f5f1bb2eb16f1718
> 
> 
> Generated by fedora-review 0.5.1 (bb9bf27) last change: 2013-12-13
> Command line :/usr/bin/fedora-review -m fedora-rawhide-i386 -rn
> Downloads/nwchem-6.3.2-4.fc21.src.rpm
> Buildroot used: fedora-rawhide-i386
> Active plugins: Generic, Shell-api, C/C++
> Disabled plugins: Java, Python, fonts, SugarActivity, Ocaml, Perl, Haskell,
> R, PHP, Ruby
> Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG

Spec URL: http://marcindulak.fedorapeople.org/packages/nwchem/r06/nwchem.spec
SRPM URL:
http://marcindulak.fedorapeople.org/packages/nwchem/r06/nwchem-6.3.2-6.fc21.src.rpm

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