[Bug 435018] New: Review Request: clipper - crystallographic object oriented library - package-review

List overview All Threads
Download

newer

[Bug 435018] New: Review Request: clipper - crystallographic object oriented library

older

[Bug 193271] New: Review Request:...

[Bug 469816] New: Review Request:...

Red Hat Bugzilla

26 Feb 2008 26 Feb '08

2:26 p.m.

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Summary: Review Request: clipper - crystallographic object oriented library Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: low Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: fenn@stanford.edu QAContact: extras-qa@fedoraproject.org CC: fedora-package-review@redhat.com,notting@redhat.com

Spec URL: http://www.stanford.edu/~fenn/packs/clipper.spec SRPM URL: http://www.stanford.edu/~fenn/packs/clipper-2.0-10.f8.src.rpm Description: The aim of the project is to produce a set of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation. The libraries are designed as a framework for new crystallographic software, which will allow the full power of modern programming techniques to be exploited by the developer. This will lead to greater functionality from simpler code which will be easier to develop and debug.

Also see: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Show replies by thread

Red Hat Bugzilla

25 May 25 May

3:22 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

Summary: Review Request: clipper - crystallographic object oriented library

https://bugzilla.redhat.com/show_bug.cgi?id=435018

------- Additional Comments From bdpepple@gmail.com 2008-05-25 16:22 EST ------- Couple of items that need to be fixed before giving this a proper review:

1. Remove Packager tag. That is set in the build system. 2. There's no URL tag. 3. The Source file doesn't contain a url. 4. Package contains static library. Refer: http://fedoraproject.org/wiki/Packaging/Guidelines#head-82d97fc4a3421310f4e2... 5. Package fails to build, due to some missing build requirements (libmmdb-devel , libgpp4-devel) that aren't available in Fedora. If you've submitted them for review, they should be a blocker on this bug.

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Red Hat Bugzilla

26 May 26 May

6:41 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

Summary: Review Request: clipper - crystallographic object oriented library

https://bugzilla.redhat.com/show_bug.cgi?id=435018

fenn@stanford.edu changed:

What |Removed |Added ---------------------------------------------------------------------------- BugsThisDependsOn| |435015

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Red Hat Bugzilla

6:42 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

Summary: Review Request: clipper - crystallographic object oriented library

https://bugzilla.redhat.com/show_bug.cgi?id=435018

fenn@stanford.edu changed:

What |Removed |Added ---------------------------------------------------------------------------- BugsThisDependsOn| |435016

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Red Hat Bugzilla

6:49 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

Summary: Review Request: clipper - crystallographic object oriented library

https://bugzilla.redhat.com/show_bug.cgi?id=435018

------- Additional Comments From fenn@stanford.edu 2008-05-26 19:49 EST ------- Sorry for my clumsiness, I'm still getting accustomed to the Fedora packaging scheme.

1. Remove Packager tag. That is set in the build system.

Done.

2. There's no URL tag.

Fixed.

3. The Source file doesn't contain a url.

Fixed, and patches separated out to delineate differences from upstream.

4. Package contains static library. Refer: http://fedoraproject.org/wiki/Packaging/Guidelines#head-82d97fc4a3421310f4e2...

Fixed (static libraries added to -static package)

5. Package fails to build, due to some missing build requirements (libmmdb-devel , libgpp4-devel) that aren't available in Fedora. If you've submitted them for review, they should be a blocker on this bug.

Done - see: https://bugzilla.redhat.com/show_bug.cgi?id=435015 https://bugzilla.redhat.com/show_bug.cgi?id=435016

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Red Hat Bugzilla

6:50 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

Summary: Review Request: clipper - crystallographic object oriented library

https://bugzilla.redhat.com/show_bug.cgi?id=435018

------- Additional Comments From fenn@stanford.edu 2008-05-26 19:50 EST ------- Updated files:

Spec URL: http://www.stanford.edu/~fenn/packs/clipper.spec SRPM URL: http://www.stanford.edu/~fenn/packs/clipper-2.0-11.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Red Hat Bugzilla

27 May 27 May

4:54 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

Summary: Review Request: clipper - crystallographic object oriented library

https://bugzilla.redhat.com/show_bug.cgi?id=435018

------- Additional Comments From fenn@stanford.edu 2008-05-27 05:54 EST ------- More updates as per

https://bugzilla.redhat.com/show_bug.cgi?id=435017#c2

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-12.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Red Hat Bugzilla

4:18 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug report.

Summary: Review Request: clipper - crystallographic object oriented library

https://bugzilla.redhat.com/show_bug.cgi?id=435018

------- Additional Comments From fenn@stanford.edu 2008-05-27 17:18 EST ------- Removed static libs.

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-13.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug, or are watching someone who is.

Red Hat Bugzilla

16 Aug 16 Aug

10:41 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Rakesh Pandit rakesh.pandit@gmail.com changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |rakesh.pandit@gmail.com

--- Comment #6 from Rakesh Pandit rakesh.pandit@gmail.com 2008-08-16 11:41:47 EDT ---

rpmlint output on srpm: [rpmbuild@rocky clipper]$ rp -i clipper-2.0-13.f8.src.rpm clipper.src:40: W: setup-not-quiet Use the -q option to the %setup macro to avoid useless build output from unpacking the sources.

clipper.src: W: summary-not-capitalized clipper C++ crystallographic library Summary doesn't begin with a capital letter.

clipper.src: W: no-version-in-last-changelog The last changelog entry doesn't contain a version. Please insert the version that is coherent with the version of the package and rebuild it.

1 packages and 0 specfiles checked; 0 errors, 3 warnings.

After using libmmdb-devel libgpp4-devel packages, clipper failed to built on my i386

make[3]: Entering directory `/home/rpmbuild/rpm/BUILD/clipper-2.0/clipper/mmdb' /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../clipper -I../../clipper -I/usr/include/gpp4 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -fno-strict-aliasing -c -o clipper_mmdb.lo clipper_mmdb.cpp mkdir .libs g++ -DHAVE_CONFIG_H -I. -I../../clipper -I../../clipper -I/usr/include/gpp4 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -fno-strict-aliasing -c clipper_mmdb.cpp -fPIC -DPIC -o .libs/clipper_mmdb.o clipper_mmdb.cpp: In member function 'void clipper::MMDBResidue::set_inscode(const clipper::String&)': clipper_mmdb.cpp:228: error: 'strncpy' was not declared in this scope make[3]: *** [clipper_mmdb.lo] Error 1 make[3]: Leaving directory `/home/rpmbuild/rpm/BUILD/clipper-2.0/clipper/mmdb' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/rpmbuild/rpm/BUILD/clipper-2.0/clipper' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/rpmbuild/rpm/BUILD/clipper-2.0/clipper' make: *** [all-recursive] Error 1 error: Bad exit status from /home/rpmbuild/rpm/tmp/rpm-tmp.54706 (%build)

RPM build errors: Bad exit status from /home/rpmbuild/rpm/tmp/rpm-tmp.54706 (%build)

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

21 Aug 21 Aug

9:36 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #7 from Tim Fenn fenn@stanford.edu 2008-08-21 10:36:13 EDT --- Sorry for the late reply, I've been away.

(In reply to comment #6)

...

rpmlint output on srpm: [rpmbuild@rocky clipper]$ rp -i clipper-2.0-13.f8.src.rpm clipper.src:40: W: setup-not-quiet Use the -q option to the %setup macro to avoid useless build output from unpacking the sources.

clipper.src: W: summary-not-capitalized clipper C++ crystallographic library Summary doesn't begin with a capital letter.

clipper.src: W: no-version-in-last-changelog The last changelog entry doesn't contain a version. Please insert the version that is coherent with the version of the package and rebuild it.

done.

...

make[3]: Entering directory clipper_mmdb.cpp: In member function 'void clipper::MMDBResidue::set_inscode(const clipper::String&)': clipper_mmdb.cpp:228: error: 'strncpy' was not declared in this scope make[3]: *** [clipper_mmdb.lo] Error 1 error: Bad exit status from /home/rpmbuild/rpm/tmp/rpm-tmp.54706 (%build)

I've included a patch to #include <string> in the appropriate files.

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-14.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

10 Sep 10 Sep

7:05 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #8 from Tim Fenn fenn@stanford.edu 2008-09-10 20:05:45 EDT --- Cleaned up most rpmlint problems with the -devel package:

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-15.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

14 Sep 14 Sep

4 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Tim Fenn fenn@stanford.edu changed:

What |Removed |Added ---------------------------------------------------------------------------- Depends on| |462250

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

4 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Tim Fenn fenn@stanford.edu changed:

What |Removed |Added ---------------------------------------------------------------------------- Depends on| |462251

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

4:06 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Tim Fenn fenn@stanford.edu changed:

What |Removed |Added ---------------------------------------------------------------------------- Depends on|462250 |

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

4:07 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Tim Fenn fenn@stanford.edu changed:

What |Removed |Added ---------------------------------------------------------------------------- Depends on|462251 |

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

29 Sep 29 Sep

7:38 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Rakesh Pandit rakesh.pandit@gmail.com changed:

--- Comment #9 from Rakesh Pandit rakesh.pandit@gmail.com 2008-09-29 08:38:17 EDT --- You are not sponsored yet. So I have added FE-NEEDSPONSOR here also.

Thanks

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

16 Oct 16 Oct

5:28 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Michael Schwendt bugs.michael@gmx.net changed:

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

23 Oct 23 Oct

1:25 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp changed:

What |Removed |Added ---------------------------------------------------------------------------- Blocks|177841 |

--- Comment #10 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-10-23 14:24:59 EDT --- (Removing NEEDSPONSOR: bug 462250)

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

30 Oct 30 Oct

2:05 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Bug 435018 depends on bug 435015, which changed state.

Bug 435015 Summary: Review Request: gpp4 - LGPL CCP4 library https://bugzilla.redhat.com/show_bug.cgi?id=435015

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

8 Nov 8 Nov

1:16 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Bug 435018 depends on bug 435016, which changed state.

Bug 435016 Summary: Review Request: mmdb - MMDB coordinate library https://bugzilla.redhat.com/show_bug.cgi?id=435016

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

11 Nov 11 Nov

12:55 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |mtasaka@ioa.s.u-tokyo.ac.jp

--- Comment #11 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-11-11 01:55:31 EDT --- Would you rewrite your spec/srpm? I guess you once want to clean up your spec file.

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

3:15 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #12 from Tim Fenn fenn@stanford.edu 2008-11-11 16:15:13 EDT --- (In reply to comment #11)

...

Would you rewrite your spec/srpm? I guess you once want to clean up your spec file.

Yes, now that all the deps are cleaned up, I did a bit of a cleaning/fixing:

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-16.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

12 Nov 12 Nov

10:21 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #13 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-11-12 11:21:55 EDT --- Rebuild failed on dist-f11: http://koji.fedoraproject.org/koji/taskinfo?taskID=928611

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

3:26 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #14 from Tim Fenn fenn@stanford.edu 2008-11-12 16:26:55 EDT --- (In reply to comment #13)

...

Rebuild failed on dist-f11: http://koji.fedoraproject.org/koji/taskinfo?taskID=928611

Added a patch to fix the build problems, tested on koji: https://koji.fedoraproject.org/koji/taskinfo?taskID=929474

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-17.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

13 Nov 13 Nov

3:35 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp changed:

--- Comment #15 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-11-13 04:35:06 EDT --- For -17:

* License - Well, the description of the license in the source codes seems somewhat confusing, however the license tag can be safe with "LGPLv2+".

* Source1 - Is this source created by yourself or can it be downloaded somewhere? (If some URL exists, write the URL like Source0)

* Dependency for -devel subpackage - Installed clipper.pc contains: -------------------------------------------------------- 8 Requires: mmdb gpp4 10 Libs: -L/usr/lib -lclipper -lsrfftw -lsfftw -lm -------------------------------------------------------- This means that -devel subpackage must have "Requires: mmdb-devel gpp4-devel fftw2-devel", however - Would you check if "Requires: gpp4" and "Libs: -lstfftw -lsfftw" are really needed? Installed clipper-devel header files do not seem to depend on any header files in gpp4-devel or fftw2-devel", so I guess these Requires and Libs can be removed

! Note: "Requires: mmdb" is still needed (this means that clipper-devel must have "Requires: mmdb-devel") because clipper/mmdb/clipper_mmdb.h contains: -------------------------------------------------------- 50 51 #include <mmdb/mmdb_manager.h> 52 --------------------------------------------------------

* %setup - I guess %setup can be replaced by -------------------------------------------------------- %prep %setup -q -c -a 1 --------------------------------------------------------

! Timestamps - Not a blocker, however for packages using "install-sh" to install files, -------------------------------------------------------- make install DESTDIR=$RPM_BUILD_ROOT CPPROG="cp -p" -------------------------------------------------------- to keep timestamps on installed files

* %defattr - Now we recommend %defattr(-,root,root,-)

* Documents - The file "INSTALL" is usually for people who wants to compile/ install the package by himself and not needed for rpm users.

* Directory ownership issue - %_includedir/clipper is not owned by any packages ref:

https://fedoraproject.org/wiki/Packaging/UnownedDirectories#Wildcarding_File...

* rpmlint -------------------------------------------------------- clipper.i386: E: zero-length /usr/share/doc/clipper-2.0/ChangeLog clipper-devel.i386: W: wrong-file-end-of-line-encoding /usr/share/doc/clipper-devel-2.0/dox/develop.dox clipper-devel.i386: W: wrong-file-end-of-line-encoding /usr/share/doc/clipper-devel-2.0/dox/coordtypes.dox clipper-devel.i386: W: spurious-executable-perm /usr/share/doc/clipper-devel-2.0/dox/wheretolook.dox -------------------------------------------------------- - Including zero size "ChangeLog" seems meaningless - Please fix CRLF (Windows-like) end-of-line endcodings. - Usually files included as %doc must have 0644 permission

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

2:49 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #16 from Tim Fenn fenn@stanford.edu 2008-11-13 15:49:56 EDT --- (In reply to comment #15)

...

For -17:

License

Well, the description of the license in the source codes seems somewhat confusing, however the license tag can be safe with "LGPLv2+".

OK.

...

Source1

Is this source created by yourself or can it be downloaded somewhere? (If some URL exists, write the URL like Source0)

Created by me - I've submitted it upstream as well.

...

Dependency for -devel subpackage
- Installed clipper.pc contains:

 8  Requires: mmdb gpp4
10  Libs: -L/usr/lib -lclipper -lsrfftw -lsfftw -lm

This means that -devel subpackage must have
"Requires: mmdb-devel gpp4-devel fftw2-devel", however
- Would you check if "Requires: gpp4" and
  "Libs: -lstfftw -lsfftw" are really needed?
  Installed clipper-devel header files do not seem to
  depend on any header files in gpp4-devel or fftw2-devel",
  so I guess these Requires and Libs can be removed

several of the functions under the ccp4/ folder are wrapped C++ calls to gpp4 functions, and functions in core/fftmap.h contain wrapped fftw calls. I've added the Requires to -devel.

...

%setup

I guess %setup can be replaced by

%prep %setup -q -c -a 1

done.

...

! Timestamps

Not a blocker, however for packages using "install-sh" to install files,

make install DESTDIR=$RPM_BUILD_ROOT CPPROG="cp -p"
to keep timestamps on installed files

done.

...

%defattr

Now we recommend %defattr(-,root,root,-)

oops, fixed.

...

Documents

The file "INSTALL" is usually for people who wants to compile/ install the package by himself and not needed for rpm users.

removed.

...

Directory ownership issue

%_includedir/clipper is not owned by any packages ref:

Ah, thanks! fixed.

...

rpmlint

clipper.i386: E: zero-length /usr/share/doc/clipper-2.0/ChangeLog clipper-devel.i386: W: wrong-file-end-of-line-encoding /usr/share/doc/clipper-devel-2.0/dox/develop.dox clipper-devel.i386: W: wrong-file-end-of-line-encoding /usr/share/doc/clipper-devel-2.0/dox/coordtypes.dox clipper-devel.i386: W: spurious-executable-perm /usr/share/doc/clipper-devel-2.0/dox/wheretolook.dox

Including zero size "ChangeLog" seems meaningless

Please fix CRLF (Windows-like) end-of-line endcodings.

Usually files included as %doc must have 0644 permission

removed the changelog file, fixed CRLF foo and file perms.

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-18.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

14 Nov 14 Nov

2:31 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #17 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-11-14 03:31:35 EDT --- For -18:

(In reply to comment #16)

...

(In reply to comment #15)

...

...

Directory ownership issue

%_includedir/clipper is not owned by any packages ref:

Ah, thanks! fixed.

- This time build.log says: ------------------------------------------------------------ 2116 + exit 0 2117 warning: File listed twice: /usr/include/clipper/ccp4 2118 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_map_io.h 2119 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_mtz_io.h 2120 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_mtz_types.h 2121 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_utils.h 2122 warning: File listed twice: /usr/include/clipper/cif ------------------------------------------------------------ As written on the wiki I quoted on my comment 15, %files entry ------------------------------------------------------------ %files %{_includedir}/clipper ------------------------------------------------------------ contains the directory %_includedir/clipper _and_ all files/directories/etc under %_includedir/clipper.

? Static linkage - The following command ------------------------------------------------------------ $ rpm -ql clipper | grep /usr/bin | xargs ldd -r ------------------------------------------------------------ shows no binaries in clipper rpm under %_bindir do not depend on libclipper.so. This seems rather strange.

For example, caniso binaries are created like: ------------------------------------------------------------ 1842 g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -fno-strict-aliasing -o caniso caniso.o ../clipper/mmdb/.libs/libclippermmdb.a ../clipper/cif/.libs/libclippercif.a ../clipper/cns/.libs/libclippercns.a ../clipper/minimol/.libs/libclipperminimol.a ../clipper/phs/.libs/libclipperphs.a ../clipper/ccp4/.libs/libclipperccp4.a -lgpp4 -lmmdb ../clipper/contrib/.libs/libclippercontrib.a ../clipper/core/.libs/libclippercore.a -lsrfftw -lsfftw -lm ------------------------------------------------------------ So these binaries use static libclipperXXXX.a. I guess these binaries should use system wide libclipper.so.

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

1:27 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #18 from Tim Fenn fenn@stanford.edu 2008-11-14 14:27:48 EDT --- (In reply to comment #17)

...

For -18:

(In reply to comment #16)

...
(In reply to comment #15)

...
...

Directory ownership issue

%_includedir/clipper is not owned by any packages ref:

Ah, thanks! fixed.

This time build.log says:

2116 + exit 0 2117 warning: File listed twice: /usr/include/clipper/ccp4 2118 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_map_io.h 2119 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_mtz_io.h 2120 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_mtz_types.h 2121 warning: File listed twice: /usr/include/clipper/ccp4/ccp4_utils.h 2122 warning: File listed twice: /usr/include/clipper/cif
As written on the wiki I quoted on my comment 15,
%files entry
%files %{_includedir}/clipper
contains the directory %_includedir/clipper _and_ all
files/directories/etc under %_includedir/clipper.

Sorry, I was rushing a bit - removed the extraneous entries.

...

? Static linkage

The following command

$ rpm -ql clipper | grep /usr/bin | xargs ldd -r
shows no binaries in clipper rpm under %_bindir do not depend
on libclipper.so. This seems rather strange.

fixed Makefile.am for the examples

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-19.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

15 Nov 15 Nov

9:42 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #19 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-11-15 10:42:00 EDT --- Created an attachment (id=323692) --> (https://bugzilla.redhat.com/attachment.cgi?id=323692) Patch to compile -19

Rebuild failed: http://koji.fedoraproject.org/koji/taskinfo?taskID=934459

The attached patch will fix this issue: http://koji.fedoraproject.org/koji/taskinfo?taskID=934517

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

9:43 a.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp changed:

What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-review? |fedora-review+

--- Comment #20 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-11-15 10:43:22 EDT --- Other things are okay.

------------------------------------------------------ This package (clipper) is APPROVED by mtasaka ------------------------------------------------------

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

5:42 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #21 from Tim Fenn fenn@stanford.edu 2008-11-15 18:42:16 EDT --- (In reply to comment #19)

...

Created an attachment (id=323692)

--> (https://bugzilla.redhat.com/attachment.cgi?id=323692) [details]

...

Patch to compile -19

Thanks, applied!

new spec: http://www.stanford.edu/~fenn/packs/clipper.spec new srpm: http://www.stanford.edu/~fenn/packs/clipper-2.0-20.f8.src.rpm

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

5:43 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #22 from Tim Fenn fenn@stanford.edu 2008-11-15 18:43:33 EDT --- New Package CVS Request ======================= Package Name: clipper Short Description: crystallographic object oriented library Owners: timfenn Branches: F-9 F-10 EL-5 InitialCC: timfenn

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

5:43 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Tim Fenn fenn@stanford.edu changed:

What |Removed |Added ---------------------------------------------------------------------------- Flag| |fedora-cvs?

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

16 Nov 16 Nov

2:32 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Kevin Fenzi kevin@tummy.com changed:

What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs? |fedora-cvs+

--- Comment #23 from Kevin Fenzi kevin@tummy.com 2008-11-16 15:32:05 EDT --- cvs done.

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

18 Nov 18 Nov

5:15 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

--- Comment #24 from Tim Fenn fenn@stanford.edu 2008-11-18 18:15:09 EDT --- cvs builds done, update request submitted to bodhi for F-9 and F-10.

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

Red Hat Bugzilla

7:26 p.m.

New subject: [Bug 435018] Review Request: clipper - crystallographic object oriented library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=435018

Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp changed:

--- Comment #25 from Mamoru Tasaka mtasaka@ioa.s.u-tokyo.ac.jp 2008-11-18 20:26:58 EDT --- Thank you.

-- Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

6089

Age (days ago)

6356

Last active (days ago)

package-review@lists.fedoraproject.org

35 comments

1 participants

tags (0)

participants (1)

Red Hat Bugzilla