Bug 236158 - Review Request: wise2 - Bioinformatics tools for comparison of biopolymers
Review Request: wise2 - Bioinformatics tools for comparison of biopolymers
Product: Fedora
Classification: Fedora
Component: Package Review (Show other bugs)
All Linux
medium Severity medium
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Assigned To: Parag AN(पराग)
Fedora Package Reviews List
Depends On:
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Reported: 2007-04-12 01:54 EDT by Alex Lancaster
Modified: 2015-02-16 09:18 EST (History)
1 user (show)

See Also:
Fixed In Version:
Doc Type: Bug Fix
Doc Text:
Story Points: ---
Clone Of:
Last Closed: 2007-04-24 01:50:14 EDT
Type: ---
Regression: ---
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oVirt Team: ---
RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: ---
panemade: fedora‑review+
limburgher: fedora‑cvs+

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Description Alex Lancaster 2007-04-12 01:54:58 EDT
Spec URL: http://allele5.biol.berkeley.edu/~alex/fedora/wise2.spec
SRPM URL: http://allele5.biol.berkeley.edu/~alex/fedora/wise2-2.2.0-1.src.rpm
Wise2 is a package focused on comparisons of biopolymers, commonly DNA
sequence and protein sequence.  A strength of Wise2 is the
comparison of DNA sequence at the level of its protein
translation. This comparison allows the simultaneous prediction of
gene structure with homology based alignment.

Parts of the code are licensed under a BSD-style license, the rest is under the GPL making the aggregate work GPL.
Comment 1 Ralf Corsepius 2007-04-12 03:07:31 EDT
+ make CC=gcc all
(cd base   ; make CC="gcc" CFLAGS="-c -O " libwisebase.a )
make[1]: Entering directory `/users/packman/src/rpms/BUILD/wise2.2.0/src/base'
gcc -c -O  wiseconfig.c
gcc -c -O  wisestring.c

=> package doesn't honour RPM_OPT_FLAGS
Comment 2 Alex Lancaster 2007-04-12 04:56:39 EDT
* Mon Apr 12 2007 Alex Lancaster <alexl@users.sourceforge.net> 2.2.0-2
- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius.

Spec URL: http://allele5.biol.berkeley.edu/~alex/fedora/wise2.spec
SRPM URL: http://allele5.biol.berkeley.edu/~alex/fedora/wise2-2.2.0-2.src.rpm

+ make CC=gcc 'CFLAGS=-c -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' all
(cd base   ; make CC="gcc" CFLAGS="-c -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" libwisebase.a )
Comment 3 Parag AN(पराग) 2007-04-23 07:24:35 EDT
+ package builds in mock (development i386).
+ rpmlint is silent for SRPM and for RPM.
+ source files match upstream url
0584240f77885e37528e99e64535ab60  wise2.2.0.tar.gz
+ package meets naming and packaging guidelines.
+ specfile is properly named, is cleanly written
+ Spec file is written in American English.
+ Spec file is legible.
+ dist tag is present.
+ build root is correct.
+ license is open source-compatible.
+ License text is included in package.
+ %doc is present.
+ BuildRequires are proper.
+ %clean is present.
+ package installed properly.
+ Macro use appears rather consistent.
+ Package contains code, not content.
+ no headers or static libraries.
+ no .pc file present.
+ no -devel subpackage
+ no .la files.
+ no translations are available
+ Does owns the directories it creates.
+ no scriptlets present.
+ no duplicates in %files.
+ file permissions are appropriate.
+ Provides: config(wise2) = 2.2.0-2.fc7
+ Requires: config(wise2) = 2.2.0-2.fc7 libc.so.6 libc.so.6(GLIBC_2.0)
libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4)
libc.so.6(GLIBC_2.4) libm.so.6 libm.so.6(GLIBC_2.0) rtld(GNU_HASH)

Comment 4 Alex Lancaster 2007-04-23 07:33:37 EDT
New Package CVS Request
Package Name: wise2
Short Description: Bioinformatics tools for comparison of biopolymers
Owners: alexl@users.sourceforge.net
Branches: FC-5 FC-6
Comment 5 Alex Lancaster 2007-04-24 01:50:14 EDT
Builds fine in all branches.  Closing.
Comment 6 Dominik 'Rathann' Mierzejewski 2015-02-15 12:04:40 EST
Package Change Request
Package Name: wise2
New Branches: el6 epel7
Owners: rathann
Comment 7 Gwyn Ciesla 2015-02-16 09:18:23 EST
Git done (by process-git-requests).

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