Red Hat Bugzilla – Bug 457038
Review Request: primer3 - PCR primer design tool
Last modified: 2008-10-30 08:55:35 EDT
Spec URL: http://pingou.fedorapeople.org/RPMs/primer3.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/primer3-1.1.4-1.fc9.src.rpm Description: Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.
build: http://koji.fedoraproject.org/koji/taskinfo?taskID=745087
- starting review - 1/ It would be fine to keep timestamps while converting README.txt to UTF8 2/ This package doesn't use our RPM_OPT_FLAGS gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 primer3_main.c 3/ It seems possible to build a Shared library : OLIGOTM_DYN_LIB = liboligotm.so.1.2.0 You can note that this library will probably need to be installed manually as oligotm.h will probably need the releated liboligotm.a (or .so) to be bundled in prism3-devel Do you know any dependent package to test primer3-devel ? I guess not all headers will be needed... 4/ Make check is usally done in a separate job control (before %clean) %check pushd src %{?_with_tests:make check} popd This will probably need to be conditionalized as some tests take time. (tested succeded on F-8 x86_64 local rpmbuild - so it's good) 5/ Why BuildRequires: perl ? This is in the default buildRequirement, but I wonder why you have added it ?
(In reply to comment #2) > 1/ It would be fine to keep timestamps while converting README.txt to UTF8 I am using now touch -r COPYING.txt README.txt after the conversion to UTF8. Is it fine ? > 2/ This package doesn't use our RPM_OPT_FLAGS > gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -DDPAL_MAX_ALIGN=36 > -DMAX_PRIMER_LENGTH=36 primer3_main.c Could you give me some insigth on how I can change this ? > 3/ It seems possible to build a Shared library : > OLIGOTM_DYN_LIB = liboligotm.so.1.2.0 > You can note that this library will probably need to be installed manually as > oligotm.h will probably need the releated liboligotm.a (or .so) to be bundled in > prism3-devel > Do you know any dependent package to test primer3-devel ? Actually, I do not know any. > I guess not all headers will be needed... I would say so to, but since I am not sure I prefered to put them all rather than miss one. > 4/ Make check is usally done in a separate job control (before %clean) > %check > pushd src > %{?_with_tests:make check} > popd added > This will probably need to be conditionalized as some tests take time. > (tested succeded on F-8 x86_64 local rpmbuild - so it's good) > 5/ Why BuildRequires: perl ? > This is in the default buildRequirement, but I wonder why you have added it ? It's the only dependency that I found on the website. I can removed it if it's there by default
There are the new files http://pingou.fedorapeople.org/RPMs/primer3.spec http://pingou.fedorapeople.org/RPMs/primer3-1.1.4-2.fc9.src.rpm %changelog * Wed Aug 06 2008 pingou <pingoufc4@yahoo.fr> 1.1.4-2 - Keep the timestamp in the README.txt - Change the CFLAG for the compilation - Remove BR perl
- README.txt convertion can be simplified. - you need to have export INIT_CFLAGS="%{optflags}" in the %build section - make test remains in the %build section. - non-standard perms for binaries, should be 755 It still seems strange if you don't install the .a or .so when you install some .h for the -devel package. Is it possible or relevant to build a shared onject library instead ?
(In reply to comment #5) > - README.txt convertion can be simplified. I have always done this in that way. Does it really matter ? I would prefer be consistent over my spec file. > - you need to have export INIT_CFLAGS="%{optflags}" in the %build section Done > - make test remains in the %build section. Done > - non-standard perms for binaries, should be 755 Done > It still seems strange if you don't install the .a or .so when you install some > .h for the -devel package. Is it possible or relevant to build a shared onject > library instead ? I have never done such sub-package could you point me to an example or so doc ? SPEC http://pingou.fedorapeople.org/RPMs/primer3.spec SRPM http://pingou.fedorapeople.org/RPMs/primer3-1.1.4-3.fc9.src.rpm
I corrected the make test to include the conditionnality --with tests does the tests (make test) defaults does not SPEC http://pingou.fedorapeople.org/RPMs/primer3.spec SRPM http://pingou.fedorapeople.org/RPMs/primer3-1.1.4-4.fc9.src.rpm
export INIT_CFLAGS="%{optflags} -fPIC -DPIC" make %{?_smp_mflags} liboligotm.so.1.2.0 make %{?_smp_mflags} make %{?_smp_mflags} primer3_core.dyn This will build a shared version of the library along with a binary linked with the shared library. Maybe -fPIC isn't needed on i386 for some little library (you need to test), but on x86_64, it is mandatory.
Ok I have removed the -devel package and I did not do the shared library because I do not know any project that needs those headers files. I am keeping this package as simple as possible. SPEC http://pingou.fedorapeople.org/RPMs/primer3.spec SRPM http://pingou.fedorapeople.org/RPMs/primer3-1.1.4-5.fc9.src.rpm
-------------------- This package (primer3) is APPROVED by me --------------------
New Package CVS Request ======================= Package Name: primer3 Short Description: PCR primer design tool Owners: pingou Branches: F-8 F-9 InitialCC:
cvs done.
primer3-1.1.4-5.fc9 has been submitted as an update for Fedora 9. http://admin.fedoraproject.org/updates/primer3-1.1.4-5.fc9
primer3-1.1.4-5.fc8 has been submitted as an update for Fedora 8. http://admin.fedoraproject.org/updates/primer3-1.1.4-5.fc8
primer3-1.1.4-5.fc9 has been pushed to the Fedora 9 stable repository. If problems still persist, please make note of it in this bug report.
primer3-1.1.4-5.fc8 has been pushed to the Fedora 8 stable repository. If problems still persist, please make note of it in this bug report.