[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Jun Aruga  changed:

   What|Removed |Added

 Resolution|DUPLICATE   |WONTFIX



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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Jun Aruga  changed:

   What|Removed |Added

 Status|POST|CLOSED
 Resolution|--- |DUPLICATE
Last Closed||2019-10-09 13:17:59



--- Comment #50 from Jun Aruga  ---
I close following ticket, as I can request the dist-git repository by my
account that has packager "user" role on Fedora.
https://bugzilla.redhat.com/show_bug.cgi?id=1759940

*** This bug has been marked as a duplicate of bug 1759940 ***

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Sam Nicholls  changed:

   What|Removed |Added

 Blocks|177841 (FE-NEEDSPONSOR) |201449 (FE-DEADREVIEW)



--- Comment #49 from Sam Nicholls  ---
Jun and I have discussed this off-thread and think this is likely the best way
forward.


Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=177841
[Bug 177841] Tracker: Review requests from new Fedora packagers who need a
sponsor
https://bugzilla.redhat.com/show_bug.cgi?id=201449
[Bug 201449] FE-DEADREVIEW -- Reviews stalled due to lack of submitter response
should be blocking this bug.
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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Zbigniew Jędrzejewski-Szmek  changed:

   What|Removed |Added

 CC||zbys...@in.waw.pl



--- Comment #48 from Zbigniew Jędrzejewski-Szmek  ---
Jan: I think you should open a new review ticket and close this one as
DEAD-REVIEW.
Sam's review request from 3 years ago is not enough for be sponsored as a
packager.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #47 from Jun Aruga  ---
> Did someone on devel say that's OK?

No. No response so far.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #46 from Jun Aruga  ---
I am asking if current htslib is valid on devel@ mailing list.
https://lists.fedoraproject.org/archives/list/de...@lists.fedoraproject.org/thread/WHZBVT3Y7TKYAEK6EXEY6L77W42T7LJX/

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #45 from Jun Aruga  ---
Dave, how you think about the fact of the libraries that is same pattern with
upstream htslib?
I do not think that your concern is valid considering the fact at the moment.

```
$ ls -l /usr/lib64/libz.so*
lrwxrwxrwx 1 root root 14 Aug 15 09:30 /usr/lib64/libz.so ->
libz.so.1.2.11*
lrwxrwxrwx 1 root root 14 Aug 15 09:30 /usr/lib64/libz.so.1 ->
libz.so.1.2.11*
-rwxr-xr-x 1 root root 128904 Aug 15 09:30 /usr/lib64/libz.so.1.2.11*

$ rpm -qf /usr/lib64/libz.so
zlib-devel-1.2.11-17.fc30.x86_64
$ rpm -qf /usr/lib64/libz.so.1
zlib-1.2.11-17.fc30.x86_64
$ rpm -qf /usr/lib64/libz.so.1.2.11
zlib-1.2.11-17.fc30.x86_64
```

Please join to discuss with us on following page, if you would like to change
the reviewer's decision.
https://github.com/samtools/htslib/issues/932#issuecomment-537694737

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #44 from Jun Aruga  ---
> https://fedoraproject.org/wiki/How_to_get_sponsored_into_the_packager_group#Submitting_quality_new_packages
> When you open your review request in bugzilla, you should block the 
> FE-NEEDSPONSOR tracking bug, that way all of the sponsors will be able to see 
> your sponsorship request. 

I blocked "FE-NEEDSPONSOR" following above document.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Jun Aruga  changed:

   What|Removed |Added

 Blocks||177841 (FE-NEEDSPONSOR)




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=177841
[Bug 177841] Tracker: Review requests from new Fedora packagers who need a
sponsor
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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #43 from Jun Aruga  ---
> I don't think this should have been waved through with the shared libraries 
> in that state.
> It may or may not strictly be incorrect to link libhts.so.1.9 with soname 
> libhts.so.2, but it's at least misleading when someone familiar with ELF 
> versioning looks at a program's dynamic linkage or what's in libdir.  Did 
> someone on devel say that's OK?

I do not say that you are wrong. I asked you to discuss on the htslib upstream,
or to send a pull-request on comment 29.
https://bugzilla.redhat.com/show_bug.cgi?id=1326504#c29

Because I am not familiar with the ELF, and I do not have an ability to fix the
spec file aligning your requests.
I thought that you declined the options because you did not have a time.
If you act to make your idea real, the situation moves forward. But otherwise
not.

By the way, my account's role is just "user", not "sponsor". I can not be a
sponsor of Sam at the moment.
So, I want to ask someone to be a sponsor of Sam.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #42 from Dave Love  ---
I don't think this should have been waved through with the shared libraries in
that state.
It may or may not strictly be incorrect to link libhts.so.1.9 with soname
libhts.so.2, but it's at least misleading when someone familiar with ELF
versioning looks at a program's dynamic linkage or what's in libdir.  Did
someone on devel say that's OK?

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #41 from Jun Aruga  ---
Hi Sam, 

Sorry, I forget the possibility for you.
You need to get a sponsor from other fedora users before requesting the
repository.
I can be a sponsor for you. Let me check the actual steps.

> https://fedoraproject.org/wiki/Package_Review_Process#Review_Process
>
> If you do not have any package already in Fedora, this means you need a 
> sponsor and to add FE-NEEDSPONSOR (Bugzilla id:177841) to the bugs being 
> blocked by your review request. For more information read the How to get 
> sponsored into the packager group wiki page.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #40 from Sam Nicholls  ---
I got:
> The Bugzilla bug's review is approved by a user that is not a packager

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #39 from Sam Nicholls  ---
Hi Jun,
Thanks for your patch. I've requested the reviews as per your instructions:

$ fedpkg request-branch --repo htslib f31
$ fedpkg request-repo htslib 1326504
https://pagure.io/releng/fedora-scm-requests/issue/17943
$ fedpkg request-branch --repo htslib f31
https://pagure.io/releng/fedora-scm-requests/issue/17944
$ fedpkg request-branch --repo htslib f30
https://pagure.io/releng/fedora-scm-requests/issue/17945
$ fedpkg request-branch --repo htslib f29
https://pagure.io/releng/fedora-scm-requests/issue/17946

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #38 from Jun Aruga  ---
> Yeah I was fearing this, alternatively create your own review request and 
> close this bug as duplicate and block this bug as FE-DEADREVIEW. If Sam 
> request the package, he will be the maintainer and not you.

Thanks for sharing the alternative way. I am okay for that Sam will be
maintainer.
Then I can ask him for me to be a co-maintainer.
I wait him today. tomorrow, if there is no response from him, I will do the
alternative way.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #37 from Robert-André Mauchin  ---
(In reply to Jun Aruga from comment #36)
> Above fedora-scm requests are declined, because I am not the creator this
> bugzilla ticket.
> I am asking Sam to request the repository and branches here.
> https://github.com/SamStudio8/htslib-pkg/pull/4

Yeah I was fearing this, alternatively create your own review request and close
this bug as duplicate and block this bug as FE-DEADREVIEW. If Sam request the
package, he will be the maintainer and not you.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #36 from Jun Aruga  ---
Above fedora-scm requests are declined, because I am not the creator this
bugzilla ticket.
I am asking Sam to request the repository and branches here.
https://github.com/SamStudio8/htslib-pkg/pull/4

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #35 from Jun Aruga  ---
Hi Robert-André Mauchin

Thanks for your review! Now I requested the repository and the branches by
"fedpkg request-repo" and "fedpkg request-branch", and waiting they will be
created.
https://fedoraproject.org/wiki/Package_Review_Process#Review_Process

$ fedpkg request-repo htslib 1326504
https://pagure.io/releng/fedora-scm-requests/issue/17763
$ fedpkg request-branch --repo htslib f31
https://pagure.io/releng/fedora-scm-requests/issue/17764
$ fedpkg request-branch --repo htslib f30
https://pagure.io/releng/fedora-scm-requests/issue/17765
$ fedpkg request-branch --repo htslib f29
https://pagure.io/releng/fedora-scm-requests/issue/17766

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Robert-André Mauchin  changed:

   What|Removed |Added

 Status|ASSIGNED|POST
 CC||zebo...@gmail.com
   Assignee|bl...@verdurin.com  |zebo...@gmail.com
  Flags|fedora-review?  |fedora-review+
   |needinfo?(bl...@verdurin.co |
   |m)  |



--- Comment #34 from Robert-André Mauchin  ---
(In reply to Jun Aruga from comment #23)
> Hi Dave,
> 
> I updated the spec file and SRPM file for below URLs.
> 
> > Spec URL: 
> > https://raw.githubusercontent.com/junaruga/htslib-pkg/hotfix/review/htslib.spec
> > SRPM URL: 
> > https://github.com/junaruga/htslib-pkg/blob/hotfix/review/htslib-1.9-1.fc32.src.rpm?raw=true
> 
> > I confess I ignore those.  I'm not at all sure it's sensible as a
> general stipulation.
> 
> I just keep it in my mind at the moment. It's not an error from rpmlint, but
> warning.
> 
> > Ah.  That probably merits a bug report.
> 
> Sure. I sent email to le...@lists.fedoraproject.org to ask the question
> about how to set Expat license. It looks Expat license is MIT license. Then
> someone replied Expat was same with MIT.
> https://lists.fedoraproject.org/archives/list/le...@lists.fedoraproject.org/
> thread/C5AHVIW3F6LF5CYLR2PSHNANFYKP327P/
> 
> > It's simply wrong.  .so.1.9 and .so.2 imply incompatible ABIs. ...
> 
> > so you probably don't want to follow it.
> 
> I simply did not understand it well. This is my first experience for RPM
> packaging of "foolib".
> I like to follow Fedora's rule as much as possible.
> 
> I defined `%global so_version 0.1` to use it like libhts.so.0.1
> I also opened the ticket to ask it on upstream.
> https://github.com/samtools/htslib/issues/932
> 
> > Also, the advice is to glob man pages in %files
> 
> done
> 
> > -fPIC is redundant in CFLAGS as it comes from the compiler specs.
> 
> done
> 
> > You should also set LDFLAGS to %build_ldflags or similar.
> 
> done
> 
> 
> What I want to ask you is when I install the binary RPM
> htslib-1.9-1.fc32.x86_64.rpm, `/usr/lib64/libhts.so.2` is installed. I do
> not know why.
> 
> 
> ```
> $ mock -i htslib-1.9-1.fc32.x86_64.rpm
> 
>  sh-5.0# ls /usr/lib64/libhts*
> /usr/lib64/libhts.so.0.1  /usr/lib64/libhts.so.2
> 
>  sh-5.0# rpm -ql /usr/lib64/libhts.so.2
> package /usr/lib64/libhts.so.2 is not installed
> ```
> 
> I ran `rm -f libhts.so.2` in %install section, also had to set `%exclude
> %{_libdir}/libhts.so.2` in %files.
> And I also below error from rpmlint might be related to this issue.
> 
> ```
> htslib.x86_64: E: no-ldconfig-symlink /usr/lib64/libhts.so.0.1
> The package should not only include the shared library itself, but also the
> symbolic link which ldconfig would produce. (This is necessary, so that the
> link gets removed by rpm automatically when the package gets removed, even if
> for some reason ldconfig would not be run at package postinstall phase.)
> ```
> 
> Do you know why?
> 
> Here is the scratch build.
> Scratch build: https://koji.fedoraproject.org/koji/taskinfo?taskID=37811950
> 
> Thank you for your patience.
> I am learning a lot from this reviewing process.

Package approved.


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]: If your application is a C or C++ application you must list a
 BuildRequires against gcc, gcc-c++ or clang.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig not called in %post and %postun for Fedora 28 and later.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

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: "Unknown or generated", "Expat License BSD 3-clause "New" or
 "Revised" License", "Expat License", "Public domain", "BSD 3-clause
 "New" or "Revised" License", "FSF All Permissive License". 107 files
 have unknown license. Detailed output of licensecheck in
 /home/bob/packaging/review/htslib/review-htslib/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[x]: If the package is under multiple licenses, the licensing breakdown
 must be documented in the spec.
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package 

[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #33 from Jun Aruga  ---
Adam, if you do not have a time to review, perhaps I can be the reviewer. In
case, Sam is reporter, and I can change the fedora-review flag to "+".

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Jun Aruga  changed:

   What|Removed |Added

  Flags||fedora-review?
   ||needinfo?(bl...@verdurin.co
   ||m)



--- Comment #32 from Jun Aruga  ---
Hi Dave,

> Sorry, it isn't my review to approve, and I can't spend much time on it.
I'm happy to be corrected about shared libraries by someone authoritative in
Fedora, and I don't know what htslib's policy is on ABI changes and whether the
ELF semantics actually do follow the upstream version number.

Yeah. Alright. Please do "I'm happy to be corrected about shared libraries by
someone authoritative in Fedora", and let me know. 


Hi Adam

https://fedoraproject.org/wiki/Package_Review_Process#Review_Process

> if you want to formally review the package, set the fedora-review flag to ? 
> and assign the bug to yourself.

I changed the flag to ? by following the the review process.
I am "packager" in the document. I already inherited from original reporter
Sam. [1]

> ACCEPT - If the package is good, set the fedora-review flag to +

I want to ask you to change "the fedora-review flag to +" from "?" if you are
okay.

[1] https://github.com/SamStudio8/htslib-pkg/pull/3#issuecomment-529875690

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Dave Love  changed:

   What|Removed |Added

  Flags|needinfo?(dave.love@manches |
   |ter.ac.uk)  |



--- Comment #31 from Dave Love  ---
Sorry, it isn't my review to approve, and I can't spend much time on it.
I'm happy to be corrected about shared libraries by someone authoritative in
Fedora, and I don't know what htslib's policy is on ABI changes and whether the
ELF semantics actually do follow the upstream version number.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Jun Aruga  changed:

   What|Removed |Added

  Flags||needinfo?(dave.love@manches
   ||ter.ac.uk)



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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #30 from Jun Aruga  ---
> Now I see not see the issue on my latest spec file.

Sorry typo. "Now I do not see the issue on my latest spec file." is correct.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #29 from Jun Aruga  ---
> Nor do I, but it shouldn't be.

Now I see not see the issue on my latest spec file.

> If you're not convinced, I should ask on the devel list, or at Red Hat,
where there are libc maintainers.

Yes, please. Thank you.

Have you read below conversation?
There are 2 patterns both glib pattern and zlib pattern.
https://github.com/samtools/htslib/issues/932

Could you send pull-request to junaruga/htslib-pkg hotfix/review branch as you
like?
Or just show me diff info?

https://github.com/junaruga/htslib-pkg/tree/hotfix/review
$ git clone g...@github.com:junaruga/htslib-pkg.git
$ cd htslib-pkg
$ git checkout hotfix/review

I am okay to follow your preference to finish the reviewing process. Because we
can change spec file later if something needs to be changed after your
clarification. As there are blocker tickets waiting this ticket, I want to
finish it as soon as possible.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #28 from Dave Love  ---
(In reply to Jun Aruga from comment #24)
> I got a great feedback from a person in the upstream on the ticket.
> The htslib's so version rule is following Fedora's glibc's rule.

glibc follows the normal rules about sonames, and has a policy to preserve
backwards compatibility, so the major version is constant.

> So, can we use the built so files without changing so version, can't we?
> If you like, I will revert my modification for %make_build and %make_install
> line.
> 
> ```
> $ rpm -qf /usr/lib64/libc-2.29.so 
> glibc-2.29-15.fc30.x86_64
> 
> $ rpm -qf /usr/lib64/libc.so.6 
> glibc-2.29-15.fc30.x86_64
> 
> $ rpm -qf /usr/lib64/libc.so
> glibc-devel-2.29-15.fc30.x86_64
> 
> $ ls -l /usr/lib64/libc[-.]*
> -rwxr-xr-x 1 root root  6699224 Jun  6 14:09 /usr/lib64/libc-2.29.so*
> -rw-r--r-- 1 root root 16258354 Jun  6 14:10 /usr/lib64/libc.a
> -rw-r--r-- 1 root root  253 Jun  6 13:55 /usr/lib64/libc.so
> lrwxrwxrwx 1 root root   12 Jun  6 13:55 /usr/lib64/libc.so.6 ->
> libc-2.29.so*

The soname is libc.so.6, and there isn't a libc.so..
If you're not convinced, I should ask on the devel list, or at Red Hat,
where there are libc maintainers.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #27 from Dave Love  ---
(In reply to Jun Aruga from comment #23)
> What I want to ask you is when I install the binary RPM
> htslib-1.9-1.fc32.x86_64.rpm, `/usr/lib64/libhts.so.2` is installed. I do
> not know why.

Nor do I, but it shouldn't be.

> htslib.x86_64: E: no-ldconfig-symlink /usr/lib64/libhts.so.0.1

Don't take rpmlint too seriously.  The link should be in the devel package.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #26 from Jun Aruga  ---
Spec URL:
https://raw.githubusercontent.com/junaruga/htslib-pkg/hotfix/review/htslib.spec
SRPM URL:
https://github.com/junaruga/htslib-pkg/blob/hotfix/review/htslib-1.9-1.fc32.src.rpm?raw=true

I updated the spec and SRPM files again.

> I renamed libhts-so.1.9 to libhts-1.9.so asking the question to the upstream 
> here https://github.com/samtools/htslib/issues/932#issuecomment-536212327 to 
> align glic(libc)'s style.

I changed again. Now using upstream libraries directly without renaming.
See https://github.com/samtools/htslib/issues/932#issuecomment-537694737
zlib on Fedora is same pattern with htslib.
I think htslib is correct.

We can update the Fedora guideine line later.
https://docs.fedoraproject.org/en-US/packaging-guidelines/#_downstream_so_name_versioning


* Koji scratch build: ok
https://koji.fedoraproject.org/koji/taskinfo?taskID=38010659
* Test to install RPMs: ok
* rpmlint: ok, as I mentioned we can fix below warning later, as this ticket
blocks other tickets right now.

```
htslib.x86_64: W: shared-lib-calls-exit /usr/lib64/libhts.so.1.9
exit@GLIBC_2.2.5
This library package calls exit() or _exit(), probably in a non-fork()
context. Doing so from a library is strongly discouraged - when a library
function calls exit(), it prevents the calling program from handling the 
error, reporting it to the user, closing files properly, and cleaning up any 
state that the program has. It is preferred for the library to return an
actual error code and let the calling program decide how to handle the 
situation.
```

As I assume that you are busy now, I will ask people to review on devel@
mailing list. :)

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #25 from Jun Aruga  ---
> Spec URL: 
> https://raw.githubusercontent.com/junaruga/htslib-pkg/hotfix/review/htslib.spec
> SRPM URL: 
> https://github.com/junaruga/htslib-pkg/blob/hotfix/review/htslib-1.9-1.fc32.src.rpm?raw=true

Hi I updated the htslib.spec and SRPM file.

I renamed libhts-so.1.9 to libhts-1.9.so asking the question to the upstream
here https://github.com/samtools/htslib/issues/932#issuecomment-536212327 to
align glic(libc)'s style.

```
 sh-5.0# ls -l /usr/lib64/libhts*
-rwxr-xr-x 1 root root 759680 Sep 28 20:29 /usr/lib64/libhts-1.9.so
lrwxrwxrwx 1 root root 13 Sep 28 20:29 /usr/lib64/libhts.so ->
libhts-1.9.so
lrwxrwxrwx 1 root root 13 Sep 28 20:29 /usr/lib64/libhts.so.2 ->
libhts-1.9.so
```

On my local Fedora 30 environment.

```
$ ls -l /usr/lib64/libc[-.]*
-rwxr-xr-x 1 root root  6699224 Jun  6 14:09 /usr/lib64/libc-2.29.so*
-rw-r--r-- 1 root root 16258354 Jun  6 14:10 /usr/lib64/libc.a
-rw-r--r-- 1 root root  253 Jun  6 13:55 /usr/lib64/libc.so
lrwxrwxrwx 1 root root   12 Jun  6 13:55 /usr/lib64/libc.so.6 ->
libc-2.29.so*
```

I think this situation is to solve the concern "It's simply wrong.  .so.1.9 and
.so.2 imply incompatible ABIs."

* rpmlint: ok.
* Test to install binary RPMs: ok
* Scratch build: ok
https://koji.fedoraproject.org/koji/taskinfo?taskID=37915859

Could you review again? Thanks.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #24 from Jun Aruga  ---
Hi Dave,

> I defined `%global so_version 0.1` to use it like libhts.so.0.1
> I also opened the ticket to ask it on upstream.
> https://github.com/samtools/htslib/issues/932

I got a great feedback from a person in the upstream on the ticket.
The htslib's so version rule is following Fedora's glibc's rule.
So, can we use the built so files without changing so version, can't we?
If you like, I will revert my modification for %make_build and %make_install
line.

```
$ rpm -qf /usr/lib64/libc-2.29.so 
glibc-2.29-15.fc30.x86_64

$ rpm -qf /usr/lib64/libc.so.6 
glibc-2.29-15.fc30.x86_64

$ rpm -qf /usr/lib64/libc.so
glibc-devel-2.29-15.fc30.x86_64

$ ls -l /usr/lib64/libc[-.]*
-rwxr-xr-x 1 root root  6699224 Jun  6 14:09 /usr/lib64/libc-2.29.so*
-rw-r--r-- 1 root root 16258354 Jun  6 14:10 /usr/lib64/libc.a
-rw-r--r-- 1 root root  253 Jun  6 13:55 /usr/lib64/libc.so
lrwxrwxrwx 1 root root   12 Jun  6 13:55 /usr/lib64/libc.so.6 ->
libc-2.29.so*
```

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Lumír Balhar  changed:

   What|Removed |Added

 Blocks||1738176




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1738176
[Bug 1738176] samtools depends on Python 2
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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #23 from Jun Aruga  ---
Hi Dave,

I updated the spec file and SRPM file for below URLs.

> Spec URL: 
> https://raw.githubusercontent.com/junaruga/htslib-pkg/hotfix/review/htslib.spec
> SRPM URL: 
> https://github.com/junaruga/htslib-pkg/blob/hotfix/review/htslib-1.9-1.fc32.src.rpm?raw=true

> I confess I ignore those.  I'm not at all sure it's sensible as a
general stipulation.

I just keep it in my mind at the moment. It's not an error from rpmlint, but
warning.

> Ah.  That probably merits a bug report.

Sure. I sent email to le...@lists.fedoraproject.org to ask the question about
how to set Expat license. It looks Expat license is MIT license. Then someone
replied Expat was same with MIT.
https://lists.fedoraproject.org/archives/list/le...@lists.fedoraproject.org/thread/C5AHVIW3F6LF5CYLR2PSHNANFYKP327P/

> It's simply wrong.  .so.1.9 and .so.2 imply incompatible ABIs. ...

> so you probably don't want to follow it.

I simply did not understand it well. This is my first experience for RPM
packaging of "foolib".
I like to follow Fedora's rule as much as possible.

I defined `%global so_version 0.1` to use it like libhts.so.0.1
I also opened the ticket to ask it on upstream.
https://github.com/samtools/htslib/issues/932

> Also, the advice is to glob man pages in %files

done

> -fPIC is redundant in CFLAGS as it comes from the compiler specs.

done

> You should also set LDFLAGS to %build_ldflags or similar.

done


What I want to ask you is when I install the binary RPM
htslib-1.9-1.fc32.x86_64.rpm, `/usr/lib64/libhts.so.2` is installed. I do not
know why.


```
$ mock -i htslib-1.9-1.fc32.x86_64.rpm

 sh-5.0# ls /usr/lib64/libhts*
/usr/lib64/libhts.so.0.1  /usr/lib64/libhts.so.2

 sh-5.0# rpm -ql /usr/lib64/libhts.so.2
package /usr/lib64/libhts.so.2 is not installed
```

I ran `rm -f libhts.so.2` in %install section, also had to set `%exclude
%{_libdir}/libhts.so.2` in %files.
And I also below error from rpmlint might be related to this issue.

```
htslib.x86_64: E: no-ldconfig-symlink /usr/lib64/libhts.so.0.1
The package should not only include the shared library itself, but also the
symbolic link which ldconfig would produce. (This is necessary, so that the
link gets removed by rpm automatically when the package gets removed, even if
for some reason ldconfig would not be run at package postinstall phase.)
```

Do you know why?

Here is the scratch build.
Scratch build: https://koji.fedoraproject.org/koji/taskinfo?taskID=37811950

Thank you for your patience.
I am learning a lot from this reviewing process.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #22 from Dave Love  ---
> A test for rpmlint. There is below warning. But I like to postpone to fix it.
> 
> ```
> htslib.x86_64: W: shared-lib-calls-exit /usr/lib64/libhts.so.1.9

I confess I ignore those.  I'm not at all sure it's sensible as a
general stipulation.

> > * licensecheck says Expat rather than MIT -- I haven't checked
> 
> There is no "Expat" in the short name list used as "License:"'s value.
> https://fedoraproject.org/wiki/Licensing:Main?rd=Licensing#SoftwareLicenses
> 
> Also below package setting "MIT" is actually detected as "Expat" by
> licensecheck command.
> https://src.fedoraproject.org/rpms/golang-uber-zap/blob/master/f/golang-uber-
> zap.spec#_33
> 
> I think "MIT" is fine.

Ah.  That probably merits a bug report.

> `make` command creates libhts.so (actual so file) and libhts.so.2 (symbolic
> link to libhts.so) on the current directory.
> But `make install prefix=$(pwd)/dist` creates below files soname:
> libhts.so.1.9 and symbolic links: libhts.so and libhts.so.2. libhts.so.1.9
> is the actual soname used in the binary RPM file.
> 
> ```
> $ ls -l dist/lib/
> total 10576
> -rw-r--r-- 1 jaruga jaruga 7165054 Sep 15 21:54 libhts.a
> lrwxrwxrwx 1 jaruga jaruga  13 Sep 15 22:01 libhts.so -> libhts.so.1.9
> -rw-r--r-- 1 jaruga jaruga 3653800 Sep 15 21:55 libhts.so.1.9
> lrwxrwxrwx 1 jaruga jaruga  13 Sep 15 22:01 libhts.so.2 -> libhts.so.1.9
> drwxr-xr-x 2 jaruga jaruga4096 Sep 15 22:01 pkgconfig/
> ```
> 
> Do you have any concerns about this situation?
> I suppose that current situation is no problem.

It's simply wrong.  .so.1.9 and .so.2 imply incompatible ABIs.  Using
1.9 suggests that it's doing the wrong thing anyhow, by using the
software version, not the ABI version, so you probably don't want to
follow it.  Without investigating, I don't know whether it would be
best to use .so.1 or .so.2 in the soname.  Then the spec should use
that explicitly in %files, not a glob, to be proof against inadvertent
changes.  For packaging info see
https://docs.fedoraproject.org/en-US/packaging-guidelines/#_downstream_so_name_versioning

Also, the advice is to glob man pages in %files 
.

If you use %make_build, it includes smp_mflags, so remove that.

-fPIC is redundant in CFLAGS as it comes from the compiler specs.  You
should also set LDFLAGS to %build_ldflags or similar.

Hope that helps.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #21 from Dave Love  ---
(In reply to Adam Huffman from comment #16)
> Dave - I could, but I'm rather out of practice.
> Seems like you're more up to date with the latest guidelines than I am...

I can have another look at the package and comment, but it is assigned to you,
and I'd prefer more of a bioinformatics eye on it.  I'm not in a good position
to exercise such things.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #20 from Jun Aruga  ---
Hi Dave,

Here is the updated spec file and srpm file after your reviewing.

Spec URL:
https://raw.githubusercontent.com/junaruga/htslib-pkg/hotfix/review/htslib.spec
SRPM URL:
https://github.com/junaruga/htslib-pkg/blob/hotfix/review/htslib-1.9-1.fc32.src.rpm?raw=true

Koji scratch build:
https://koji.fedoraproject.org/koji/taskinfo?taskID=37675570
A test to install binary RPMs: ok
A test for rpmlint. There is below warning. But I like to postpone to fix it.

```
htslib.x86_64: W: shared-lib-calls-exit /usr/lib64/libhts.so.1.9
exit@GLIBC_2.2.5
This library package calls exit() or _exit(), probably in a non-fork()
context. Doing so from a library is strongly discouraged - when a library
function calls exit(), it prevents the calling program from handling the-
error, reporting it to the user, closing files properly, and cleaning up any-
state that the program has. It is preferred for the library to return an
actual error code and let the calling program decide how to handle the-
situation.
```

Below is the response for your review.

> * licensecheck says Expat rather than MIT -- I haven't checked

There is no "Expat" in the short name list used as "License:"'s value.
https://fedoraproject.org/wiki/Licensing:Main?rd=Licensing#SoftwareLicenses

Also below package setting "MIT" is actually detected as "Expat" by
licensecheck command.
https://src.fedoraproject.org/rpms/golang-uber-zap/blob/master/f/golang-uber-zap.spec#_33

I think "MIT" is fine.

> * You could use %make_build in %build

done.

> * Remove the obsolete rm -rf from %install

done

> * To support EPEL, use %ldconfig_scriptlets instead of %post...

done.

I found a good example for that.
https://src.fedoraproject.org/rpms/libmodulemd/c/75a7af962341becaa6a7076e0b1e68c874acc7f9

> * The library needs sorting out.  Its soname is libhts.so.2, but
  it's installed as libhts.so.1.9 with a symlink to libhts.so.2.  I
  haven't checked what's going on.  The %files entry for it should
  be libhts.so.2*, so you know if it changes.  If the version is
  actually taken from the release version -- I dont know -- it
  shouldn't be, and could be set to 0 for Fedora.

I checked the upstream's behavior.

```
$ git clone g...@github.com:samtools/htslib.git
$ cd htslib
$ git checkout 1.9
$ make
$ make install prefix=$(pwd)/dist
```

`make` command creates libhts.so (actual so file) and libhts.so.2 (symbolic
link to libhts.so) on the current directory.
But `make install prefix=$(pwd)/dist` creates below files soname: libhts.so.1.9
and symbolic links: libhts.so and libhts.so.2. libhts.so.1.9 is the actual
soname used in the binary RPM file.

```
$ ls -l dist/lib/
total 10576
-rw-r--r-- 1 jaruga jaruga 7165054 Sep 15 21:54 libhts.a
lrwxrwxrwx 1 jaruga jaruga  13 Sep 15 22:01 libhts.so -> libhts.so.1.9
-rw-r--r-- 1 jaruga jaruga 3653800 Sep 15 21:55 libhts.so.1.9
lrwxrwxrwx 1 jaruga jaruga  13 Sep 15 22:01 libhts.so.2 -> libhts.so.1.9
drwxr-xr-x 2 jaruga jaruga4096 Sep 15 22:01 pkgconfig/
```

Do you have any concerns about this situation?
I suppose that current situation is no problem.

And as an additional change, as Makefile "install" task includes "install-so"
task, I removed "make "install-so" command line in htslib.spec. "make install"
is good enough.

Thanks!

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #19 from Jun Aruga  ---
> By the way, as I failed to run `fedora-review -b 1326504`, I reported opening 
> the ticket to fedora-review: 
> https://bugzilla.redhat.com/show_bug.cgi?id=1650620 .

Mistake. This URL. https://bugzilla.redhat.com/show_bug.cgi?id=1751630

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #18 from Jun Aruga  ---
Created attachment 1614420
  --> https://bugzilla.redhat.com/attachment.cgi?id=1614420=edit
review.txt by fedora-review command

I attach review.txt file that is the result of the fedora-review command.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #17 from Jun Aruga  ---
Dave, Adam thanks for the reviewing.

By the way, as I failed to run `fedora-review -b 1326504`, I reported opening
the ticket to fedora-review:
https://bugzilla.redhat.com/show_bug.cgi?id=1650620 .
`fedora-review -n /path/to/htslib-1.9-1.fc32.src.rpm --rpm-spec` worked.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Adam Huffman  changed:

   What|Removed |Added

  Flags|needinfo?(samstudio8@gmail. |
   |com)|
   |needinfo?(bl...@verdurin.co |
   |m)  |



--- Comment #16 from Adam Huffman  ---
Dave - I could, but I'm rather out of practice.
Seems like you're more up to date with the latest guidelines than I am...

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Dave Love  changed:

   What|Removed |Added

  Flags||needinfo?(bl...@verdurin.co
   ||m)



--- Comment #15 from Dave Love  ---
Adam: can you still review this?

From a quick look:

licensecheck says Expat rather than MIT -- I haven't checked

You could use %make_build in %build

Remove the obsolete rm -rf from %install

To support EPEL, use %ldconfig_scriptlets instead of %post...

The library needs sorting out.  Its soname is libhts.so.2, but
it's installed as libhts.so.1.9 with a symlink to libhts.so.2.  I
haven't checked what's going on.  The %files entry for it should
be libhts.so.2*, so you know if it changes.  If the version is
actually taken from the release version -- I dont know -- it
shouldn't be, and could be set to 0 for Fedora.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #14 from Jun Aruga  ---
> Hi I updated htslib.spec upgrading it to the latest version 1.9.
Here is the pull-request.
> https://github.com/SamStudio8/htslib-pkg/pull/3

The pull-request was merged.
Here are new URLs.

Spec URL:
https://raw.githubusercontent.com/SamStudio8/htslib-pkg/master/htslib.spec
SRPM URL:
https://github.com/SamStudio8/htslib-pkg/blob/master/htslib-1.9-1.fc32.src.rpm?raw=true

Koji scratch build:
https://koji.fedoraproject.org/koji/taskinfo?taskID=37509125

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #13 from Jun Aruga  ---
Hi I updated htslib.spec upgrading it to the latest version 1.9.
Here is the pull-request.
https://github.com/SamStudio8/htslib-pkg/pull/3

Here is the scratch build.
https://koji.fedoraproject.org/koji/taskinfo?taskID=37504280

Below are the files on
https://github.com/junaruga/htslib-pkg/tree/feature/update-to-1.9 .

Spec URL:
https://raw.githubusercontent.com/junaruga/htslib-pkg/feature/update-to-1.9/htslib.spec
SRPM URL:
https://github.com/junaruga/htslib-pkg/blob/feature/update-to-1.9/htslib-1.9-1.fc32.src.rpm?raw=true

Could you review the pull-request or Spec/SRPM URLs?
Thanks.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #12 from Jun Aruga  ---
What is the current items to fix for below htslib.spec?
https://github.com/SamStudio8/htslib-pkg/blob/master/htslib.spec

Someone, could you summarize it?

I can send a pull-request to SamStudio8/htslib-pkg repository, or I just can
share my updated htslib.spec.
As current htslib latest version is 1.9, I like updating it to 1.9.
https://github.com/samtools/htslib

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats ( required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #11 from Adam Huffman  ---
Hi Sam,

Any news on this?

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats ( required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Adam Huffman  changed:

   What|Removed |Added

 CC||samstud...@gmail.com
  Flags||needinfo?(samstudio8@gmail.
   ||com)



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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats ( required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #10 from Adam Huffman  ---
(In reply to Sam Nicholls from comment #9)
> Hi Dave,
> With regards to the source URL, Adam's PR
> (https://github.com/SamStudio8/htslib-pkg/pull/1), notes that an issue with
> rpmlint has been reported upstream for invalid-url errors. Otherwise I'm
> stumped!
> 
> I've added an appropriate comment and formatted the changelog appropriately
> (although I can't seem to shake the no-version-in-last-changelog).

Yes, I was just about to post a link to the two relevant BZ reports:

https://bugzilla.redhat.com/show_bug.cgi?id=1326855

https://bugzilla.redhat.com/show_bug.cgi?id=1328319

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats ( required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #9 from Sam Nicholls  ---
Hi Dave,
With regards to the source URL, Adam's PR
(https://github.com/SamStudio8/htslib-pkg/pull/1), notes that an issue with
rpmlint has been reported upstream for invalid-url errors. Otherwise I'm
stumped!

I've added an appropriate comment and formatted the changelog appropriately
(although I can't seem to shake the no-version-in-last-changelog).

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats ( required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #8 from Adam Huffman  ---
(In reply to Dave Love from comment #7)
> (In reply to Sam Nicholls from comment #6)
> > Could you describe the issue with the source URL
> > (https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.
> > bz2 works for me, for example).
> 
> I don't know what I saw at the tine, but now I see from rpmlint:
> 
> htslib.spec: W: invalid-url Source0:
> https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.
> bz2 HTTP Error 403: Forbidden
> 
> I don't know why, since that URL does work with wget, and don't have time to
> debug it.

I saw this with a different package. It's to do with the way Github handle
encryption, which they said they're unlikely to change, when I reported it to
them.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats ( required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #7 from Dave Love  ---
(In reply to Sam Nicholls from comment #6)
> Could you describe the issue with the source URL
> (https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.
> bz2 works for me, for example).

I don't know what I saw at the tine, but now I see from rpmlint:

htslib.spec: W: invalid-url Source0:
https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2
HTTP Error 403: Forbidden

I don't know why, since that URL does work with wget, and don't have time to
debug it.

> With regards to bzip2/lzma, I was under the impression the support is a
> little shaky at this time (see
> https://github.com/samtools/htslib/blob/develop/Makefile#L36-38) but support
> is optional, not required, for CRAM.

Fair enough, but worth a comment in the spec.

The changelog is garbled.  You should use rpmlint, or preferably fedora-review
(which includes rpmlint) which the package has basically to pass anyhow.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats ( required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #6 from Sam Nicholls  ---
Thanks for your time, Dave.
I've added LICENSE and NEWS to %doc, removed the unnecessary DESTDIR and
Provides.
I believe I have already solved the debuginfo issue with Adam's help off-list.

Could you describe the issue with the source URL
(https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2
works for me, for example).

With regards to bzip2/lzma, I was under the impression the support is a little
shaky at this time (see
https://github.com/samtools/htslib/blob/develop/Makefile#L36-38) but support is
optional, not required, for CRAM.

I'll take a look at running tests in a %check block.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #5 from Adam Huffman  ---

Thanks for taking a look, Dave. Sam and I had been e-mailing privately about
this and updating on Github, but it's better handled here.

(In reply to Dave Love from comment #4)
> In the meantime, I looked at building this for an updated samtools and
> noticed these:
> 
> Install LICENSE, and probably NEWS
> 
> Add a proper %changelog
> 
> Remove the explicit Provides
> 
> Source URL is wrong
> 
> Run "chmod 755" on the library for correct debuginfo packaging
> 
> Run tests (in a %check section)
> 
> Is there a good reason not to include bzip2 and/or lzma support?  Maybe
> comment if so.
> 
> DESTDIR=... is redundant with %make_install

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Dave Love  changed:

   What|Removed |Added

 CC||d.l...@liverpool.ac.uk



--- Comment #4 from Dave Love  ---
In the meantime, I looked at building this for an updated samtools and noticed
these:

Install LICENSE, and probably NEWS

Add a proper %changelog

Remove the explicit Provides

Source URL is wrong

Run "chmod 755" on the library for correct debuginfo packaging

Run tests (in a %check section)

Is there a good reason not to include bzip2 and/or lzma support?  Maybe comment
if so.

DESTDIR=... is redundant with %make_install

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #3 from Sam Nicholls  ---
Hi Adam,
That does appear to be a rather serious problem, I've updated the SPEC and SRPM
(available via the same URLs) in the hope that the package no longer
effectively requires itself as a dependency.

Sam

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504



--- Comment #2 from Adam Huffman  ---
See also:

- Development (unversioned) .so files in -devel subpackage, if present.
  Note: Unversioned so-files directly in %_libdir.
  See: http://fedoraproject.org/wiki/Packaging/Guidelines#DevelPackages
- Static libraries in -static or -devel subpackage, providing -devel if
  present.
  Note: Package has .a files: htslib-devel. Does not provide -static:
  htslib-devel.
  See: http://fedoraproject.org/wiki/Packaging/Guidelines#StaticLibraries

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Adam Huffman  changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
 CC||bl...@verdurin.com
   Assignee|nob...@fedoraproject.org|bl...@verdurin.com



--- Comment #1 from Adam Huffman  ---
Hi Sam,

There are some issues fedora-review found, which I'll come to, but perhaps most
seriously there's a problem with the dependencies when I try to install it:

Examining htslib-1.3-1.fc23.x86_64.rpm: htslib-1.3-1.fc23.x86_64
Marking htslib-1.3-1.fc23.x86_64.rpm to be installed
Resolving Dependencies
--> Running transaction check
---> Package htslib.x86_64 0:1.3-1.fc23 will be installed
--> Processing Dependency: libhts.so.1()(64bit) for package:
htslib-1.3-1.fc23.x86_64
--> Finished Dependency Resolution
Error: Package: htslib-1.3-1.fc23.x86_64 (/htslib-1.3-1.fc23.x86_64)
   Requires: libhts.so.1()(64bit)

Please see https://fedoraproject.org/wiki/PackagingDrafts/SharedLibraries for
guidance on the packaging of shared libraries.

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[Bug 1326504] Review Request: htslib - C library for high-throughput sequencing data formats (required for `samtools`)

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1326504

Sam Nicholls  changed:

   What|Removed |Added

 Blocks||1131121




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1131121
[Bug 1131121] samtools-1.2 is available
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