Debian Bug report logs - #879619
ncbi-tools6: Please provide autopkgtest

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: ncbi-tools6: Please provide autopkgtest

Date: Mon, 23 Oct 2017 16:18:20 +0200

Package: ncbi-tools6
Severity: minor

Please provide an autopkgtest for this package.
Note: This package is a bit more complex than others so it
might make sense to pick a beginners problem first.


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Message #10 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: debian-med@lists.debian.org

Cc: 879619@bugs.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Tue, 27 Mar 2018 12:48:56 +0200

Dear Liubov,

On Sat, Mar 24, 2018 at 06:45:42PM +0000, Liubov Chuprikova wrote:
> > I once had the idea in the figtree package to use xvfb-run[1].  It was
> > not really successful and most probably the answer is: No, there is no
> > sensible way to test X applications right now.
> 
> Thank you for the comprehensive answers and interesting example provided! I
> have looked through it and I will return to this subject after completing
> with *ncbi-tools-bin*.

I can confirm that the test works for me (now since I'm able to build
the package - thanks to Aaron for the quick response).
 
> > >From my personal point of view I would add a copyright notice right
> > when injecting additional files that need to be mentioned.  Its just
> > that the memory is fresh what was done to get the file.
> >
> 
> Yes, I haven't thought that it would be a better practice! I'll try to
> follow your advice.

I noticed that you pushed a commit featuring the copyright information
of the test data.  Do you consider the package ready for upload now or
are you busy to enhance the test?  From my point of view an upload with
the current status would be fine but I'm waiting for your OK for the
upload.  In any case I added a closes: #879619 (which should mark the
bug "pending upload" if the hook on Salsa works properly which I hereby
want to test).

Kind regards

      Andreas.

-- 
http://fam-tille.de

Message #15 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: debian-med@lists.debian.org, 879619@bugs.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Tue, 27 Mar 2018 13:33:58 +0000

[Message part 1 (text/plain, inline)]

Dear Andreas,

вт, 27 мар. 2018 г. в 12:49, Andreas Tille <andreas@an3as.eu>:

> Dear Liubov,
>
> On Sat, Mar 24, 2018 at 06:45:42PM +0000, Liubov Chuprikova wrote:
> > > I once had the idea in the figtree package to use xvfb-run[1].  It was
> > > not really successful and most probably the answer is: No, there is no
> > > sensible way to test X applications right now.
> >
> > Thank you for the comprehensive answers and interesting example
> provided! I
> > have looked through it and I will return to this subject after completing
> > with *ncbi-tools-bin*.
>
> I can confirm that the test works for me (now since I'm able to build
> the package - thanks to Aaron for the quick response).
>

Thanks a lot for helping me out with this project! I saw your messages to
Aaron and it was a relief for me that there was a "real" problem to build
the package. I had it too, but thought, this was with updating package
dependencies on my computer..


>
> > > >From my personal point of view I would add a copyright notice right
> > > when injecting additional files that need to be mentioned.  Its just
> > > that the memory is fresh what was done to get the file.
> > >
> >
> > Yes, I haven't thought that it would be a better practice! I'll try to
> > follow your advice.
>
> I noticed that you pushed a commit featuring the copyright information
> of the test data.  Do you consider the package ready for upload now or
> are you busy to enhance the test?  From my point of view an upload with
> the current status would be fine but I'm waiting for your OK for the
> upload.  In any case I added a closes: #879619 (which should mark the
> bug "pending upload" if the hook on Salsa works properly which I hereby
> want to test).
>

Sorry, but yes, I had no time to enhance the test by this evening. The
package has more commands to test and I need to figure out how. I will be
able to finish it no later than tomorrow's evening.  I will let you know
once it will be done.

With regards,
Liubov

[Message part 2 (text/html, inline)]

Message #20 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: <879619@bugs.debian.org>, Andreas Tille <andreas@an3as.eu>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Tue, 27 Mar 2018 23:07:38 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Thanks a lot for helping me out with this project! I saw your messages to
> Aaron and it was a relief for me that there was a "real" problem to build
> the package. I had it too, but thought, this was with updating package
> dependencies on my computer..

Thanks for adding these tests, and sorry you ran into dpkg errors along
the way!  Please let me know if you have usage questions about any of
this package's tools.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #25 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>

Cc: 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 29 Mar 2018 14:35:01 +0000

[Message part 1 (text/plain, inline)]

Dear Andreas, dear Aaron,

ср, 28 мар. 2018 г. в 5:07, Aaron M. Ucko <ucko@debian.org>:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > Thanks a lot for helping me out with this project! I saw your messages to
> > Aaron and it was a relief for me that there was a "real" problem to build
> > the package. I had it too, but thought, this was with updating package
> > dependencies on my computer..
>
> Thanks for adding these tests, and sorry you ran into dpkg errors along
> the way!  Please let me know if you have usage questions about any of
> this package's tools.


вт, 27 мар. 2018 г. в 16:01, Andreas Tille <andreas@an3as.eu>:

> On Tue, Mar 27, 2018 at 01:33:58PM +0000, Liubov Chuprikova wrote:
>
> > > I noticed that you pushed a commit featuring the copyright information
> > > of the test data.  Do you consider the package ready for upload now or
> > > are you busy to enhance the test?  From my point of view an upload with
> > > the current status would be fine but I'm waiting for your OK for the
> > > upload.  In any case I added a closes: #879619 (which should mark the
> > > bug "pending upload" if the hook on Salsa works properly which I hereby
> > > want to test).
> > >
> >
> > Sorry, but yes, I had no time to enhance the test by this evening. The
> > package has more commands to test and I need to figure out how. I will be
> > able to finish it no later than tomorrow's evening.  I will let you know
> > once it will be done.
>
> That's perfectly fine and I'll stay patient.  Feel free to take all time
> you need.
>

Thanks a lot for your attention to my work on the project! Frankly, I am
stunned with the huge amount of different file formats required or
generated! :-) Unfortunately, I could not add tests for all commands in the
package so far. It appears I need more time to recognise what their inputs
should look like and where to find them.

Please, have an eye on my last commits
<https://salsa.debian.org/med-team/ncbi-tools6/commits/master>! I'd like to
ask one question (most likely it is to Aaron): Are there tools that I
didn't include, but you would strongly recommend for testing? Then I will
concentrate on them to finish.

Kind regards,
Liubov

[Message part 2 (text/html, inline)]

Message #30 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>, <879619@bugs.debian.org>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 29 Mar 2018 13:30:14 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Please, have an eye on my last commits
> <https://salsa.debian.org/med-team/ncbi-tools6/commits/master>! I'd like to
> ask one question (most likely it is to Aaron): Are there tools that I
> didn't include, but you would strongly recommend for testing? Then I will
> concentrate on them to finish.

These tests are shaping up nicely; thanks again for putting them
together.  Of the remaining tools, I would prioritize testing tbl2asn
and perhaps asnmacro.  (Also, please fix the typo in the asn2gb test's
leading echo statement.)

Спасибо!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #35 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>

Cc: 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Tue, 03 Apr 2018 22:37:20 +0000

[Message part 1 (text/plain, inline)]

Dear Andreas, dear Aaron,

On Thu, 29 Mar 2018 at 18:14 Andreas Tille <andreas@an3as.eu> wrote:

> On Thu, Mar 29, 2018 at 02:35:01PM +0000, Liubov Chuprikova wrote:
> >
> > Thanks a lot for your attention to my work on the project!
>
> I'd like to confirm that this is because of your pretty good work. ;-)


Thanks again!

On Thu, 29 Mar 2018 at 19:30 Aaron M. Ucko <ucko@debian.org> wrote:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > Please, have an eye on my last commits
> > <https://salsa.debian.org/med-team/ncbi-tools6/commits/master>! I'd
> like to
> > ask one question (most likely it is to Aaron): Are there tools that I
> > didn't include, but you would strongly recommend for testing? Then I will
> > concentrate on them to finish.
>
> These tests are shaping up nicely; thanks again for putting them
> together.  Of the remaining tools, I would prioritize testing tbl2asn
> and perhaps asnmacro.  (Also, please fix the typo in the asn2gb test's
> leading echo statement.)
>

Sorry for the delay in continuing the work! Last two days I have been
figuring out how to test *tbl2asn* and *asnmacro*. Please, take a look at
the last commits
<https://salsa.debian.org/med-team/ncbi-tools6/commits/master>. I could not
understand where a macro file for *asnmacro* can be taken from. Is it
possible to generate such a file by any program? I have included one as an
example, containing only a simple action (it is generated during
*run-unit-test* script execution).

Спасибо!
>

Oops! I have not paid attention to the fact that the date and time
headlines are written on my native language. Fixed it! ;-)

Regards,
Liubov

[Message part 2 (text/html, inline)]

Message #40 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>, <879619@bugs.debian.org>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Tue, 03 Apr 2018 19:41:05 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Sorry for the delay in continuing the work!

No problem.

> Last two days I have been figuring out how to test *tbl2asn* and
> *asnmacro*. Please, take a look at the last commits
> <https://salsa.debian.org/med-team/ncbi-tools6/commits/master>.

These all look OK offhand, apart from one purely cosmetic consideration:
Sc_16.sbt has a lot of trailing whitespace that would be best to clean up.

> I could not understand where a macro file for *asnmacro* can be taken
> from. Is it possible to generate such a file by any program?

Just by a generic text editor, sorry.  However, this package does
already ship a macro file you may be able to test with:
/usr/share/ncbi/data/autofix.prt.

Thanks!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #45 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>

Cc: 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 05 Apr 2018 21:02:01 +0000

[Message part 1 (text/plain, inline)]

Hi Aaron, Hi Andreas,

On Wed, 4 Apr 2018 at 01:41 Aaron M. Ucko <ucko@debian.org> wrote:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > Last two days I have been figuring out how to test *tbl2asn* and
> > *asnmacro*. Please, take a look at the last commits
> > <https://salsa.debian.org/med-team/ncbi-tools6/commits/master>.
>
> These all look OK offhand, apart from one purely cosmetic consideration:
> Sc_16.sbt has a lot of trailing whitespace that would be best to clean up.


Did it and also configured my vim to always show them.


> > I could not understand where a macro file for *asnmacro* can be taken
> > from. Is it possible to generate such a file by any program?
>
> Just by a generic text editor, sorry.  However, this package does
> already ship a macro file you may be able to test with:
> /usr/share/ncbi/data/autofix.prt.


Thanks, I've included this macro file into the test. Also, I've added a
test for *vecscreen *since I've noticed UniVec database already built at
the same directory. What do you think about the whole test at this stage?

With regards,
Liubov

[Message part 2 (text/html, inline)]

Message #50 received at 879619@bugs.debian.org (full text, mbox, reply):

From: amu@alum.mit.edu (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>, <879619@bugs.debian.org>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 05 Apr 2018 17:30:33 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Did it and also configured my vim to always show them.

Thanks!

> Thanks, I've included this macro file into the test. Also, I've added a
> test for *vecscreen *since I've noticed UniVec database already built at
> the same directory. What do you think about the whole test at this stage?

Great, thanks!  I suppose you could check for specific output contents
(via grep, not necessarily 100% identity), but this otherwise all looks
good, and is a clear improvement over not having autopkgtests at all.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #55 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <amu@alum.mit.edu>

Cc: Andreas Tille <andreas@an3as.eu>, 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 12 Apr 2018 14:24:12 +0000

[Message part 1 (text/plain, inline)]

Hi Aaron,

On Thu, 5 Apr 2018 at 23:30 Aaron M. Ucko <amu@alum.mit.edu> wrote:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > the same directory. What do you think about the whole test at this stage?
>
> Great, thanks!  I suppose you could check for specific output contents
> (via grep, not necessarily 100% identity), but this otherwise all looks
> good, and is a clear improvement over not having autopkgtests at all.
>

I have added simple checks for specific output content. What do you think
about my last commits? Is it an acceptable way to check or maybe you have
another idea how it should look like?

Apart from that, could you please help me with *taxblast*. I have tried to
run it providing SeqAnnot ASN.1 file as required. But I got the same error
message each time:

[taxblast] REJECT: Secure socket layer (SSL) has not been properly
initialized in the NCBI Toolkit.  Have you forgotten to call
SOCK_SetupSSL()?
[taxblast] ERROR: [URL_Connect;
https://www.ncbi.nlm.nih.gov:443/Service/dispd.cgi?service=TaxService&address=stretch.localdomain(127.0.1.1)&platform=LINUX
]  Failed to connect: Not supported
... (here the previous line repets)
[taxblast] ERROR: [HTTP;
https://www.ncbi.nlm.nih.gov/Service/dispd.cgi?service=TaxService&address=stretch.localdomain(127.0.1.1)&platform=LINUX
]  Too many failed attempts (3), giving up
[taxblast] ERROR: [TaxService]  Service not found
[taxblast] ERROR: [TaxService]  Cannot connect to service
[taxblast] ERROR: NI_ServiceGet [no error] ()

Do you have any suggestions what could be wrong with it?

Thank you,
Liubov

[Message part 2 (text/html, inline)]

Message #60 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 12 Apr 2018 16:39:47 +0200

Hi Liubov,

On Thu, Apr 12, 2018 at 02:24:12PM +0000, Liubov Chuprikova wrote:
> >
> > Great, thanks!  I suppose you could check for specific output contents
> > (via grep, not necessarily 100% identity), but this otherwise all looks
> > good, and is a clear improvement over not having autopkgtests at all.
> >
> 
> I have added simple checks for specific output content. What do you think
> about my last commits? Is it an acceptable way to check or maybe you have
> another idea how it should look like?

Just from reading the shell script it looks fine.  Requiring bash is
also OK.
 
> Apart from that, could you please help me with *taxblast*. I have tried to
> run it providing SeqAnnot ASN.1 file as required. But I got the same error
> message each time:
> 
> [taxblast] REJECT: Secure socket layer (SSL) has not been properly
> initialized in the NCBI Toolkit.  Have you forgotten to call
> SOCK_SetupSSL()?
> [taxblast] ERROR: [URL_Connect;
> https://www.ncbi.nlm.nih.gov:443/Service/dispd.cgi?service=TaxService&address=stretch.localdomain(127.0.1.1)&platform=LINUX
> ]  Failed to connect: Not supported
> ... (here the previous line repets)
> [taxblast] ERROR: [HTTP;
> https://www.ncbi.nlm.nih.gov/Service/dispd.cgi?service=TaxService&address=stretch.localdomain(127.0.1.1)&platform=LINUX
> ]  Too many failed attempts (3), giving up
> [taxblast] ERROR: [TaxService]  Service not found
> [taxblast] ERROR: [TaxService]  Cannot connect to service
> [taxblast] ERROR: NI_ServiceGet [no error] ()
> 
> Do you have any suggestions what could be wrong with it?

I hope Aaron will give a more authoritative answer but when I'm reading
SSL I'm getting suspicious:  The test suite needs to be run in a machine
that is disconnected from the internet (similarly when the package is
build).

In some rules file this is somehow faked by using

  export http_proxy=http://127.0.0.1:9/

I'm absolutely not sure that this has any chance to work in the test
suite.  If the test needs network access to succeed than the only way is
to skip that test.

Kind regards

      Andreas.

-- 
http://fam-tille.de

Message #65 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 12 Apr 2018 15:19:27 +0000

[Message part 1 (text/plain, inline)]

On Thu, 12 Apr 2018 at 16:40 Andreas Tille <andreas@an3as.eu> wrote:

>
> Just from reading the shell script it looks fine.  Requiring bash is
> also OK.
>

Ok, thanks!

SSL I'm getting suspicious:  The test suite needs to be run in a machine
> that is disconnected from the internet (similarly when the package is
> build).
>

Ops, it's escaped my attention somehow that tests are usually run on a
disconnected machine. I thought the opposite way.. Then I also need to
comment tests for *insdseqget* and *idfetch*.. Thank you for the
clarification!

With regards,
Liubov

[Message part 2 (text/html, inline)]

Message #70 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: <879619@bugs.debian.org>, Andreas Tille <andreas@an3as.eu>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 12 Apr 2018 11:30:40 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Ops, it's escaped my attention somehow that tests are usually run on a
> disconnected machine. I thought the opposite way.. Then I also need to
> comment tests for *insdseqget* and *idfetch*.. Thank you for the
> clarification!

That said, you did catch a bug in taxblast; I'll push a fix this
evening.  (The binary will still require a network connection, just
actually be able to use it now).

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #75 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>

Cc: 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 12 Apr 2018 15:36:12 +0000

[Message part 1 (text/plain, inline)]

On Thu, 12 Apr 2018 at 17:30 Aaron M. Ucko <ucko@debian.org> wrote:

>
> That said, you did catch a bug in taxblast; I'll push a fix this
> evening.  (The binary will still require a network connection, just
> actually be able to use it now).
>

Ok, thank you!

With regards,
Liubov

[Message part 2 (text/html, inline)]

Message #80 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: "Aaron M. Ucko" <ucko@debian.org>, <879619@bugs.debian.org>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 12 Apr 2018 20:04:11 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> On Thu, 12 Apr 2018 at 17:30 Aaron M. Ucko <ucko@debian.org> wrote:
>
>>
>> That said, you did catch a bug in taxblast; I'll push a fix this
>> evening.  (The binary will still require a network connection, just
>> actually be able to use it now).
>>
>
> Ok, thank you!

Fix pushed, no problem.  I'd also be happy to sponsor the upload if
you'd like.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #85 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>

Cc: 879619@bugs.debian.org, debian-med@lists.debian.org, Andreas Tille <andreas@an3as.eu>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Mon, 16 Apr 2018 21:45:15 +0000

[Message part 1 (text/plain, inline)]

Hi Aaron,

On Fri, 13 Apr 2018 at 02:04 Aaron M. Ucko <ucko@debian.org> wrote:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > On Thu, 12 Apr 2018 at 17:30 Aaron M. Ucko <ucko@debian.org> wrote:
> >
> >>
> >> That said, you did catch a bug in taxblast; I'll push a fix this
> >> evening.  (The binary will still require a network connection, just
> >> actually be able to use it now).
> >>
> >
> > Ok, thank you!
>
> Fix pushed, no problem.  I'd also be happy to sponsor the upload if
> you'd like.
>

Sorry for a delay, but I was planning to make one more effort on extending
the set of tests. At the moment, the following commands are still lacking
tests:

   - *asn2ff*, *gbseqget*, *findspl* (their output indicates they are
   obsolete and/or unsupported)
   - *asndhuff*, *nps2gps* (I can't figure out what kind of inputs they
   require)
   - *fa2htgs*, *spidey* (they look too complicated for me and require much
   time to understand how they work)
   - *taxblast* doesn't generate an output file and only generates an
   *incomplete* html
   - *errhdr*, *sortbyquote* (I can't figure out even what they are
   supposed to do)

If nothing critical is left without a test, then I'd like to ask you to
sponsor the upload. If you need any additional information about *taxblast*,
I'll be happy to provide it.

Thank you,
Liubov

[Message part 2 (text/html, inline)]

Message #90 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: "Aaron M. Ucko" <ucko@debian.org>, <879619@bugs.debian.org>, <debian-med@lists.debian.org>, Andreas Tille <andreas@an3as.eu>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Mon, 16 Apr 2018 21:48:44 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Sorry for a delay, but I was planning to make one more effort on extending
> the set of tests.

No problem.

> At the moment, the following commands are still lacking tests:
>
>    - *asn2ff*, *gbseqget*, *findspl* (their output indicates they are
>    obsolete and/or unsupported)

- asn2ff plays the same general role as asn2flat, and should be possible to
  test similarly.
- gbseqget is like insdseqget, but formally uses GenBank-specific
  notation; as such, it requires network access.
- findspl also requires network access, and will need to be patched in the
  same fashion as taxblast; I'll take care of it when I get a chance.

>    - *asndhuff*, *nps2gps* (I can't figure out what kind of inputs they
>    require)

- I'm not sure where you'd find input for asndhuff.
- nps2gps takes a text Bioseq-set or Seq-entry of class nuc-prot, as
  obtained by (for instance) idfetch -g1234.

>    - *fa2htgs*, *spidey* (they look too complicated for me and require much
>    time to understand how they work)

That's fair.  You can always come back to them later if you feel inspired.

>    - *taxblast* doesn't generate an output file and only generates an
>    *incomplete* html

I'm not sure what's up with that, but as previously noted, it requires
network access anyway.

>    - *errhdr*, *sortbyquote* (I can't figure out even what they are
>    supposed to do)

- errhdr is a developer tool, working with files of the format found in
  errmsg/.
- sortbyquote is also a developer tool, essentially a variant of sort
  that ignores everything outside quotation marks (and generally has far
  fewer options).

> If nothing critical is left without a test, then I'd like to ask you to
> sponsor the upload. If you need any additional information about *taxblast*,
> I'll be happy to provide it.

OK, thanks.  I'm not sure any of these is critical to test, but some
should be relatively straightforward to work in at this point, and as
noted I'm not quite ready to upload a new version anyway.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #95 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>

Cc: 879619@bugs.debian.org, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Tue, 22 May 2018 01:01:55 +0200

[Message part 1 (text/plain, inline)]

Hi Aaron, Hi Andreas,

Please, have a look at my two last commits (
https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually,
the first one was made a month ago.

On Tue, 17 Apr 2018 at 03:48 Aaron M. Ucko <ucko@debian.org> wrote:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > At the moment, the following commands are still lacking tests:
> >
> >    - *asn2ff*, *gbseqget*, *findspl* (their output indicates they are
> >    obsolete and/or unsupported)
>
> - asn2ff plays the same general role as asn2flat, and should be possible to
>   test similarly.
>

I tried to run it in a similar way to *asn2asn*. It throws an error which
starts with "The asn2ff flatfile generator is obsolete and unsupported.  Please
switch to using asn2gb/SeqEntryToGnbk in the future."

- gbseqget is like insdseqget, but formally uses GenBank-specific
>   notation; as such, it requires network access.


I added a test for *gbseqget* within if statement which checks for internet
connection.


> - findspl also requires network access, and will need to be patched in the
>
  same fashion as taxblast; I'll take care of it when I get a chance.
>
> >    - *asndhuff*, *nps2gps* (I can't figure out what kind of inputs they
> >    require)
>
> - I'm not sure where you'd find input for asndhuff.
> - nps2gps takes a text Bioseq-set or Seq-entry of class nuc-prot, as
>   obtained by (for instance) idfetch -g1234.


A test for *nps2gps* also presents now.


> >    - *fa2htgs*, *spidey* (they look too complicated for me and require
> much
>
>    time to understand how they work)
>
> That's fair.  You can always come back to them later if you feel inspired.
>

I have also finished with *spidey* and *fa2htgs* today.


> >    - *taxblast* doesn't generate an output file and only generates an
> >    *incomplete* html
>
> I'm not sure what's up with that, but as previously noted, it requires
> network access anyway.
>
> >    - *errhdr*, *sortbyquote* (I can't figure out even what they are
> >    supposed to do)
>
> - errhdr is a developer tool, working with files of the format found in
>   errmsg/.
> - sortbyquote is also a developer tool, essentially a variant of sort
>   that ignores everything outside quotation marks (and generally has far
>   fewer options).



> I'm not sure any of these is critical to test, but some
>
should be relatively straightforward to work in at this point, and as
> noted I'm not quite ready to upload a new version anyway.
>

Aaron, thank you for the explanations! They helped me a lot!

Aaron, Andreas: what is your opinion about the whole test? Could we
consider it as completed?

With regards,
Liubov

[Message part 2 (text/html, inline)]

Message #100 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@fam-tille.de>

To: 879619@bugs.debian.org

Cc: "Aaron M. Ucko" <ucko@debian.org>, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Tue, 22 May 2018 06:47:08 +0200

Hi Liubov,

On Tue, May 22, 2018 at 01:01:55AM +0200, Liubov Chuprikova wrote:
> 
> Aaron, thank you for the explanations! They helped me a lot!

+1
 
> Aaron, Andreas: what is your opinion about the whole test? Could we
> consider it as completed?

Your work looks very fine grained but for the decision of "completed"
Aaron is the expert we both need to trust.  Aaron, let me know if you
want me to upload or if you want to do it yourself.

Kind regards

      Andreas.

-- 
http://fam-tille.de

Message #105 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: <879619@bugs.debian.org>, "Aaron M. Ucko" <ucko@debian.org>, Andreas Tille <andreas@an3as.eu>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Wed, 23 May 2018 14:36:06 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Please, have a look at my two last commits (
> https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually,
> the first one was made a month ago.

All looks good except for one formality -- Lintian considers your
additions to debian/copyright to be incomplete:

W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph at line 16)
W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright (paragraph at line 16)
W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph at line 24)
W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright (paragraph at line 24)
W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph at line 30)
W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright (paragraph at line 30)
W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph at line 35)
W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright (paragraph at line 35)

(It also issues a few unrelated complaints, which I'll be happy to
address myself.)

> I tried to run it in a similar way to *asn2asn*. It throws an error which
> starts with "The asn2ff flatfile generator is obsolete and unsupported.  Please
> switch to using asn2gb/SeqEntryToGnbk in the future."

Ah, got it.  No test needed here, then.

> Aaron, thank you for the explanations! They helped me a lot!

No problem; thanks for the tests!

> Your work looks very fine grained but for the decision of "completed"
> Aaron is the expert we both need to trust.  Aaron, let me know if you
> want me to upload or if you want to do it yourself.

I'll do it myself, thanks, adding a few other small changes along the way.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #110 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>

Cc: 879619@bugs.debian.org, Andreas Tille <andreas@an3as.eu>, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Wed, 23 May 2018 22:14:56 +0200

[Message part 1 (text/plain, inline)]

On Wed, 23 May 2018 at 20:36 Aaron M. Ucko <ucko@debian.org> wrote:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > Please, have a look at my two last commits (
> > https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually,
> > the first one was made a month ago.
>
> All looks good except for one formality -- Lintian considers your
> additions to debian/copyright to be incomplete:
>
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 16)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 16)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 24)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 24)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 30)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 30)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 35)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 35)
>
> (It also issues a few unrelated complaints, which I'll be happy to
> address myself.)
>

I cannot reproduce the same lintian output on my computer. I tried it like
this:
            lintian -i -I --show-overrides
ncbi-tools6_6.1.20170106-3_amd64.changes
I mistakenly decided that if NCBI copyright had already mentioned I could
skip it
for test data files as they were also taken from NCBI, except one...
            trnascan-se_sample.output
I generated that file by running *trnascan-se* (another Debian Med
package), so I have no
idea what the license and copyright should be written for it. Could you
help me with this
problem?

__
Liubov

[Message part 2 (text/html, inline)]

Message #115 received at 879619@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: "Aaron M. Ucko" <ucko@debian.org>

Cc: 879619@bugs.debian.org, Andreas Tille <andreas@an3as.eu>, debian-med@lists.debian.org

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Thu, 24 May 2018 15:19:28 +0200

[Message part 1 (text/plain, inline)]

Hi Aaron,

On Wed, 23 May 2018 at 20:36 Aaron M. Ucko <ucko@debian.org> wrote:

> Liubov Chuprikova <chuprikovalv@gmail.com> writes:
>
> > Please, have a look at my two last commits (
> > https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually,
> > the first one was made a month ago.
>
> All looks good except for one formality -- Lintian considers your
> additions to debian/copyright to be incomplete:
>
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 16)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 16)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 24)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 24)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 30)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 30)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright license (paragraph
> at line 35)
> W: ncbi-tools6 source: missing-field-in-dep5-copyright copyright
> (paragraph at line 35)


Andreas helped me to figure out how to fill in the copyright and license
fields for the test data. I have just pushed these changes. Let me know if
something wrong.

With regards,
Liubov

[Message part 2 (text/html, inline)]

Message #120 received at 879619@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: Liubov Chuprikova <chuprikovalv@gmail.com>

Cc: "Aaron M. Ucko" <ucko@debian.org>, <879619@bugs.debian.org>, Andreas Tille <andreas@an3as.eu>, <debian-med@lists.debian.org>

Subject: Re: Bug#879619: Autopkgtest for ncbi-tools6

Date: Fri, 25 May 2018 10:10:07 -0400

Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> Andreas helped me to figure out how to fill in the copyright and license
> fields for the test data. I have just pushed these changes. Let me know if
> something wrong.

Looks good now, thanks; I'll take it from here.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

Message #125 received at 879619-close@bugs.debian.org (full text, mbox, reply):

From: ucko@debian.org (Aaron M. Ucko)

To: 879619-close@bugs.debian.org

Subject: Bug#879619: fixed in ncbi-tools6 6.1.20170106-3

Date: Sun, 24 Jun 2018 17:04:24 +0000

Source: ncbi-tools6
Source-Version: 6.1.20170106-3

We believe that the bug you reported is fixed in the latest version of
ncbi-tools6, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 879619@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Aaron M. Ucko <ucko@debian.org> (supplier of updated ncbi-tools6 package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Sun, 24 Jun 2018 12:06:15 -0400
Source: ncbi-tools6
Binary: libncbi6 libncbi6-dev ncbi-data ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 libvibrant6b libvibrant6-dev
Architecture: source
Version: 6.1.20170106-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Aaron M. Ucko <ucko@debian.org>
Description:
 libncbi6   - NCBI libraries for biology applications
 libncbi6-dev - NCBI libraries for biology applications (development files)
 libvibrant6-dev - NCBI libraries for graphic biology applications (development file
 libvibrant6b - NCBI libraries for graphic biology applications
 ncbi-data  - Platform-independent data for the NCBI toolkit
 ncbi-rrna-data - large rRNA BLAST databases distributed with the NCBI toolkit
 ncbi-tools-bin - NCBI libraries for biology applications (text-based utilities)
 ncbi-tools-x11 - NCBI libraries for biology applications (X-based utilities)
Closes: 879619
Changes:
 ncbi-tools6 (6.1.20170106-3) unstable; urgency=medium
 .
   [ Liubov Chuprikova ]
   * Added autopkgtest for ncbi-tools-bin.
     Closes: #879619
 .
   [ Aaron M. Ucko ]
   * debian/{*.gif,ncbi2.css}: Add local copies of NCBI resources used by HTML
     docs.
   * debian/control:
     - Repoint Vcs-* at salsa.debian.org.
     - Standards-Version: 4.1.4 (already compliant).
     - Rules-Requires-Root: no (confirmed safe).
   * debian/{libncbi6,ncbi-tools-x11}.docs: Install resources from debian/ as
     needed.
   * debian/source/format: Set to 3.0 (quilt) to accommodate binary test data.
   * debian/source/include-binaries: List debian/tests/test-data/nc0305.aso.gz
     and (individually) debian/*.gif.
   * debian/source/options: single-debian-patch (tracking changes purely
     with git for now).
   * debian/source/patch-header: "Combined patches from git."
   * demo/{findspl,taxblast_main}.c: Call SOCK_SetupSSL (accidentally missed
     earlier).
   * doc/{dispatcher,firewall}.html: Patch to use (newly supplied) local
     resources, addressing a generic privacy breach caught by Lintian.
   * make/make{demo,net}.unx: Link findspl and taxblast against $(LIBTLS)
     and $(GNUTLS_LIBS).
Checksums-Sha1:
 f6fbcd24f42ac9c269f7e98a3a021cbd1dee37b7 2784 ncbi-tools6_6.1.20170106-3.dsc
 23b929d007656ece3be1f42b28b7900522896479 1508492 ncbi-tools6_6.1.20170106-3.debian.tar.xz
Checksums-Sha256:
 75bdc16a44e881eb9fe377a291d6e77640f808befb119b9e2746ab3d1a9b9bd6 2784 ncbi-tools6_6.1.20170106-3.dsc
 27bd32f67059699a060ba59ad7ec83199768197f4fc1dc47dd426af2825572a8 1508492 ncbi-tools6_6.1.20170106-3.debian.tar.xz
Files:
 a26a154b48b513e2802c55fb2f429506 2784 libdevel optional ncbi-tools6_6.1.20170106-3.dsc
 87458976a920bb735aab2d335e8ca3bd 1508492 libdevel optional ncbi-tools6_6.1.20170106-3.debian.tar.xz

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