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Old 05-19-2012, 12:56 PM
Onkar Shinde
 
Default RFS: cdk 1.4.9-1

Hi all,

I am looking for sponsorship for cdk 1.4.9-1. The packaging bits have
been updated in pkg-java svn. I have also uploaded new source package
on mentors.d.n
http://mentors.debian.net/debian/pool/main/c/cdk/cdk_1.4.9-1.dsc

Please note that the upload will go through binary new as it adds a
new -doc package containing API documentation.

Latest changelog entry
cdk (1:1.4.9-1) unstable; urgency=low

* New upstream release. (Closes: #635182, LP: #280189)
* Build -doc package containing api docs.
* Refresh patch as per latest upstream source.
* Exclude modules inchi, libiocml, signature, smsd, tautomer, iordf as their
build dependencies are not in packaged yet.


Cheers,
Onkar
--
Passion - Some people climb mountains - others write Free software.
Don't ask why - the reason is the same.


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Old 05-23-2012, 08:04 AM
Niels Thykier
 
Default RFS: cdk 1.4.9-1

On 2012-05-19 14:56, Onkar Shinde wrote:
> Hi all,
>
> I am looking for sponsorship for cdk 1.4.9-1. The packaging bits have
> been updated in pkg-java svn. I have also uploaded new source package
> on mentors.d.n
> http://mentors.debian.net/debian/pool/main/c/cdk/cdk_1.4.9-1.dsc
>
> Please note that the upload will go through binary new as it adds a
> new -doc package containing API documentation.
>
> Latest changelog entry
> cdk (1:1.4.9-1) unstable; urgency=low
>
> * New upstream release. (Closes: #635182, LP: #280189)
> * Build -doc package containing api docs.
> * Refresh patch as per latest upstream source.
> * Exclude modules inchi, libiocml, signature, smsd, tautomer, iordf as their
> build dependencies are not in packaged yet.
>
>
> Cheers,
> Onkar

Hi,

It seems that some public methods are changing signature and also that
some public constants are disappearing in this release (compared to our
current version). Have you (build-)tested the reverse dependencies of cdk?

The new doc package does not get any recommends despite using jh_depends
- I am not entirely sure what goes wrong because the javadoc is at least
linked against default-jdk-doc and at first sight the d/control looks
correct.

~Niels



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Old 05-23-2012, 11:37 AM
Egon Willighagen
 
Default RFS: cdk 1.4.9-1

NIels,

On Wed, May 23, 2012 at 10:04 AM, Niels Thykier <niels@thykier.net> wrote:
> On 2012-05-19 14:56, Onkar Shinde wrote:
> It seems that some public methods are changing signature and also that
> some public constants are disappearing in this release (compared to our
> current version).

Which ones are those? The 1.4 series should be API stable... I love to
hear how you tested that!

> Have you (build-)tested the reverse dependencies of cdk?

I do not think there are any reverse dependencies... ? I wish there
were, and I hope Bioclipse will be one of those; but at this moment I
cannot think of any... I cannot find right now where to find that rev
dep info...

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
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Old 05-23-2012, 12:45 PM
Niels Thykier
 
Default RFS: cdk 1.4.9-1

On 2012-05-23 13:37, Egon Willighagen wrote:
> NIels,
>
> On Wed, May 23, 2012 at 10:04 AM, Niels Thykier <niels@thykier.net> wrote:
>> On 2012-05-19 14:56, Onkar Shinde wrote:
>> It seems that some public methods are changing signature and also that
>> some public constants are disappearing in this release (compared to our
>> current version).
>
> Which ones are those? The 1.4 series should be API stable... I love to
> hear how you tested that!
>

Hi,

I "just" read the diff between our current version (1.2.10) and the RFS
version 1.4.9. Actually, thanks you just made me realize that it FTBFS
when built twice in a row!

Anyhow, it is quite possible that I saw false positives as I just read
the diff once without considering new interfaces/super classes and
whether the methods were "defined internal" (despite being public).
Anyhow, to mention examples:

PartialFilledStructureMerger:
-public IAtomContainer generate() throws CDKException
+public IAtomContainer generate(IAtomContainerSet atomContainers)
throws CDKException

SmilesParser:
-private IAtom assembleAtom(String s) throws InvalidSmilesException
+private IAtom assembleAtom(String s, IAtom lastNode, boolean
bondExists) throws InvalidSmilesException

CDKSourceCodeWriter*:
-public void writeAtomContainer(IAtomContainer molecule)
throws Exception {
+private void writeAtomContainer(IAtomContainer molecule)
throws Exception {


IChemObjectBuilder lost a lof interface methods and it does not extend
any other interface that could have gained those methods.

IBond:
-public int getStereo();
+public IBond.Stereo getStereo();

These are examples of what I found; they may (or may not) be an issue.
I also noticed now that some of the files disappearing appears to
auto-generated JJTree or so? Anyway, with the clean rule not working my
diff is currently a bit tainted.


*) Probably intended to be private from the beginning, but changing the
visiblity from public -> private is a possible source of breakage.

>> Have you (build-)tested the reverse dependencies of cdk?
>
> I do not think there are any reverse dependencies... ? I wish there
> were, and I hope Bioclipse will be one of those; but at this moment I
> cannot think of any... I cannot find right now where to find that rev
> dep info...
>
> Egon
>

For reverse dependencies (not including build-depends) I notice at least
3 (potentional) rdeps in Debian:

$ apt-cache rdepends libcdk-java
libcdk-java
Reverse Depends:
debichem-cheminformatics
science-chemistry
python-cinfony

Actually, the first two turns out to be meta-packages, but
python-cinfony appears to be a genuine reverse dependency.

~Niels


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Old 05-23-2012, 02:07 PM
Egon Willighagen
 
Default RFS: cdk 1.4.9-1

Hi Niels,

On Wed, May 23, 2012 at 2:45 PM, Niels Thykier <niels@thykier.net> wrote:
> I "just" read the diff between our current version (1.2.10) and the RFS
> version 1.4.9. *Actually, thanks you just made me realize that it FTBFS
> when built twice in a row!

Ah, right! Yes, from 1.2 to 1.4 there are API changes...

Please do provide me details about build fails... part of it is prob
Debian specific, but some perhaps also CDK specific... the latter I
like to hear about

> Anyhow, it is quite possible that I saw false positives as I just read
> the diff once without considering new interfaces/super classes and
> whether the methods were "defined internal" (despite being public).
> Anyhow, to mention examples:
>
> PartialFilledStructureMerger:
> *-public IAtomContainer generate() throws CDKException
> *+public IAtomContainer generate(IAtomContainerSet atomContainers)
> * * * * throws CDKException
>
> SmilesParser:
> *-private IAtom assembleAtom(String s) throws InvalidSmilesException
> *+private IAtom assembleAtom(String s, IAtom lastNode, boolean
> * * * * *bondExists) throws InvalidSmilesException
>
> CDKSourceCodeWriter*:
> -public void writeAtomContainer(IAtomContainer molecule)
> * * * * throws Exception {
> +private void writeAtomContainer(IAtomContainer molecule)
> * * * * throws Exception {

>From 1.2 to 1.4 that actually makes sense...

> IChemObjectBuilder lost a lof interface methods and it does not extend
> any other interface that could have gained those methods.

Yes, this one has seen a major rewrite in 1.4.

> These are examples of what I found;

Thanx for the detail!

> they may (or may not) be an issue.
> I also noticed now that some of the files disappearing appears to
> auto-generated JJTree or so? *Anyway, with the clean rule not working my
> diff is currently a bit tainted.

Yes, some source code files are generated indeed.

>>> Have you (build-)tested the reverse dependencies of cdk?
>>
>> I do not think there are any reverse dependencies... ? I wish there
>> were, and I hope Bioclipse will be one of those; but at this moment I
>> cannot think of any... I cannot find right now where to find that rev
>> dep info...
>
> For reverse dependencies (not including build-depends) I notice at least
> 3 (potentional) rdeps in Debian:
>
> $ apt-cache rdepends libcdk-java
> libcdk-java
> Reverse Depends:
> *debichem-cheminformatics
> *science-chemistry
> *python-cinfony
>
> Actually, the first two turns out to be meta-packages, but
> python-cinfony appears to be a genuine reverse dependency.

Stupid of me to forget about Cinfony!

Cinfony 1.1 should work fine with CDK 1.4.x:
http://baoilleach.blogspot.com/2011/12/cinfony-11-released.html

That post tells about a compile against 1.4.5, but as said, within
1.4.x there are no API changes (or very minor ones).

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


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Old 05-23-2012, 02:15 PM
Niels Thykier
 
Default RFS: cdk 1.4.9-1

On 2012-05-23 16:07, Egon Willighagen wrote:
> Hi Niels,
>
> On Wed, May 23, 2012 at 2:45 PM, Niels Thykier <niels@thykier.net> wrote:
>> I "just" read the diff between our current version (1.2.10) and the RFS
>> version 1.4.9. Actually, thanks you just made me realize that it FTBFS
>> when built twice in a row!
>
> Ah, right! Yes, from 1.2 to 1.4 there are API changes...
>
> Please do provide me details about build fails... part of it is prob
> Debian specific, but some perhaps also CDK specific... the latter I
> like to hear about
>

The issue is that it fails to clean properly - at least some (java)doc
files are not cleaned, but also some non-text files (can't remember - I
didn't pay too much attention to it). I haven't actually investigated
the failure that deeply, so it may be trivial to fix.

>> [...]
>>
>> Actually, the first two turns out to be meta-packages, but
>> python-cinfony appears to be a genuine reverse dependency.
>
> Stupid of me to forget about Cinfony!
>
> Cinfony 1.1 should work fine with CDK 1.4.x:
> http://baoilleach.blogspot.com/2011/12/cinfony-11-released.html
>
> That post tells about a compile against 1.4.5, but as said, within
> 1.4.x there are no API changes (or very minor ones).
>
> Egon
>

Good to know, looks like the reverse-dependencies will not pose an issue
then.

~Niels


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Old 05-23-2012, 02:23 PM
Egon Willighagen
 
Default RFS: cdk 1.4.9-1

On Wed, May 23, 2012 at 4:15 PM, Niels Thykier <niels@thykier.net> wrote:
> The issue is that it fails to clean properly - at least some (java)doc
> files are not cleaned, but also some non-text files (can't remember - I
> didn't pay too much attention to it). *I haven't actually investigated
> the failure that deeply, so it may be trivial to fix. *

I'm happy to look at a full error report! (Not sure I can get around
to setting up an environment for building it myself... (I've done it
in the past, but have to relearn the steps each time...)

>> Cinfony 1.1 should work fine with CDK 1.4.x:
>> http://baoilleach.blogspot.com/2011/12/cinfony-11-released.html
>>
>> That post tells about a compile against 1.4.5, but as said, within
>> 1.4.x there are no API changes (or very minor ones).
>
> Good to know, looks like the reverse-dependencies will not pose an issue
> then. *

Except that the python-cinfony package needs updating too, and that
may imply having to updated rdkit and openbabel as well... (nothing
wrong with that, of course!

Egon


--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


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Old 05-24-2012, 04:25 AM
Onkar Shinde
 
Default RFS: cdk 1.4.9-1

On Wed, May 23, 2012 at 7:53 PM, Egon Willighagen
<egon.willighagen@gmail.com> wrote:
> On Wed, May 23, 2012 at 4:15 PM, Niels Thykier <niels@thykier.net> wrote:
>> The issue is that it fails to clean properly - at least some (java)doc
>> files are not cleaned, but also some non-text files (can't remember - I
>> didn't pay too much attention to it). *I haven't actually investigated
>> the failure that deeply, so it may be trivial to fix. *
>
> I'm happy to look at a full error report! (Not sure I can get around
> to setting up an environment for building it myself... (I've done it
> in the past, but have to relearn the steps each time...)

I will look into the build failure over weekend. I think one reason
might be that I forgot to clean javadocs in the clean target in
d/rules.

>
>>> Cinfony 1.1 should work fine with CDK 1.4.x:
>>> http://baoilleach.blogspot.com/2011/12/cinfony-11-released.html
>>>
>>> That post tells about a compile against 1.4.5, but as said, within
>>> 1.4.x there are no API changes (or very minor ones).
>>
>> Good to know, looks like the reverse-dependencies will not pose an issue
>> then. *
>
> Except that the python-cinfony package needs updating too, and that
> may imply having to updated rdkit and openbabel as well... (nothing
> wrong with that, of course!

A quick check of packages suggests that openbabel and rdkit are recent
enough for cinfony 1.1. But it seems to have gained new
(build)dependencies. So I am not sure how easy the task will be for
packaging latest cinfony.
Given this scenario, my suggestion is to target the cdk packaging for
'experimental' and then file a wishlist bug against cinfony for the
upgrade request (or simply test current version against new cdk). If
we are lucky then both will make into archives before freeze. Let me
know what you think.

Cheers,
Onkar
--
Passion - Some people climb mountains - others write Free software.
Don't ask why - the reason is the same.


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Old 05-24-2012, 07:54 AM
Niels Thykier
 
Default RFS: cdk 1.4.9-1

On 2012-05-24 06:25, Onkar Shinde wrote:
> On Wed, May 23, 2012 at 7:53 PM, Egon Willighagen
> <egon.willighagen@gmail.com> wrote:
>> [...]
>>
>> I'm happy to look at a full error report! (Not sure I can get around
>> to setting up an environment for building it myself... (I've done it
>> in the past, but have to relearn the steps each time...)
>
> I will look into the build failure over weekend. I think one reason
> might be that I forgot to clean javadocs in the clean target in
> d/rules.
>

Seems like a plausible reason.

>>
>> [...]
>>
>> Except that the python-cinfony package needs updating too, and that
>> may imply having to updated rdkit and openbabel as well... (nothing
>> wrong with that, of course!
>
> A quick check of packages suggests that openbabel and rdkit are recent
> enough for cinfony 1.1. But it seems to have gained new
> (build)dependencies. So I am not sure how easy the task will be for
> packaging latest cinfony.
> Given this scenario, my suggestion is to target the cdk packaging for
> 'experimental' and then file a wishlist bug against cinfony for the
> upgrade request (or simply test current version against new cdk). If
> we are lucky then both will make into archives before freeze. Let me
> know what you think.
>
> Cheers,
> Onkar

Personally I have no issues with targetting this for experimental; in
fact I think it makes perfect sense to use experimental for possible
API/ABI issues[1].

~Niels

[1] https://wiki.debian.org/Teams/ReleaseTeam/Transitions

"""
[...], you are more than welcome (and even encouraged) to use experimental.
"""


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Old 08-05-2012, 08:02 AM
Egon Willighagen
 
Default RFS: cdk 1.4.9-1

Hi Niels, Onkar,

On Thu, May 24, 2012 at 9:54 AM, Niels Thykier <niels@thykier.net> wrote:
> Personally I have no issues with targetting this for experimental; in
> fact I think it makes perfect sense to use experimental for possible
> API/ABI issues[1].

Daniel Leidert and I met up in Utrecht along with some 10 other Debian
developers for a lunch.

We briefly spoke about the CDK package, and I'm happy to see that
Cinfony 1.1 is in testing, which means that libcdk-java should be
upgraded without much trouble... I will have a look the JavaDoc
cleaning thing now...

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


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