doxygen-users — List for users of doxygen

Re: [Doxygen-users] doxywizard can't run PlantUML

[rkennerly <rke...@gm...>]

Christoph Lipka wrote
> Am 01.07.2015 um 18:32 schrieb rkennerly:
>> MikePelley wrote
>>> I am trying to use the doxywizard with PlantUML.  PlantUML works fine by
>>> itself.  But when the doxywizard gets to the step to invoke PlantUML, it
>>> throws up a dialog saying "choose the program you want to use to open
>>> this
>>> file: java.exe".  Why is it trying to "open" java.exe?  It should just
>>> run
>>> it!  I'm on Windows 7 Professional, 64-bit.  Doxygen is 1.8.9.1
>>> installed
>>> from the binary distribution doxygen-1.8.9.1-setup.exe.
>>>
>>> Any help is appreciated!
>> I found a work-around for this exact problem by side-stepping the
>> "java.exe"
>> shortcut that is installed by the java installer (java version
>> "1.8.0_45")
>> at "C:\ProgramData\Oracle\Java\javapath".  Look at your "Path"
>> environment
>> variable in a command prompt window (type "path") and see if the
>> directory
>> for java includes symlink entries as it does on my system (Win7 64 bit). 
>> If
>> you look at "properties" for the shortcut called "java.exe" you can see
>> where it points to the real executable:
>>
>> C:\ProgramData\Oracle\Java\javapath>dir
>>   Directory of C:\ProgramData\Oracle\Java\javapath
>> ...
>> 07/01/2015  09:01 AM    
> <SYMLINK>
>       java.exe [C:\Program Files
>> (x86)\Java\jre1.8.0_45\bin\java.exe]
>>
>> So, I wrote a short batch file to prepend the actual install directory of
>> java to the front of my path that I can run before running doxygen (in
>> the
>> same Command Prompt window):
> 
> That's becoming a pain though as soon as the JRE is updated.
> 
> I had this issue, too; it appears that, as of recently, Windows refuses 
> to execute symbolic links with an ".exe" extension. On the interwebs 
> there are some hints that this change in behaviour was introduced with 
> security update KB3039066 (see 
> https://support.microsoft.com/en-us/kb/3039066), and indeed selectively 
> uninstalling that update fixed the problem for me. (Obviously you'll 
> have to live with an unpatched potential security issue instead, so you 
> may choose not to go that way.)

Yes - I see the problem has wider scope than I thought; I tried other
symlinks (created with mklink.exe from command prompt) and indeed I cannot
execute programs through these symlinks via explorer but can use them
successfully from command prompt.

I'm not a Java developer (C++) so I don't know what the scope of this
problem is (how many programs are affected given that there are other ways
to run java), but I found a link about this problem on an Oracle discussion
thread from April 1, 2015, so the problem has been around for at least three
months:

https://community.oracle.com/thread/3695801
<https://community.oracle.com/thread/3695801>  

As of now, I'm launching doxygen from Visual Studio in an nmake project and
I'm patching the path there (as above) - this will have to suffice until
Oracle fixes the problem or offers a safe alternative.




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Re: [Doxygen-users] Turn off warnings for 3rd party files

[Allen W. <wi...@kd...>]

On Thursday, July 02, 2015 09:09:43 AM Ferro, Alasdair wrote:
> Hi,
> 
> [Using Doxygen 1.8.9.1, on CentOS6.6]
> 
> I'm adding Doxygen to a fairly new project, which uses Qt. I've added some of the Qt header directories to Doxygen's INPUT list, so that Doxygen can extract some information (mostly class hierarchy & methods). However, this also causes *lots* of warnings to be emitted, for the Qt headers, which I don't own (obviously) so cannot fix. Is there any way to turn off warnings for those files, but keep them turned on for our code? When compiling, I use GCC's -isystem option to disable warnings from headers in those directories - does / could Doxygen have something similar?
> 
> BTW, I also get "QGDict::hashAsciiKey: Invalid null key" appearing (around 2800 times) - I guess it caused by the undocumented code in the Qt headers? Is this a known issue or should I submit a bug report?
> 
> Thanks for a great tool!
> 
Alasdair,

You want to point to the Qt tags files, not process the Qt headers directly.
as described in:
http://stackoverflow.com/questions/22244779/doxygen-generated-documentation-with-auto-generated-links-to-qt-project
and
http://www.stack.nl/~dimitri/doxygen/manual/external.html

Re: [Doxygen-users] doxywizard can't run PlantUML

[Christoph L. <chr...@li...>]

Am 01.07.2015 um 18:32 schrieb rkennerly:
> MikePelley wrote
>> I am trying to use the doxywizard with PlantUML.  PlantUML works fine by
>> itself.  But when the doxywizard gets to the step to invoke PlantUML, it
>> throws up a dialog saying "choose the program you want to use to open this
>> file: java.exe".  Why is it trying to "open" java.exe?  It should just run
>> it!  I'm on Windows 7 Professional, 64-bit.  Doxygen is 1.8.9.1 installed
>> from the binary distribution doxygen-1.8.9.1-setup.exe.
>>
>> Any help is appreciated!
> I found a work-around for this exact problem by side-stepping the "java.exe"
> shortcut that is installed by the java installer (java version "1.8.0_45")
> at "C:\ProgramData\Oracle\Java\javapath".  Look at your "Path" environment
> variable in a command prompt window (type "path") and see if the directory
> for java includes symlink entries as it does on my system (Win7 64 bit).  If
> you look at "properties" for the shortcut called "java.exe" you can see
> where it points to the real executable:
>
> C:\ProgramData\Oracle\Java\javapath>dir
>   Directory of C:\ProgramData\Oracle\Java\javapath
> ...
> 07/01/2015  09:01 AM    <SYMLINK>      java.exe [C:\Program Files
> (x86)\Java\jre1.8.0_45\bin\java.exe]
>
> So, I wrote a short batch file to prepend the actual install directory of
> java to the front of my path that I can run before running doxygen (in the
> same Command Prompt window):

That's becoming a pain though as soon as the JRE is updated.

I had this issue, too; it appears that, as of recently, Windows refuses 
to execute symbolic links with an ".exe" extension. On the interwebs 
there are some hints that this change in behaviour was introduced with 
security update KB3039066 (see 
https://support.microsoft.com/en-us/kb/3039066), and indeed selectively 
uninstalling that update fixed the problem for me. (Obviously you'll 
have to live with an unpatched potential security issue instead, so you 
may choose not to go that way.)

[Doxygen-users] Turn off warnings for 3rd party files

[Ferro, A. <Ala...@me...>]

Hi,

[Using Doxygen 1.8.9.1, on CentOS6.6]

I'm adding Doxygen to a fairly new project, which uses Qt. I've added some of the Qt header directories to Doxygen's INPUT list, so that Doxygen can extract some information (mostly class hierarchy & methods). However, this also causes *lots* of warnings to be emitted, for the Qt headers, which I don't own (obviously) so cannot fix. Is there any way to turn off warnings for those files, but keep them turned on for our code? When compiling, I use GCC's -isystem option to disable warnings from headers in those directories - does / could Doxygen have something similar?

BTW, I also get "QGDict::hashAsciiKey: Invalid null key" appearing (around 2800 times) - I guess it caused by the undocumented code in the Qt headers? Is this a known issue or should I submit a bug report?

Thanks for a great tool!

Alasdair

Re: [Doxygen-users] doxywizard a command line client

[Dimitri v. H. <do...@gm...>]

Hi Andreas,

> On 30 Jun 2015, at 13:28 , Andreas Tscharner <an...@vi...> wrote:
> 
> Hello World,
> 
> I've just installed doxygen 1.8.10. When I start doxywizard the first 
> thing that gets started is a command line shell and then the GUI gets 
> started. It didn't do that in 1.8.9.1.
> 
> Is this a bug or intentional?

It was a bug and has been fixed in the meantime.
Just download and reinstall the binary and the console is gone
(and also the binary will now work on Windows XP again).

Regards,
  Dimitri

Re: [Doxygen-users] doxywizard can't run PlantUML

[rkennerly <rke...@gm...>]

MikePelley wrote
> I am trying to use the doxywizard with PlantUML.  PlantUML works fine by
> itself.  But when the doxywizard gets to the step to invoke PlantUML, it
> throws up a dialog saying "choose the program you want to use to open this
> file: java.exe".  Why is it trying to "open" java.exe?  It should just run
> it!  I'm on Windows 7 Professional, 64-bit.  Doxygen is 1.8.9.1 installed
> from the binary distribution doxygen-1.8.9.1-setup.exe.
> 
> Any help is appreciated!

I found a work-around for this exact problem by side-stepping the "java.exe"
shortcut that is installed by the java installer (java version "1.8.0_45")
at "C:\ProgramData\Oracle\Java\javapath".  Look at your "Path" environment
variable in a command prompt window (type "path") and see if the directory
for java includes symlink entries as it does on my system (Win7 64 bit).  If
you look at "properties" for the shortcut called "java.exe" you can see
where it points to the real executable:

C:\ProgramData\Oracle\Java\javapath>dir
 Directory of C:\ProgramData\Oracle\Java\javapath
...
07/01/2015  09:01 AM    <SYMLINK>      java.exe [C:\Program Files
(x86)\Java\jre1.8.0_45\bin\java.exe]

So, I wrote a short batch file to prepend the actual install directory of
java to the front of my path that I can run before running doxygen (in the
same Command Prompt window):

REM Put the "real" java path in front of the one with a symlink to work with
doxygen:
set Path=C:\Program Files (x86)\Java\jre1.8.0_45\bin;%Path%

Now Plantuml diagrams are created fine via doxygen.

I would NOT recommend modifying your "Path" environment variable permanently
because this could open various security holes or break other things.

Hopefully someone will figure out the underlying problem with how java is
launched from doxygen and make plantuml work out-of-the-box.




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Re: [Doxygen-users] doxygen sort order

[woody <kn...@re...>]

At 01:02 PM 6/30/2015 -0400, Ron W wrote:
>On Tue, Jun 30, 2015 at 12:17 PM, woody 
><<mailto:kn...@re...>kn...@re...> wrote:
>When I ran doxygen and output a .rtf file, doxygen sorted the fields in a 
>structure by name,
>rather than by order of definition.
>How do you override this behavior so it will do it in line number order 
>(the way the structure
>is laid out).  It is a pain having to sort these by hand.
>
>
>In your Doxygen config:
>
>SORT_MEMBER_DOCS = NO

Thank you.   When I read that, it implied that the documents would be 
sorted somehow.

SORT_STRUCTURE_MEMBERS would have communicated it better I think.

I will change that for the next configuration.  I just completed a massive 
copy, delete, and paste effort on the .rtf file..... sigh..

Re: [Doxygen-users] doxygen sort order

[Ron W <ron...@gm...>]

On Tue, Jun 30, 2015 at 12:17 PM, woody <kn...@re...> wrote:

> When I ran doxygen and output a .rtf file, doxygen sorted the fields in a
> structure by name,
> rather than by order of definition.
> How do you override this behavior so it will do it in line number order
> (the way the structure
> is laid out).  It is a pain having to sort these by hand.
>
>
In your Doxygen config:

SORT_MEMBER_DOCS = NO

Re: [Doxygen-users] adding doxygen comments to code

[Ron W <ron...@gm...>]

On Tue, Jun 30, 2015 at 9:51 AM, woody <kn...@re...> wrote:

>
> How do you create the custom directives?
>

See: http://www.stack.nl/~dimitri/doxygen/manual/custcmd.html

"@req" is just a short hand for "@par Requirements".

"@range" is defined as:
        ALIASES += range{1}="@par Range @f[ @1 @f]"

"@issue" works like "@todo" and is defined as:
        ALIASES += issue="\xrefitem issues,\"Issue\",\"Issues Addressed\""

[Doxygen-users] doxygen sort order

[woody <kn...@re...>]

When I ran doxygen and output a .rtf file, doxygen sorted the fields in a 
structure by name,
rather than by order of definition.
How do you override this behavior so it will do it in line number order 
(the way the structure
is laid out).  It is a pain having to sort these by hand.

[Doxygen-users] doxywizard a command line client

[Andreas T. <an...@vi...>]

Hello World,

I've just installed doxygen 1.8.10. When I start doxywizard the first 
thing that gets started is a command line shell and then the GUI gets 
started. It didn't do that in 1.8.9.1.

Is this a bug or intentional?

Thanks for this great product!

Best regards
	Andreas
-- 
       ("`-''-/").___..--''"`-._
        `o_ o  )   `-.  (     ).`-.__.`)
        (_Y_.)'  ._   )  `._ `. ``-..-'
      _..`--'_..-_/  /--'_.' .'
     (il).-''  (li).'  ((!.-'

Andreas Tscharner   an...@vi...   ICQ-No. 14356454

[Doxygen-users] Building doxygen 1.8.10 with custom tools

[Ferro, A. <Ala...@me...>]

Hi,

I'm trying to build the latest Doxygen release with a custom Python and Flex build (for various reasons I still have to build on SLES10...). Previously (i.e. with 1.8.9.1) I used:

./configure \
   --prefix /install/path \
   --english-only \
   --python python2.7 \
   --flex /path/to/flex-2.5.35/bin/flex
make -j && make docs && make install

What options can I pass to cmake to replicate the above configuration options?

Thanks,

Alasdair

Re: [Doxygen-users] Doxygen does not generate documentation from html pages

[didje <dia...@pd...>]

Hi Albert, I did search the forums, without success - I was perhaps being too
specific about my search term, checking for "html" related answers only.
However, I did not check the FAQ, the one you mention answers my question.
Thanks.



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Re: [Doxygen-users] adding doxygen comments to code

[Ron W <ron...@gm...>]

On Mon, Jun 29, 2015 at 4:32 PM, woody <kn...@re...> wrote:

> The html documentation has the line numbers, as does the rtf file, so
> obviously it is tracking at some level.
>
> I see that the call graphs are interspersed through the rtf file, but they
> are not really grouped into a coherent structure.
> And I never found them at all in the html generated stuff.
>
>
> *::#define CONTROL_TABLE 1 *Definition at line 388 of file
> medbest_310_o_split.c.
>
> *::void adc_window_complete ()*


I meant for the references. I know it records the line numbers of the
definitions.


>
> There is the @brief and a ton more.
>

We use "AUTO_BRIEF" in our Doxygen configuration so we rarely need @brief
or @details. Besides @return, we use @f$, @f[ and @f] (for formulae),
@note, @internal/@endinternal, @ref, @see, @page, @section, @test, @todo,
and a few custom directives.* But, most of the time, we only need
descriptive prose.

> I don't know what requirements IEC 62304 imposes, particularly on "in
> line" code documentation.
>
>
> It is a very long discussion
>

Looks very similar to ISO-26262. Doxygen helps us here because we can
define the interfaces directly at the code level and generate an interface
document from that. Otherwise, Doxygen's strength is in generating low
level documentation. Higher level documentation, we use Dia to create
diagrams and charts and Libre Office to write prose.

* Our custom Doxygen directives include @req (for denoting requirements (by
ReqID)), @range (for annotating limits and constraints) and @issue (for
annotating code changes made per issue tracking).

Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10

[Robert H. <he...@de...>]

At Mon, 29 Jun 2015 21:36:15 +0200 Dimitri van Heesch <do...@gm...> wrote:

> 
> 
> > On 29 Jun 2015, at 21:29 , Dimitri van Heesch <do...@gm...> wrote:
> > 
> > Hi Jean,
> > 
> >> On 29 Jun 2015, at 10:05 , Jean Audibert <jau...@eu...> wrote:
> >> 
> >> Hi!
> >> 
> >> Until the release 1.8.9.1, I was able to build Doxygen (binaires ands RPMs) with this command:
> >> $ rpmbuild -ta doxygen-<VERSION>.src.tar.gz
> >> 
> >> With the last release, this command fails: "error: Failed to read spec file from doxygen-1.8.10.src.tar.gz"
> >> 
> >> I think it's related to the CMake build. So now, what is the best way to achieve build of RPMs?
> > 
> > Unfortunately, the spec file has not been updated to the new build system yet :-(
> > Since this was a third party contribution in the past, I'm open for suggestions on how to correct it.
> 
> This looks like a promising starting point:
> https://schneide.wordpress.com/2013/02/11/build-a-rpm-package-using-cmake/

The *big downside* to using CPack to make the *binary* RPMs is that the RPM(s)
can only be made with CPack -- you don't get a .src.rpm, so it is not possible
to later rebuild the RPM using rpmbuild (say if you want to rebuild the Fedora
RPM for EL6, because of differences in the Glibc version or something, or want
to build it for a different machine type, etc.). With the CPack RPM, all you
get is a binary RPM and anyone downsteam *has* to know how to build the
package using CMake's tools (which is non-obvious to someone not familure with
CMake or CPack). It also breaks things for distro repackagers, who take source
RPMs from one distro and rebuild them for another, including creating derived
distros. For *most* packages one just gets the source RPMs and does a rpmbuild
--rebuild on them -- this process can be automated easily. Using CPack breaks
this, requiring manual hand hackery.

When I created RPMs (and also debs) for xtrkcad, I created my own spec file 
and used rpmbuild to create source and binary RPMs and skipped using CPack.

(BTW: CPack is a bit broken in that it fails to build proper source archives 
under some situations.)

> 
> Regards,
>   Dimitri
> ------------------------------------------------------------------------------
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Re: [Doxygen-users] adding doxygen comments to code

[woody <kn...@re...>]

>Doxygen might only save the names of functions where each variable and 
>function are referenced, but not the line numbers.

The html documentation has the line numbers, as does the rtf file, so 
obviously it is tracking at some level.

I see that the call graphs are interspersed through the rtf file, but they 
are not really grouped into a coherent structure.
And I never found them at all in the html generated stuff.

::#define CONTROL_TABLE 1
Definition at line 388 of file medbest_310_o_split.c.
::void adc_window_complete ()

Definition at line 5983 of file medbest_310_o_split.c.
  5984     {
  5985     }
::void adc_window_interrupt ()

Definition at line 5970 of file medbest_310_o_split.c.
  5971     {
  5972     }
::data char beep_count

Definition at line 1052 of file medbest_310_o_split.c.
::data int beep_duration

Definition at line 1053 of file medbest_310_o_split.c.
And the .rtf file lists the code for each function.


>The HTML source listings Doxygen can generate contain algorithmically 
>generated anchors to serve as target for links from the generated 
>documentation, so line numbers are not needed.
>
>Certainly would be good if it could produce a cross-reference with line 
>numbers.
>Well, consider the issue raised :D .  It just seems obvious.
>
>
>I'm just a user of Doxygen.Â



I wonder if Dimitri monitors this list....

>>Even after comments blocks are automatically inserted, I would think you 
>>will still have to do extensive editing to include descriptive prose.
>You might, but they would just be padding on existing lines more or 
>less.  So yes, but it is a lot easier and quicker to go into the code and 
>add the comments or descriptive prose to an
>existing comment block.   1. You don't have to remember how to create 
>the block.   2. with the blocks in place, documentation would certainly 
>be easier.
>
>
>My team and I have templates defined in the source code editors we use. 
>When reviewing/studying legacy code, we can insert the relevant temple and 
>fill in the descriptive prose. Or, more often, since what Doxygen needs is 
>so minimal, just type. for example:
>  /** One line description.
>   * More detail....
>   * @return Description of what's returned.
>   */
>or:
>  /**< One line description after a parameter or variable definition. More 
> detail.... */

There is the @brief and a ton more.

>One of the things coming down in the medical device world, is compliance 
>with IEC 62304.  One part of this requires detailed 
>architectural  descriptions and diagrams.  Current code will ultimately
>have to be brought up to that standard, and all over the medical world, 
>people are having to back document programs.
>
>
>I don't know what requirements IEC 62304 imposes, particularly on "in 
>line" code documentation.

It is a very long discussion :(  But essentially it means for class A and 
B, you have to document each software item, and create architectural 
documents, etc.
For class C (stuff that can kill you) it gets really detailed, with having 
to document all boundry conditions code flow and on and on...
  part of the checklist B and C are classes.

[B, C] The manufacturer transformed the requirements for the medical device 
software into a documented architecture that describes the software’s 
structure and identifies the software items
[B, C] The manufacturer developed and documented an architecture for the 
interfaces between the software items and the components external to the 
software items (both software and hardware), and between the software items
[B, C] If a software item is identified as soup, the manufacturer specified 
functional and performance requirements for the soup item that are 
necessary for its intended use
[B, C] If a software item is identified as soup, the manufacturer specified 
the system hardware and software necessary to support the proper operation 
of the soup item
[C] The manufacturer identified the segregation between software items that 
is essential to risk control, and state how to ensure that the segregation 
is effective

[B, C] The manufacturer verified and document that:
a) the architecture of the software implements system and software 
requirements including those relating to risk control
b) the software architecture is able to support interfaces between software 
items and between software items and hardware
c) the medical device architecture supports proper operation of any soup items
[B, C] The manufacturer refined the software architecture until it is 
represented by software units
[C] The manufacturer developed and documented a detailed design for each 
software unit of the software item


>Feeding the output of Doxygen back in to the source files is possible. 
>Most probably something to be done using a post processor.
>Â
>I have attached a file, and hope it comes through.
>
>current_intensity is the variable.  This shows that build_array uses it, 
>as do a bunch of the routines that build array calls.
>There are many other places in the code where this variable are referenced.
>
>
>Right now, Doxygen can produce a call graph similar to what your charts 
>shows in relation to "build_array" and what it calls.
>
>Enhancing Doxygen to product a (textural) cross-reference should not be 
>hard. However, I can't speak to the internals of Doxygen.
>
>The chart you produced with Source Insight is a hybrid of a call graph and 
>a graphical cross-reference. That is most likely best implemented as a 
>post processor.

Probably.  You can turn off the cross reference, in which case it is a call 
graph.

>Â
>Doxygen has the info to do this, or would with an extension.  I was 
>hoping that graphvis would be able to take Doxygen's data
>and produce this kind of diagram automatically for each function, 
>variable, and data structure.
>
>
>With a cross-reference and the output Doxygen currently produces, post 
>processing should be able to produce most kinds of (code) relationship 
>diagrams.




>Flow diagrams would require help from additional analysis tools. 
>Unfortunately, all such tools I know of that provide the kind of 
>sophisticated analysis that Source Insight does are expensive, proprietary 
>tools that work much like you describe Source Insight, unless you add 
>expensive, optional reporting extensions.

Well source insight isn't exactly cheap, around 239.00 or so.  But it isn't 
a flow analysis tool per se.
http://www.sourceinsight.com/eval.html  you can download a 30 day trial, 
and there are keys on the net.
I was one of Ray Grahms early beta testers.

It is one of the coolest editors ever, with full syntax coloring and 
parsing for literally dozens of languages, and a fully documented api that 
you can extend.
an more nifty features than you can shake a stick at.



>Graphvis is just a tool for interpreting description in DOT notation in to 
>graphical charts. It has no analysis capability. Doxygen uses it because 
>it was much easier to use it than to attempt to produce such diagrams directly.

Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10

[Jean A. <jau...@eu...>]

Hi Dimitri,

Thanks for your e-mails.

In my team we build&package several tools (like Git and CMake) to keep dev boxes (from el5 to el7) up-to-date.
So we had to work/rework spec files and builds.

Let me see with my colleagues what we can provide/suggest. It would a pleasure to contribute.
The current spec file and your link are very good starting points.

Best,

Jean

----- Message d'origine -----
De : Dimitri van Heesch [mailto:do...@gm...]
Envoyé : Monday, June 29, 2015 09:36 PM
À : Jean Audibert
Cc : dox...@li... <dox...@li...>
Objet : Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10


> On 29 Jun 2015, at 21:29 , Dimitri van Heesch <do...@gm...> wrote:
> 
> Hi Jean,
> 
>> On 29 Jun 2015, at 10:05 , Jean Audibert <jau...@eu...> wrote:
>> 
>> Hi!
>> 
>> Until the release 1.8.9.1, I was able to build Doxygen (binaires ands RPMs) with this command:
>> $ rpmbuild -ta doxygen-<VERSION>.src.tar.gz
>> 
>> With the last release, this command fails: "error: Failed to read spec file from doxygen-1.8.10.src.tar.gz"
>> 
>> I think it's related to the CMake build. So now, what is the best way to achieve build of RPMs?
> 
> Unfortunately, the spec file has not been updated to the new build system yet :-(
> Since this was a third party contribution in the past, I'm open for suggestions on how to correct it.

This looks like a promising starting point:
https://schneide.wordpress.com/2013/02/11/build-a-rpm-package-using-cmake/

Regards,
  Dimitri

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Re: [Doxygen-users] adding doxygen comments to code

[Ron W <ron...@gm...>]

On Mon, Jun 29, 2015 at 10:58 AM, woody <kn...@re...> wrote:
>
> It *has* to have the information though, whether or not it organizes it.
> When it scan a program, indentifies a symbol, it reports which line the
> symbol is defined on.  It could and should
> also have an option to report ALL the lines.
>

Doxygen might only save the names of functions where each variable and
function are referenced, but not the line numbers.

The HTML source listings Doxygen can generate contain algorithmically
generated anchors to serve as target for links from the generated
documentation, so line numbers are not needed.

Certainly would be good if it could produce a cross-reference with line
numbers.

Well, consider the issue raised :D .  It just seems obvious.
>

I'm just a user of Doxygen.

> Even after comments blocks are automatically inserted, I would think you
> will still have to do extensive editing to include descriptive prose.
>
>
> You might, but they would just be padding on existing lines more or less.
> So yes, but it is a lot easier and quicker to go into the code and add the
> comments or descriptive prose to an
> existing comment block.   1. You don't have to remember how to create the
> block.   2. with the blocks in place, documentation would certainly be
> easier.
>

My team and I have templates defined in the source code editors we use.
When reviewing/studying legacy code, we can insert the relevant temple and
fill in the descriptive prose. Or, more often, since what Doxygen needs is
so minimal, just type. for example:
       /** One line description.
        * More detail....
        * @return Description of what's returned.
        */
or:
        /**< One line description after a parameter or variable definition.
More detail.... */

One of the things coming down in the medical device world, is compliance
> with IEC 62304.  One part of this requires detailed architectural
> descriptions and diagrams.  Current code will ultimately
> have to be brought up to that standard, and all over the medical world,
> people are having to back document programs.
>

I don't know what requirements IEC 62304 imposes, particularly on "in line"
code documentation.

Doxygen is meant to make generating a separate document from special
comments contained in the code. The (limited) source analysis capability
Doxygen has is there to make adding and maintaining those comments easier
by allowing the coder/documentor to follow the principle of "Do Not Repeat
Yourself".

Feeding the output of Doxygen back in to the source files is possible. Most
probably something to be done using a post processor.


> I have attached a file, and hope it comes through.
>
> current_intensity is the variable.  This shows that build_array uses it,
> as do a bunch of the routines that build array calls.
> There are many other places in the code where this variable are referenced.
>

Right now, Doxygen can produce a call graph similar to what your charts
shows in relation to "build_array" and what it calls.

Enhancing Doxygen to product a (textural) cross-reference should not be
hard. However, I can't speak to the internals of Doxygen.

The chart you produced with Source Insight is a hybrid of a call graph and
a graphical cross-reference. That is most likely best implemented as a post
processor.


> Doxygen has the info to do this, or would with an extension.  I was hoping
> that graphvis would be able to take Doxygen's data
> and produce this kind of diagram automatically for each function,
> variable, and data structure.
>

With a cross-reference and the output Doxygen currently produces, post
processing should be able to produce most kinds of (code) relationship
diagrams.

Flow diagrams would require help from additional analysis tools.
Unfortunately, all such tools I know of that provide the kind of
sophisticated analysis that Source Insight does are expensive, proprietary
tools that work much like you describe Source Insight, unless you add
expensive, optional reporting extensions.

Graphvis is just a tool for interpreting description in DOT notation in to
graphical charts. It has no analysis capability. Doxygen uses it because it
was much easier to use it than to attempt to produce such diagrams directly.

Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10

[Dimitri v. H. <do...@gm...>]

> On 29 Jun 2015, at 21:29 , Dimitri van Heesch <do...@gm...> wrote:
> 
> Hi Jean,
> 
>> On 29 Jun 2015, at 10:05 , Jean Audibert <jau...@eu...> wrote:
>> 
>> Hi!
>> 
>> Until the release 1.8.9.1, I was able to build Doxygen (binaires ands RPMs) with this command:
>> $ rpmbuild -ta doxygen-<VERSION>.src.tar.gz
>> 
>> With the last release, this command fails: "error: Failed to read spec file from doxygen-1.8.10.src.tar.gz"
>> 
>> I think it's related to the CMake build. So now, what is the best way to achieve build of RPMs?
> 
> Unfortunately, the spec file has not been updated to the new build system yet :-(
> Since this was a third party contribution in the past, I'm open for suggestions on how to correct it.

This looks like a promising starting point:
https://schneide.wordpress.com/2013/02/11/build-a-rpm-package-using-cmake/

Regards,
  Dimitri

Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10

[Dimitri v. H. <do...@gm...>]

Hi Jean,

> On 29 Jun 2015, at 10:05 , Jean Audibert <jau...@eu...> wrote:
> 
> Hi!
> 
> Until the release 1.8.9.1, I was able to build Doxygen (binaires ands RPMs) with this command:
> $ rpmbuild -ta doxygen-<VERSION>.src.tar.gz
> 
> With the last release, this command fails: "error: Failed to read spec file from doxygen-1.8.10.src.tar.gz"
> 
> I think it's related to the CMake build. So now, what is the best way to achieve build of RPMs?

Unfortunately, the spec file has not been updated to the new build system yet :-(
Since this was a third party contribution in the past, I'm open for suggestions on how to correct it.

Regards,
  Dimitri

[Doxygen-users] Fw: background colour

[<pa...@ar...>]

Hi Phil. Thanks for the reply.
Please forgive my boldness, but next time please click on reply to all, so that every body in the mailing list is able to learn from your reply.

Have a wonderful and joyful day friend. 

From: Phil Dixon 
Sent: Monday, June 29, 2015 3:56 AM
To: pa...@ar... 
Subject: Re: [Doxygen-users] background colour

The background appears blue as default.  If you use the wizzard you can change the colour to anything at all but I've no idea where the colour is held which is a bit of a pain when setting up a project.


On 29 June 2015 at 06:27, <pa...@ar...> wrote:

  I have noticed the doxygen home page has a colour blue in the title bar, matching the logo. I would like to have the same effect on my page, how can I do that?

  thanks 



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Re: [Doxygen-users] Doxygen does not generate documentation from html pages

[Albert <alb...@gm...>]

Did you have a look at the FAQs especially the one "My file with a custom
extension is not parsed (properly) (anymore)." or the forums where this
topic hs been handled a number of times?

Albert

On Mon, Jun 29, 2015 at 1:50 PM, didje <dia...@pd...> wrote:

> Doxygen 1.8.10.
>
> I generate documentation from a mix of .h files and .html files.
> I was using Doxygen 1.8.7 and the documentation was generated correctly
> from
> these sources.
> However, I have just installed 1.8.10 and see that the .html files I
> reference in my INPUT tag do not generate anything in the output
> documentation.
>
> I presume nothing was changed between 1.8.7 and 1.8.10 to prevent the use
> of
> .html files for generating doxygen output, so I presume it must be a
> configuration issue of some sort - however, when I look at the doxyfile
> configuration file, there is no setting which has been added connected to
> this, as far as I can see.
>
>
>
>
>
> --
> View this message in context:
> http://doxygen.10944.n7.nabble.com/Doxygen-does-not-generate-documentation-from-html-pages-tp7236.html
> Sent from the Doxygen - Users mailing list archive at Nabble.com.
>
>
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>

Re: [Doxygen-users] Doxygen-users Digest, Vol 109, Issue 5

[woody <kn...@re...>]

>
>
>
>Doxygen can produce and XML file containing the information it extracted 
>and/or derived from the source files. With out testing, I don't know if 
>contains any line numbers. (This is intended to be used by "add on" report 
>generators.)
>
>Anyway, Â it should be possible to create a "post processor" that would 
>read this XML and generate, for example, a set of sed scripts that could 
>insert comment blocks into copies of your source files.

Sound like it.  I know nothing about XML unfortunately :(



>This is a separate issue. I don't think Doxygen has any option to generate 
>a cross reference. If it does, Then it certainly should also have an 
>option to produce it as part of a "document all" operation.

I agree. I *has* to have the information though, whether or not it 
organizes it.  When it scan a program, indentifies a symbol, it reports 
which line the symbol is defined on.  It could and should
also have an option to report ALL the lines.  I would think it would be a 
"simple" [I know, there are NO simple program changes :) ]  matter to 
attach to the defined line, another data structure that would
contain a line number for each non comment line that it finds the 
symbol.  It might just be a matter of making a linked list of line numbers, 
using the defined line as the head of the list, and just adding to
it as lines are found.


> >you don't need to add the comments to the code to get them (but I think
> >normally you want to go in and improve on them).
>
>yes, but on a multi thousand line code base that would be very expensive in
>terms of time and money.  It seems so logical to have Doxygen be able to 
>do it
>for you on a one time basis to get a start.  It baffles me that it
>can't.  It certainly has the information.  It would make it a much more
>complete documentation tool.
>
>
>Because Doxygen doesn't need comments to produce the default 
>documentation, nobody saw a need to create an "add on" to automatically 
>insert comment blocks.

Well, consider the issue raised :D .  It just seems obvious.

>Â
>Here is the problem.  The major use case for doxygen is to come in behind
>some guy who wrote a bunch of code, and gain
>some idea of how the code works, so you can maintain it, and create a
>documentation package for it.
>
>...Â
>Doxygen is most of the way there, but it
>desperately needs a way to be able
>to insert the comments it can generate, into the source.
>
>
> From looking at the "C Doc" generated comment sample you provided, you 
> appear to want Doxygen (or an add on to Doxygen) to insert the generated 
> pieces of documentation into comment blocks before each function, global 
> variable and other "document-able objects".

Absolutely.  Once that is done, then going back and maintaining the 
comments will be much easier, and the documentation will be much nicer.


>A tool to do this (based on information extracted by Doxygen) could 
>certainly be made.
>I would have to do extensive editing to the code to embed the comments
>that doxygen can use to create the documentation correctly.
>
>
>Even after comments blocks are automatically inserted, I would think you 
>will still have to do extensive editing to include descriptive prose.

You might, but they would just be padding on existing lines more or 
less.  So yes, but it is a lot easier and quicker to go into the code and 
add the comments or descriptive prose to an
existing comment block.   1. You don't have to remember how to create the 
block.   2. with the blocks in place, documentation would certainly be easier.

My way of looking at code is that it is the crystallized thoughts and 
thought process of the programmer.  One should write code for the guy 
coming behind.  The compiler doesn't care about comments
and will generate the code regardless of comments.  But comment blocks etc, 
especially of the kind that Doxygen uses would be very helpful.

One of the things coming down in the medical device world, is compliance 
with IEC 62304.  One part of this requires detailed 
architectural  descriptions and diagrams.  Current code will ultimately
have to be brought up to that standard, and all over the medical world, 
people are having to back document programs.

>Â
>I have yet to get doxygen to do a flow tree, though I have enabled the
>"dot" stuff and have graphviz in the path.  It created flows only
>for certain structures, and those are really not right.
>
>
>Doxygen really only "creates" call graphs and a few other basic 
>relationship graphs. It was not intended as a source code analyzer.
>Â
>I am aware that *IF* you have the right headers, Doxygen can do this and a
>whole lot more.
>
>
>I'm not sure how much of the needed information would (or could) be in 
>Doxygen's output to create comment blocks with the "fields" needed. 
>Enhancing Doxygen to generate a cross reference seems reasonably possible. 
>But, as I said above, Doxygen was not intended to be a source code 
>analyzer. Output from a proper source code analyzer may also be needed.

I have attached a file, and hope it comes through.

This file was generated by Source Insight, the source editor I use.  Ray 
Grahm has done a fantastic job with this tool.   This is the kind of 
diagram that I would like to be able to generate via Doxygen and
other tools.

The problem with doing this with Source Insight, is that you have to click 
on one variable at a time, and then do a screen capture.  It is fraught 
with problems.  missing one, the long manaul series of
operations, and on and on.
Notice that this produces the kind of "flow" diagram needed.

current_intensity is the variable.  This shows that build_array uses it, as 
do a bunch of the routines that build array calls.
There are many other places in the code where this variable are referenced.

Doxygen has the info to do this, or would with an extension.  I was hoping 
that graphvis would be able to take Doxygen's data
and produce this kind of diagram automatically for each function, variable, 
and data structure.



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Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10

[Robert H. <he...@de...>]

At Mon, 29 Jun 2015 13:40:44 +0000 Jean Audibert <jau...@eu...> wrote:

> 
> Hi Robert,
> 
> Thanks for your answer.
> 
> Sorry, but I'm not sure to understand.
> You mean that the SPEC file in
> doxygen-1.8.10.src.tar.gz\doxygen-1.8.10.src.tar\doxygen-1.8.10\packages\rpm\doxygen.spec.in
> is useless?

Its in the wrong place for rpmbuild -ta. I am not sure what CMake's idea of
subverting rpmbuild is. For rpmbuild -ta ...tar.gz to work, the SPEC file
needs to be at the toplevel of the tarball. I believe CMake has some other
ideas, including *NOT* using rpmbuild, but using its own 'logic' that
*replaces* rpmbuild instead. I think you have to unpack the archive, build the
package 'normally', *then* run some *special* CMake command to build the RPM
from the build binaries (I don't really know the exact incantation). You
*don't* get a package-version.src.rpm this way. I think esentually you end up
building a binary-only (batch) of RPM(s). Which is stupid and unhelpful for
anyone 'downstream' of whoever is distributing the RPMs -- eg it means that
anyone who needs to rebuild the RPM(s), have to get the original source and
built it from scratch. It also means it is not possible to build RPMs with
distro-specific patches. And thus, it is probably less than useful for these
and other related reasons.

> 
> So, what is the new procedure to build RPM?
> 
> Thanks,
> 
> Jean
> 
> -----Original Message-----
> From: Robert Heller [mailto:he...@de...] 
> Sent: lundi 29 juin 2015 14:22
> To: Jean Audibert
> Cc: 'dox...@li...'; Robert Heller
> Subject: Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10
> 
> At Mon, 29 Jun 2015 08:05:40 +0000 Jean Audibert <jau...@eu...> wrote:
> 
> > 
> > Hi!
> > 
> > Until the release 1.8.9.1, I was able to build Doxygen (binaires ands RPMs) with this command:
> > $ rpmbuild -ta doxygen-<VERSION>.src.tar.gz
> > 
> > With the last release, this command fails: "error: Failed to read spec file from doxygen-1.8.10.src.tar.gz"
> > 
> > I think it's related to the CMake build. So now, what is the best way to achieve build of RPMs?
> >
> 
> No, more likely simply that somehow the spec file was left out of the source archive.  The *might* be related to the CMake build, in that possibly the spec file was left out of the CMake equivelant of AutoMake's 'EXTRA_DIST' variable. 
> 
>  
> > Thanks a lot!
> > 
> > Jean
> > 
> > 
> > _________________________________________________________________
> > 
> > This message may contain confidential information and is intended for specific recipients unless explicitly noted otherwise. If you have reason to believe you are not an intended recipient of this message, please delete it and notify the sender. This message may not represent the opinion of Euronext N.V. or any of its subsidiaries or affiliates, and does not constitute a contract or guarantee. Unencrypted electronic mail is not secure and the recipient of this message is expected to provide safeguards from viruses and pursue alternate means of communication where privacy or a binding message is desired.
> > 
> > 
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> >                                                                                                                               
> 

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Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10

[Jean A. <jau...@eu...>]

Hi Robert,

Thanks for your answer.

Sorry, but I'm not sure to understand.
You mean that the SPEC file in doxygen-1.8.10.src.tar.gz\doxygen-1.8.10.src.tar\doxygen-1.8.10\packages\rpm\doxygen.spec.in is useless?

So, what is the new procedure to build RPM?

Thanks,

Jean

-----Original Message-----
From: Robert Heller [mailto:he...@de...] 
Sent: lundi 29 juin 2015 14:22
To: Jean Audibert
Cc: 'dox...@li...'; Robert Heller
Subject: Re: [Doxygen-users] Unable to build RPMs for Doxygen v1.8.10

At Mon, 29 Jun 2015 08:05:40 +0000 Jean Audibert <jau...@eu...> wrote:

> 
> Hi!
> 
> Until the release 1.8.9.1, I was able to build Doxygen (binaires ands RPMs) with this command:
> $ rpmbuild -ta doxygen-<VERSION>.src.tar.gz
> 
> With the last release, this command fails: "error: Failed to read spec file from doxygen-1.8.10.src.tar.gz"
> 
> I think it's related to the CMake build. So now, what is the best way to achieve build of RPMs?
>

No, more likely simply that somehow the spec file was left out of the source archive.  The *might* be related to the CMake build, in that possibly the spec file was left out of the CMake equivelant of AutoMake's 'EXTRA_DIST' variable. 

 
> Thanks a lot!
> 
> Jean
> 
> 
> _________________________________________________________________
> 
> This message may contain confidential information and is intended for specific recipients unless explicitly noted otherwise. If you have reason to believe you are not an intended recipient of this message, please delete it and notify the sender. This message may not represent the opinion of Euronext N.V. or any of its subsidiaries or affiliates, and does not constitute a contract or guarantee. Unencrypted electronic mail is not secure and the recipient of this message is expected to provide safeguards from viruses and pursue alternate means of communication where privacy or a binding message is desired.
> 
> 
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>                                                                                                                               

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Deepwoods Software        -- Custom Software Services
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he...@de...       -- Webhosting Services
                                                                          

_________________________________________________________________

This message may contain confidential information and is intended for specific recipients unless explicitly noted otherwise. If you have reason to believe you are not an intended recipient of this message, please delete it and notify the sender. This message may not represent the opinion of Euronext N.V. or any of its subsidiaries or affiliates, and does not constitute a contract or guarantee. Unencrypted electronic mail is not secure and the recipient of this message is expected to provide safeguards from viruses and pursue alternate means of communication where privacy or a binding message is desired.