Re: java9 javadoc errors (package htsjdk debianmed)

[olivier sallou]

Le lun. 16 avr. 2018 à 18:05, olivier sallou  a écrit :

> Hi,
>
> I face several javadoc errors (ending with NullPointerException) with
> openjdk 9 while updating package htsjdk.
>
> I saw on internet several bugs related to javadoc.
>
> Error ends with :
>
> javadoc: error - An exception occurred while building a component:
> TagInfo
>  (java.lang.NullPointerException)
>
> If I delete impacted files from doc, I go further but many files are
> impacted.
>
> Anyone faced and could solve this?
> It used to work on JDK8.
>
> Example impacted "doc":
>
> /**
>  * Calls close() on all elements of objs that implement
> Closeable
>  *
>  * @param objs   A list of potentially closeable objects
>  *
>  * NOTE: This method must take a List, not
> List, otherwise the overload above will be selected
>  * if the argument is not exactly List.
>  */
>
> Removing the last 2 lines part works.
>

It also occured on other files after a warning (not error):

/opt/debian/build-area/htsjdk-2.14.3+dfsg/src/main/java/htsjdk/samtools/util/BlockGunzipper.java:104:
warning - Parameter "compressedBlock" is documented more than once.


Removing duplicate declaration works. But javadoc should not fail on a
warning... (with an exception).

I am using opensjdk-9-jdk 9.0.4+12-4




>
> Last option would be to remove javadoc package or patch all files... :-(
>
>
> Olivier
>

java9 javadoc errors (package htsjdk debianmed)

[olivier sallou]

Hi,

I face several javadoc errors (ending with NullPointerException) with
openjdk 9 while updating package htsjdk.

I saw on internet several bugs related to javadoc.

Error ends with :

javadoc: error - An exception occurred while building a component:
TagInfo
 (java.lang.NullPointerException)

If I delete impacted files from doc, I go further but many files are
impacted.

Anyone faced and could solve this?
It used to work on JDK8.

Example impacted "doc":

/**
 * Calls close() on all elements of objs that implement
Closeable
 *
 * @param objs   A list of potentially closeable objects
 *
 * NOTE: This method must take a List, not
List, otherwise the overload above will be selected
 * if the argument is not exactly List.
 */

Removing the last 2 lines part works.

Last option would be to remove javadoc package or patch all files... :-(

Olivier

Re: Bug#879619: Autopkgtest for ncbi-tools6

[Liubov Chuprikova]

Hi Aaron,

On Fri, 13 Apr 2018 at 02:04 Aaron M. Ucko  wrote:

> Liubov Chuprikova  writes:
>
> > On Thu, 12 Apr 2018 at 17:30 Aaron M. Ucko  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

Re: Bug#879619: Autopkgtest for ncbi-tools6

[Aaron M. Ucko]

Liubov Chuprikova  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/?a...@monk.mit.edu