Re: 8.0.32-1ubuntu1.3~ppa2 patches not in tomcat8 8.0.32-1ubuntu1.4

[Jack Howarth]

Nish,
   Can you recreate your test packaging on
https://launchpad.net/~nacc/+archive/ubuntu/tomcat8v2/+packages based off
of the current tomcat8 package in xenial? I would be happy to test if your
proposed bug fixes resolve the problems with ubuntu's tomcat failing to run
the MetaboAnalyst war application properly.
  Jack

On Thu, Jul 27, 2017 at 4:23 PM, Nish Aravamudan <
nish.aravamu...@canonical.com> wrote:

> On Thu, Jul 27, 2017 at 12:00 PM, Robie Basak 
> wrote:
> > On Thu, Jul 27, 2017 at 09:48:06AM -0400, Jack Howarth wrote:
> >>Is there a reason that the patches present in the test tomcat8
> >> 8.0.32-1ubuntu1.3~ppa2 were dropped from tomcat8 8.0.32-1ubuntu1.4?
> >
> > Where were you getting 8.0.32-1ubuntu1.3~ppa2 from? That doesn't sound
> > like something that would have been published by Ubuntu.
>
> I believe that is referring to the version in  my PPA at
> https://launchpad.net/~nacc/+archive/ubuntu/tomcat8v2/+packages. It
> feels more productive to contact me directly, but on the list is fine
> too.
>
> That test build was for several LP bugs for tomcat8.
>
> https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1593854 - no
> response to latest testing yet
> https://bugs.launchpad.net/ubuntu/+source/tomcat7/+bug/1482893 - no
> testing feedback
> https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1606331 -
> tested successfully
> https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1644144 - no
> testing feedback
>
> It's hard for me, with confidence, to upload fixes to the archive with
> no testing feedback. And, it's not uncommon for there to be "races"
> between uploaders -- in this case, ubuntu1.4 has a fix for a totally
> unrelated bug to the above.
>
> -Nish
>
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Re: 8.0.32-1ubuntu1.3~ppa2 patches not in tomcat8 8.0.32-1ubuntu1.4

[Jack Howarth]

Nish,
 Nevermind. I manually installed your previous test packages under
current xenial and those changes don't solve the breakage in running the
MetaboAnalyst war under tomcat8 on ubuntu. As I mentioned before, when
using glassfish there is no problems running MetaboAnalyst but under
tomca8, one gets...

HTTP Status 404 -
type Status report
message
description The requested resource is not available.
Apache Tomcat/8.0.32 (Ubuntu)

for http://localhost:8080/MetaboAnalyst/faces/ModuleView.xhtml.

I know that tomcat 8.0.32 should be able to run this war as we do it in the
fink project on MacOS against the Oracle JDK 1.8.
 Jack
ps I have attached the /var/lib/tomcat8/logs directory from my installation
which contains the files created after...

installing authbind, libcommons-collections3-java, libcommons-dbcp-java,
libcommons-pool-java, libecj-java, libjakarta-taglibs-standard-java, libjax
p1.3-java, libjstl1.1-java, libtomcat8-java, libxalan2-java,
libxerces2-java, libxml-commons-external-java,  libxml-commons-resolver1.1-j
ava,  tomcat8, tomcat8-admin, tomcat8-common, tomcat8-docs,
tomcat8-examples, and tomcat8-user using your test tomcat packages and then
executing...

$ sudo -u tomcat8 R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Rserve)
> Rserve()

followed by entering the url...

http://localhost:8080/MetaboAnalyst/faces/ModuleView.xhtml

into the browser which produces the error message I cited earlier.

Note that this works fine under glassfish with the caveat that glassfish4
as well as R and the launched Rserve are all run as the current user.
However, steps that I am using for running under tomcat8 as its user work
fine on MacOS so this failure on ubuntu is all very confusing.

Also note that Rutter's R and cran's have to be used since current
Bioconductor requires R 3.4.





On Thu, Jul 27, 2017 at 8:14 PM, Nish Aravamudan <
nish.aravamu...@canonical.com> wrote:

> On Thu, Jul 27, 2017 at 5:04 PM, Jack Howarth
>  wrote:
> > Nish,
> >Can you recreate your test packaging on
> > https://launchpad.net/~nacc/+archive/ubuntu/tomcat8v2/+packages based
> off of
> > the current tomcat8 package in xenial? I would be happy to test if your
> > proposed bug fixes resolve the problems with ubuntu's tomcat failing to
> run
> > the MetaboAnalyst war application properly.
>
> Yep, I'm happy to do that hopefully tomorrow. Do you know which bug is
> affecting you from the ones I listed?
>
> Thanks,
> Nish
>


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Re: 8.0.32-1ubuntu1.3~ppa2 patches not in tomcat8 8.0.32-1ubuntu1.4

[Nish Aravamudan]

Hi Jack,

On Thu, Jul 27, 2017 at 5:33 PM, Jack Howarth
 wrote:
> Nish,
>  Nevermind. I manually installed your previous test packages under
> current xenial and those changes don't solve the breakage in running the
> MetaboAnalyst war under tomcat8 on ubuntu. As I mentioned before, when using
> glassfish there is no problems running MetaboAnalyst but under tomca8, one
> gets...

At this point, please file a bug:
https://bugs.launchpad.net/ubuntu/+source/tomcat8/+filebug with the
below information.

Thanks,
Nish

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Re: 8.0.32-1ubuntu1.3~ppa2 patches not in tomcat8 8.0.32-1ubuntu1.4

[Nish Aravamudan]

On Thu, Jul 27, 2017 at 5:04 PM, Jack Howarth
 wrote:
> Nish,
>Can you recreate your test packaging on
> https://launchpad.net/~nacc/+archive/ubuntu/tomcat8v2/+packages based off of
> the current tomcat8 package in xenial? I would be happy to test if your
> proposed bug fixes resolve the problems with ubuntu's tomcat failing to run
> the MetaboAnalyst war application properly.

Yep, I'm happy to do that hopefully tomorrow. Do you know which bug is
affecting you from the ones I listed?

Thanks,
Nish

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GCC 7 default update planned for early August

[Matthias Klose]

Hi,

it's this time of the year where you go to your vacation, and look at a new
shiny new GCC version in the archive when you come back.  Well, not exactly ...

I'm planning to change the default on Aug 03/04, and then working to get things
migrated and buildable again, including two transitions for GCC runtime
libraries.  Fixing things pro-actively is appreciated.  If there are questions,
please use the #ubuntu-devel irc channel.  Resources for the GCC 7 update are:

Results of a test rebuild using GCC 7:

  http://qa.ubuntuwire.org/ftbfs/rebuilds/test-rebuild-20170706-gcc7-artful.html

The ubuntu-toolchain-r/test PPA has the updated defaults packages.

Distro specific informations (and bugs filed for Debian only):

  https://wiki.debian.org/GCC7

Upstream documentation for porting:

  https://gcc.gnu.org/gcc-7/porting_to.html

Thanks for your support for this update!

  Matthias

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Re: 8.0.32-1ubuntu1.3~ppa2 patches not in tomcat8 8.0.32-1ubuntu1.4

[Nish Aravamudan]

On Thu, Jul 27, 2017 at 12:00 PM, Robie Basak  wrote:
> On Thu, Jul 27, 2017 at 09:48:06AM -0400, Jack Howarth wrote:
>>Is there a reason that the patches present in the test tomcat8
>> 8.0.32-1ubuntu1.3~ppa2 were dropped from tomcat8 8.0.32-1ubuntu1.4?
>
> Where were you getting 8.0.32-1ubuntu1.3~ppa2 from? That doesn't sound
> like something that would have been published by Ubuntu.

I believe that is referring to the version in  my PPA at
https://launchpad.net/~nacc/+archive/ubuntu/tomcat8v2/+packages. It
feels more productive to contact me directly, but on the list is fine
too.

That test build was for several LP bugs for tomcat8.

https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1593854 - no
response to latest testing yet
https://bugs.launchpad.net/ubuntu/+source/tomcat7/+bug/1482893 - no
testing feedback
https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1606331 -
tested successfully
https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1644144 - no
testing feedback

It's hard for me, with confidence, to upload fixes to the archive with
no testing feedback. And, it's not uncommon for there to be "races"
between uploaders -- in this case, ubuntu1.4 has a fix for a totally
unrelated bug to the above.

-Nish

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Re: 8.0.32-1ubuntu1.3~ppa2 patches not in tomcat8 8.0.32-1ubuntu1.4

[Robie Basak]

On Thu, Jul 27, 2017 at 09:48:06AM -0400, Jack Howarth wrote:
>Is there a reason that the patches present in the test tomcat8
> 8.0.32-1ubuntu1.3~ppa2 were dropped from tomcat8 8.0.32-1ubuntu1.4?

Where were you getting 8.0.32-1ubuntu1.3~ppa2 from? That doesn't sound
like something that would have been published by Ubuntu.


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8.0.32-1ubuntu1.3~ppa2 patches not in tomcat8 8.0.32-1ubuntu1.4

[Jack Howarth]

   Is there a reason that the patches present in the test tomcat8
8.0.32-1ubuntu1.3~ppa2 were dropped from tomcat8 8.0.32-1ubuntu1.4? I
ask because the Metaboanalyst server war has been broken under the
ubuntu tomcat7 and tomcat8 for quire some time and this is widely
reported by end users...

https://stackoverflow.com/questions/42707456/how-to-deply-a-war-file-via-the-gui-admin-console-glassfish

when configuring the server as described in

http://www.metaboanalyst.ca/MetaboAnalyst/faces/docs/Resources.xhtml

Note that the MetaboAnalyst.war is over the size limit for the tomcat
admin deployment feature so that the war has to be manuallty deployed
or the minimum size limit bumped...

https://tecadmin.net/increase-tomcat-upload-file-size-limit/

The ubuntu tomcat packaging produces a server which fails to load the
Metabolyst server page...

 http://localhost:8080/MetaboAnalyst/faces/ModuleView.xhtml

with the error web page...

HTTP Status 404 -
type Status report
message
description The requested resource is not available.
Apache Tomcat/8.0.32 (Ubuntu)

Ubuntu users have been forced to resort to a manual installation of
glassfish4 which always works.
Jack
ps Note that I packaged the MetaboAnalyst server for use with tomcat
under the fink packaging system on MacOS

http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.9-libcxx/stable/main/finkinfo/sci/metaboanalyst3-r.info?revision=1.3=markup

and it has no issues there when used against the Orcale JDK 1.8
release and tomcat. So there is some Debian/Ubuntu patch or packaging
change being made to tomcat which breaks its ability to run the
MetaboAnalyst war.

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