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.aravamudan at canonical.com> wrote:

> On Thu, Jul 27, 2017 at 5:04 PM, Jack Howarth
> <howarth.mailing.lists at gmail.com> 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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