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

[Jack Howarth]

Nish,
     If you are interested at looking at the MetaboAnalyst war issue
directly, you can do so as follows on xenial x86_64...

sudo add-apt-repository ppa:marutter/c2d4u
sudo add-apt-repository ppa:marutter/rrutter
sudo apt-get update
sudo apt-get
install r-cran-bh r-cran-bitops r-cran-boot r-cran-cairo  r-cran-car
r-cran-caret r-cran-catools r-cran-class r-cran-cluster
r-cran-codetools r-cran-colorspace r-cran-curl r-cran-devtools
r-cran-dichromat r-cran-digest r-cran-e1071 r-cran-ellipse
r-cran-foreach r-cran-foreign r-cran-gdata r-cran-gdtools
r-cran-ggplot2 r-cran-git2r r-cran-gplots r-cran-gtable r-cran-gtools
r-cran-httr r-cran-igraph r-cran-irlba r-cran-iterators
r-cran-jsonlite  r-cran-kernsmooth r-cran-labeling r-cran-lattice
r-cran-lazyeval r-cran-lme4 r-cran-magrittr r-cran-mass r-cran-matrix
r-cran-matrixmodels r-cran-memoise r-cran-mgcv r-cran-mime
r-cran-minqa r-cran-modelmetrics r-cran-multicore r-cran-munsell
r-cran-nlme r-cran-nloptr r-cran-nnet
 r-cran-openssl r-cran-pbkrtest r-cran-pheatmap r-cran-pkgconfig
r-cran-pls r-cran-plyr r-cran-proc r-cran-quantreg r-cran-r6
r-cran-randomforest r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen
r-cran-reshape2 r-cran-rjsonio r-cran-rlang r-cran-rocr r-cran-rpart
r-cran-rserve r-cran-rstudioapi r-cran-scales r-cran-scatterplot3d
 r-cran-som r-cran-sparsem r-cran-spatial r-cran-stringi
r-cran-stringr r-cran-survival r-cran-svglite r-cran-tibble
r-cran-whisker r-cran-withr r-cran-xtable

then download the R_bioc_local_lib.tar.bz2 from
https://www.dropbox.com/s/x7o8596k3nnzq99/R_bioc_local_lib.tar.bz2?dl=0 and
execute...

cd /usr/local/lib
mv R R.sav
sudo tar -jxvf  <path_to>/R_bioc_local_lib.tar.bz2

to obtain the required Bioconductor R modules. Also, execute...

sudo apt-get install libnetcdf-dev build-essential libboost-dev libxml2-dev

to make sure all the dependencies for the pre-built Bioconductor modules
are satisfied.

Now you should be able to run a MetaboAnalyst server by 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()

in one terminal and copying the MetaboAnalyst.war (obtained from
https://dl.dropboxusercontent.com/u/95163184/MetaboAnalyst.war)
into /var/lib/tomcat8/webapps to deploy it. On MacOS, these steps allow the
URL

http://localhost:8080/MetaboAnalyst/

to display the same web pages seen at http://www.metaboanalyst.ca/ main
server.
                        Jack
ps You should also be able to confirm that if you use the glassfish4 4.1.2
server on ubuntu as follows...

unzip glassfish-4.1.2.zip
glassfish4/bin/asadmin start-domain

quit R and kill any running Rserve daemons followed by

$ 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()

and finally deploy the  MetaboAnalyst.war in glassfish4 that the URL

http://localhost:8080/MetaboAnalyst/

works fine under glassfish4.

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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