<div dir="ltr">Nish,<div> If you are interested at looking at the MetaboAnalyst war issue directly, you can do so as follows on xenial x86_64...</div><div><br></div><div>sudo add-apt-repository ppa:marutter/c2d4u<br></div><div>sudo add-apt-repository ppa:marutter/rrutter<br></div><div>sudo apt-get update</div><div>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</div><div><br></div><div>then download the R_bioc_local_lib.tar.bz2 from <a href="https://www.dropbox.com/s/x7o8596k3nnzq99/R_bioc_local_lib.tar.bz2?dl=0">https://www.dropbox.com/s/x7o8596k3nnzq99/R_bioc_local_lib.tar.bz2?dl=0</a> and execute...</div><div><br></div><div>cd /usr/local/lib</div><div>mv R R.sav</div><div>sudo tar -jxvf <path_to>/R_bioc_local_lib.tar.bz2</div><div><br></div><div>to obtain the required Bioconductor R modules. Also, execute...</div><div><br></div><div>sudo apt-get install libnetcdf-dev build-essential libboost-dev libxml2-dev<br></div><div><br></div><div>to make sure all the dependencies for the pre-built Bioconductor modules are satisfied.</div><div><br></div><div>Now you should be able to run a MetaboAnalyst server by executing...</div><div><br></div><div><div>$ sudo -u tomcat8 R</div><div><br></div><div>R version 3.4.1 (2017-06-30) -- "Single Candle"</div><div>Copyright (C) 2017 The R Foundation for Statistical Computing</div><div>Platform: x86_64-pc-linux-gnu (64-bit)</div><div><br></div><div>R is free software and comes with ABSOLUTELY NO WARRANTY.</div><div>You are welcome to redistribute it under certain conditions.</div><div>Type 'license()' or 'licence()' for distribution details.</div><div><br></div><div> Natural language support but running in an English locale</div><div><br></div><div>R is a collaborative project with many contributors.</div><div>Type 'contributors()' for more information and</div><div>'citation()' on how to cite R or R packages in publications.</div><div><br></div><div>Type 'demo()' for some demos, 'help()' for on-line help, or</div><div>'help.start()' for an HTML browser interface to help.</div><div>Type 'q()' to quit R.</div><div><br></div><div>> library(Rserve)</div><div>> Rserve()</div></div><div><br></div><div>in one terminal and copying the MetaboAnalyst.war (obtained from <a href="https://dl.dropboxusercontent.com/u/95163184/MetaboAnalyst.war">https://dl.dropboxusercontent.com/u/95163184/MetaboAnalyst.war</a>) into /var/lib/tomcat8/webapps to deploy it. On MacOS, these steps allow the URL</div><div><br></div><div><a href="http://localhost:8080/MetaboAnalyst/">http://localhost:8080/MetaboAnalyst/</a><br></div><div><br></div><div>to display the same web pages seen at <a href="http://www.metaboanalyst.ca/">http://www.metaboanalyst.ca/</a> main server.</div><div> Jack</div><div>ps You should also be able to confirm that if you use the glassfish4 4.1.2 server on ubuntu as follows...</div><div><br></div><div>unzip glassfish-4.1.2.zip</div><div>glassfish4/bin/asadmin start-domain<br></div><div><br></div><div>quit R and kill any running Rserve daemons followed by</div><div><br></div><div>$ R<br></div><div><br></div><div>R version 3.4.1 (2017-06-30) -- "Single Candle"</div><div>Copyright (C) 2017 The R Foundation for Statistical Computing</div><div>Platform: x86_64-pc-linux-gnu (64-bit)</div><div><br></div><div>R is free software and comes with ABSOLUTELY NO WARRANTY.</div><div>You are welcome to redistribute it under certain conditions.</div><div>Type 'license()' or 'licence()' for distribution details.</div><div><br></div><div> Natural language support but running in an English locale</div><div><br></div><div>R is a collaborative project with many contributors.</div><div>Type 'contributors()' for more information and</div><div>'citation()' on how to cite R or R packages in publications.</div><div><br></div><div>Type 'demo()' for some demos, 'help()' for on-line help, or</div><div>'help.start()' for an HTML browser interface to help.</div><div>Type 'q()' to quit R.</div><div><br></div><div>> library(Rserve)</div><div>> Rserve()</div><div><br></div><div>and finally deploy the MetaboAnalyst.war in glassfish4 that the URL</div><div><br></div><div><a href="http://localhost:8080/MetaboAnalyst/">http://localhost:8080/MetaboAnalyst/</a><br></div><div><br></div><div>works fine under glassfish4.</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 27, 2017 at 8:14 PM, Nish Aravamudan <span dir="ltr"><<a href="mailto:nish.aravamudan@canonical.com" target="_blank">nish.aravamudan@canonical.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On Thu, Jul 27, 2017 at 5:04 PM, Jack Howarth<br>
<<a href="mailto:howarth.mailing.lists@gmail.com">howarth.mailing.lists@gmail.<wbr>com</a>> wrote:<br>
> Nish,<br>
> Can you recreate your test packaging on<br>
> <a href="https://launchpad.net/~nacc/+archive/ubuntu/tomcat8v2/+packages" rel="noreferrer" target="_blank">https://launchpad.net/~nacc/+<wbr>archive/ubuntu/tomcat8v2/+<wbr>packages</a> based off of<br>
> the current tomcat8 package in xenial? I would be happy to test if your<br>
> proposed bug fixes resolve the problems with ubuntu's tomcat failing to run<br>
> the MetaboAnalyst war application properly.<br>
<br>
</span>Yep, I'm happy to do that hopefully tomorrow. Do you know which bug is<br>
affecting you from the ones I listed?<br>
<br>
Thanks,<br>
Nish<br>
</blockquote></div><br></div></div>