Topicmodels not supported by ShinyApps?

[Ali Kazmi]

Hi,

Is the package topicmodels not supported by the current build of ShinyApps?

I get the following error message when deploying my app to Shiny server:

Error: Unhandled Exception: Child Task 543319 failed: Error building image: Error building topicmodels (0.2-1). Build exited with non-zero status: 1

Thanks in advance!

[Andy Kipp]

Hi,

Can you send along the full output?

Thanks

-Andy

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[Ali Kazmi]

Hi Andy,

Thanks for replying.

Here is the full (quite long) output. The error occurs at the very end of the log.

Preparing to deploy application...DONE
Uploading application bundle...DONE
Deploying application: 14989...
Waiting for task: 546206
  building: Parsing manifest
  building: Installing package: stringr (0.6.2)
  building: Installing package: xtable (1.7-3)
  building: Installing package: fastcluster (1.1.13)
  building: Installing package: RColorBrewer (1.0-5)
  building: Installing package: dichromat (2.0-0)
  building: Installing package: bitops (1.0-6)
  building: Installing package: caTools (1.17)
  building: Installing package: digest (0.6.4)
  building: Installing package: NLP (0.1-3)
  building: Installing package: gtable (0.1.2)
  building: Installing package: MASS (7.3-31)
  building: Installing package: lattice (0.20-29)
  building: Installing package: Matrix (1.1-3)
  building: Installing package: munsell (0.4.2)
  building: Installing package: RCurl (1.95-4.1)
  building: Installing package: RJSONIO (1.2-0.2)
  building: Installing package: igraph (0.7.1)
  building: Installing package: Rcpp (0.11.2)
  building: Installing package: plyr (1.8.1)
  building: Installing package: reshape2 (1.4)
  building: Installing package: scales (0.2.4)
  building: Installing package: httpuv (1.3.0)
  building: Installing package: shiny (0.10.0)
  building: Installing package: rJava (0.9-6)
  building: Installing package: RWekajars (3.7.11-1)
  building: Installing package: RWeka (0.4-23)
  building: Building package: topicmodels (0.2-1)
################################## Begin Log ##################################
[2014-07-14T17:25:55.340155007+0000] Installing R package: stringr (0.6.2)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘stringr’ ...
* DONE (stringr)
[2014-07-14T17:25:56.713137725+0000] Installing R package: xtable (1.7-3)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘xtable’ ...
* DONE (xtable)
[2014-07-14T17:25:58.356135105+0000] Installing R package: labeling (0.2)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘labeling’ ...
* DONE (labeling)
[2014-07-14T17:25:59.439921795+0000] Installing R package: fastcluster (1.1.13)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘fastcluster’ ...
* DONE (fastcluster)
[2014-07-14T17:26:00.928208909+0000] Installing R package: RColorBrewer (1.0-5)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘RColorBrewer’ ...
* DONE (RColorBrewer)
[2014-07-14T17:26:02.513560197+0000] Installing R package: proto (0.3-10)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘proto’ ...
* DONE (proto)
[2014-07-14T17:26:03.912078276+0000] Installing R package: dichromat (2.0-0)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘dichromat’ ...
* DONE (dichromat)
[2014-07-14T17:26:05.163830408+0000] Installing R package: bitops (1.0-6)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘bitops’ ...
* DONE (bitops)
[2014-07-14T17:26:06.488240020+0000] Installing R package: caTools (1.17)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘caTools’ ...
* DONE (caTools)
[2014-07-14T17:26:07.800147378+0000] Installing R package: digest (0.6.4)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘digest’ ...
* DONE (digest)
[2014-07-14T17:26:09.368392930+0000] Installing R package: slam (0.1-32)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘slam’ ...
* DONE (slam)
[2014-07-14T17:26:10.768293345+0000] Installing R package: NLP (0.1-3)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘NLP’ ...
* DONE (NLP)
[2014-07-14T17:26:12.099928177+0000] Installing R package: htmltools (0.2.4)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘htmltools’ ...
* DONE (htmltools)
[2014-07-14T17:26:13.172003283+0000] Installing R package: gtable (0.1.2)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘gtable’ ...
* DONE (gtable)
[2014-07-14T17:26:14.532173744+0000] Installing R package: MASS (7.3-31)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘MASS’ ...
* DONE (MASS)
[2014-07-14T17:26:15.915643627+0000] Installing R package: lattice (0.20-29)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘lattice’ ...
* DONE (lattice)
[2014-07-14T17:26:17.305559188+0000] Installing R package: Matrix (1.1-3)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘Matrix’ ...
* DONE (Matrix)
[2014-07-14T17:26:18.999889726+0000] Installing R package: colorspace (1.2-4)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘colorspace’ ...
* DONE (colorspace)
[2014-07-14T17:26:20.508383497+0000] Installing R package: munsell (0.4.2)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘munsell’ ...
* DONE (munsell)
[2014-07-14T17:26:21.468380431+0000] Installing R package: RCurl (1.95-4.1)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘RCurl’ ...
* DONE (RCurl)
[2014-07-14T17:26:22.812228478+0000] Installing R package: modeltools (0.2-21)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘modeltools’ ...
* DONE (modeltools)
[2014-07-14T17:26:24.280803234+0000] Installing R package: RJSONIO (1.2-0.2)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘RJSONIO’ ...
* DONE (RJSONIO)
[2014-07-14T17:26:25.739985408+0000] Installing R package: igraph (0.7.1)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘igraph’ ...
* DONE (igraph)
[2014-07-14T17:26:27.499538695+0000] Installing R package: Rcpp (0.11.2)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘Rcpp’ ...
* DONE (Rcpp)
[2014-07-14T17:26:29.660200322+0000] Installing R package: plyr (1.8.1)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘plyr’ ...
* DONE (plyr)
[2014-07-14T17:26:31.027717414+0000] Installing R package: reshape2 (1.4)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘reshape2’ ...
* DONE (reshape2)
[2014-07-14T17:26:32.368070375+0000] Installing R package: scales (0.2.4)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘scales’ ...
* DONE (scales)
[2014-07-14T17:26:34.048046532+0000] Installing R package: ggplot2 (1.0.0)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘ggplot2’ ...
* DONE (ggplot2)
[2014-07-14T17:26:35.719828536+0000] Installing R package: httpuv (1.3.0)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘httpuv’ ...
* DONE (httpuv)
[2014-07-14T17:26:37.184305629+0000] Installing R package: shiny (0.10.0)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘shiny’ ...
* DONE (shiny)
[2014-07-14T17:26:38.561650400+0000] Execute script: packages/build/rJava.sh
+ set -e
+ /usr/bin/R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.7.0_51
Java home path   : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar


trying to compile and link a JNI progam
detected JNI cpp flags    : -I$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR




JAVA_HOME        : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/../include
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.


[2014-07-14T17:26:40.122977809+0000] Installing R package: rJava (0.9-6)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘rJava’ ...
* DONE (rJava)
[2014-07-14T17:26:41.172438482+0000] Installing R package: RWekajars (3.7.11-1)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘RWekajars’ ...
* DONE (RWekajars)
[2014-07-14T17:26:42.820118336+0000] Installing R package: RWeka (0.4-23)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘RWeka’ ...
* DONE (RWeka)
[2014-07-14T17:26:43.927799735+0000] Installing R package: tm (0.6)
* installing to library ‘/usr/local/lib/R/site-library’
* installing *binary* package ‘tm’ ...
* DONE (tm)
[2014-07-14T17:26:45.431826436+0000] Building R package: topicmodels (0.2-1)
/mnt/packages/build /mnt
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘topicmodels’ ...
** package ‘topicmodelsâ€################################### End Log ###################################
Error: Unhandled Exception: Child Task 546208 failed: Error building image: Error building topicmodels (0.2-1). Build exited with non-zero status: 1

[Andy Kipp]

Ali,

It looks like topicmodels packages depends on the GNU scientific library. I went ahead and added this dependency, so please try again.

Thanks

-Andy

To view this discussion on the web visit https://groups.google.com/d/msgid/shinyapps-users/0eaab74a-91ea-4379-b6ac-aba9cae32a47%40googlegroups.com.

[Ali Kazmi]

Andy,

Thanks! That resulted in a successful deployment.

However, I am now getting another error, which is not related to the topicmodels package so I may have to open a new thread.

Thanks for the help.

[Thuy Luong]

Hi Andy,

I face the same error with different error output from the log.

The log is shown below 

[2014-08-01T01:08:38.722299055+0000] Building R package: topicmodels (0.2-1)

/mnt/packages/build /mnt

* installing to library ‘/usr/local/lib/R/site-library’

* installing *source* package ‘topicmodels’ ...

** package ‘topicmodels’ successfully unpacked and MD5 sums checked

** libs

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c cokus.c -o cokus.o

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c common.c -o common.o

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c ctm.c -o ctm.o

g++ -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-s################################### End Log ################################### 

Error: Unhandled Exception: Child Task 761086 failed: Error building image: Error building topicmodels (0.2-1). Build exited with non-zero status: 1

Thank you for helping!

Thuy