package ‘Rclipper’ is not available (for R version 3.4.4) | installation of package ‘CodeDepends’ had non-zero exit status

[aliraza0337]

Hi, I have been working with RClipper and I realized my code was breaking because of dependencies! Here i the log while initializing the container and I can see there are some package that aren't being installed because of some issue. Any help will be greatly appreciated.

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-library/XML’
ERROR: dependencies ‘graph’, ‘XML’ are not available for package ‘CodeDepends’
* removing ‘/usr/local/lib/R/site-library/CodeDepends’

The downloaded source packages are in
	‘/tmp/RtmphodDKW/downloaded_packages’
[1] "Failed to install library: CodeDepends"
[1] "Proceeding with deserialization. Model inference may fail if this library is required!"
Warning messages:
1: In install.packages(lib_dep) :
  installation of package ‘runjags’ had non-zero exit status
2: package ‘ecoforecastR’ is not available (for R version 3.4.4) 
3: In install.packages(lib_dep) :
  installation of package ‘rjags’ had non-zero exit status
4: package ‘Rclipper’ is not available (for R version 3.4.4) 
5: In install.packages(lib_dep) :
  installation of package ‘XML’ had non-zero exit status
6: In install.packages(lib_dep) :
  installation of package ‘CodeDepends’ had non-zero exit status
7: In install.packages(lib_dep) :
  installation of package ‘roprov’ had non-zero exit status
8: In install.packages(lib_dep) :
  installation of package ‘histry’ had non-zero exit status
9: In install.packages(lib_dep) :
  installation of package ‘XML’ had non-zero exit status
10: In install.packages(lib_dep) :
  installation of package ‘CodeDepends’ had non-zero exit status
Starting container RPC with clipper ip: query_frontend-68729 and port: 7000

[csmithnm]

I am having the same issue. There are some serious compatibility issues with the packages of R and what the RClipper requires. I was able to get around the issues on the initial Rscript local model build, but I had to do a lot of manual installs outside of R to get it to work. There was error after error with the Rclipper required dependency packages especially around CodeDepends. To get XML to install for the build_model step I had to resort to apt-get's sudo apt-get install r-cran-zml plus a lot of other Googled fixes. In the end, when I tried to deploy the built model, I could NOT get the deployed model to work because that process only allows for simple R package installs via the install_container_dependencies.R
I even tried to create my own Docker image/container clipper/r-container-base:develop using the base template RContainerDockerfile with the XML apt-get install, but when I deployed the model the ipython deploy_model step got hung up.

What really needs to happen, instead of all the work arounds I tried, is to fix the Rclipper and CodeDepends dependency issues.

[kheraAniruddh]

Did you guys have any success on this?

[csmithnm]

No, I didn't have any luck. I have given up playing around with the RClipper code - which I have tired to get to work off and on for months. Also I have not heard a thing from the Clipper Team on this RClipper issue for over a month. I am now looking to try out AWS SageMaker which seems to cover the entire model life cycle. It is supposed to work with R, supports batch and REST APIs: Using R with Amazon SageMaker. Best of luck.