notebook build errors -- unexpected operator

[jeremydouglass]

While building, the log shows repeated

"/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator"

The error looks like it might be an expecting-bash-but-ran-in-sh problem:

• http://stackoverflow.com/questions/3411048/unexpected-operator-in-shell-programming
• http://stackoverflow.com/questions/2011160/unexpected-operator-error

Docker build log:

Step 12 : RUN Rscript -e 'install.packages("mallet", repos="http://cran.rstudio.com/")'
 ---> Running in e8c819c09034
/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator
trying URL 'http://cran.rstudio.com/src/contrib/mallet_1.0.tar.gz'
Content type 'application/x-gzip' length 4460706 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator
/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator
* installing *source* package ‘mallet’ ...
** package ‘mallet’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator
* DONE (mallet)

The downloaded source packages are in
	‘/tmp/Rtmp8dDq5e/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
 ---> 83e37ef1de7b
Removing intermediate container e8c819c09034
Step 13 : RUN Rscript -e 'devtools::install_github("agoldst/dfrtopics", quiet = TRUE)'
 ---> Running in 81731fc33920
/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator
Installing 10 packages: DBI, dplyr, lattice, Matrix, R6, Rcpp, RcppEigen, stringi, stringr, tibble
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In utils::install.packages(pkgs, repos = repos, type = type, dependencies = dependencies,  :
  installation of package ‘Rcpp’ had non-zero exit status
2: In utils::install.packages(pkgs, repos = repos, type = type, dependencies = dependencies,  :
  installation of package ‘stringi’ had non-zero exit status
 ---> 3a2475da200c
Removing intermediate container 81731fc33920
Successfully built 3a2475da200c

[jeremydouglass]

• https:// github.com/jupyter/docker-stacks/ issues/210
• https:// github.com/ContinuumIO/anaconda-issues/ issues/1063
• https:// github.com/jupyterhub/jupyterhub/ issues/800

Two resolutions:

datascience-notebook:54552d36cf0a works for me. I can plot again!

And:

With irkernel 0.7 and conda r-base 3.3.1-3, I can crash the kernel by simply entering x <- 1 in a new notebook. The error on the console is the same ....
Switching back to r-base 3.3.1-1 resolves the issue. It seems that conda 3.3.1-3 build is the culprit again.

[jeremydouglass]

Our RUN Rscript -e lines may be failing due to Rscript exec happening through sh rather than bash. Still not sure why it worked on all our earlier builds and then just stopped working -- perhaps jupyter, perhaps anaconda.

We might try mapping the command to bash using the RUN command form:

RUN ["/bin/bash", "-c", "echo hello"]

so:

RUN ["/bin/bash", "-c", "RUN Rscript -e etc etc etc"]

as per:

• https:// github.com/docker/docker/issues/ 8100
• https:// github.com/docker/docker/issues/ 7281
• moby/moby@55dc4f2

[jeremydouglass]

Nope. Looks like the Jupyter R is just damaged (probably as per 120 ?). Running from jupyter bash:

jovyan@717fbe331266:~/work$ Rscript -e 'install.packages("mallet", repos="http://cran.rstudio.com/")'                              
/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator                                                                          
trying URL 'http://cran.rstudio.com/src/contrib/mallet_1.0.tar.gz'

...and running from Jupyter R repl:

> install.packages("mallet", repos="http://cran.rstudio.com/")                                                                     
trying URL 'http://cran.rstudio.com/src/contrib/mallet_1.0.tar.gz'                                                                 
Content type 'application/x-gzip' length 4460706 bytes (4.3 MB)                                                                    
==================================================                                                                                 
downloaded 4.3 MB                                                                                                                  

/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator                                                                          
/opt/conda/lib/R/bin/R: 12: [: Linux: unexpected operator                                                                          
* installing *source* package ‘mallet’ ...