TERR + Debian + Geospatial

[ismailsunni]

Always had a problem with libproj not found on Debian based. Changed to use Ubuntu base image. It works.

[ismailsunni]

Not able to install rJava. The error message:

checking Java support in R... configure: error: absent
R was configured without Java support. Please run
R CMD javareconf
as root to add Java support to R.

If you do not have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
* Removing directory 'rJava' from library directory '/home/docker/tibco/site-library' because of installation error
Warning message:
In do.call(what, args, quote, envir) : closing unused connection 3 (https://cloud.r-project.org/src/contrib/Rcpp_1.0.3.tar.gz)
Error in source2binary.configure(sourceDir, binaryDir, pkgName, insta : rJava/configure reported failure
    Cannot install package from /tmp/TERR_15c26b8b45671/source_15c2625558ec8/rJava

Trying to run R CMD javareconf

Got this error :

Cannot find executable 'javareconf'.

It seems the javareconf is specific to GNU R. Checking the R --help I got this message:

Or: TERR CMD command args

where 'command' is one of
  build                 Build a package
  check                 Run package checks
  INSTALL               Install a package
  Rdconv                Convert Rd files

So, it is indeed no javareconf.

Alternative solutions:

• Check what R CMD javareconf does, and replicate it
• Ignore packages that needs rJava

[ismailsunni]

Failed to install an installed package:

> install.packages('sf')
Trying to download URL 'https://cloud.r-project.org/src/contrib/sf_0.8-0.tar.gz' to file '/tmp/TERR_00016b8b45671/downloaded_packages/sf_0.8-0.tar.gz'
  Downloaded 8607770 bytes
* unpacking *source* package sf from "/tmp/TERR_00016b8b45671/downloaded_packages/sf_0.8-0.tar.gz" to "/tmp/TERR_00016b8b45671/source_000174b0dc515"
* checking MD5 checksums
    MD5 checksums ok
* installing *source* package from "/tmp/TERR_00016b8b45671/source_000174b0dc515/sf" to "/home/docker/tibco/site-library"
Error in source2binary(dir, install_opts = install_opts) : Cannot rename old binaryDir from '/home/docker/tibco/site-library/sf' to '/home/docker/tibco/site-library/00LOCK--sf'
    Cannot install package from /tmp/TERR_00016b8b45671/source_000174b0dc515/sf

[nuest]

Looking at https://github.com/ismailsunni/dockeRs/blob/master/terr-5.0.0-debian-geospatial/Dockerfile you do not install Java... how should rJava work then?

[ismailsunni]

Reproducible example of failure in installing an existing package:

docker run  -it --rm ismailsunni/terr-5.0.0-ubuntu-geospatial

It will open a TERR session. Then run this code:

install.packages('RSQLite')

or

install.packages('sf')

It seems, if the package need another R package (dependency) that already installed, it will give the error.

[nuest]

For RSQLite I do get a few warnings, but can load the package:

> library("RSQLite")
The following object(s) are masked _from_ 'package:methods':

    show
Warning messages:
1: In .loadNamespaceImpl(package, path, keep.source, partial) : package 'blob': S3method declaration for 'vec_ptype2.blob' ignored: cannot find generic
2: In .loadNamespaceImpl(package, path, keep.source, partial) : package 'blob': S3method declaration for 'vec_ptype2.list.blob' ignored: cannot find generic

For sf, I get an error, but sf is already installed - why do you need to install it again?

> install.packages("sf")
Trying to download URL 'https://cloud.r-project.org/src/contrib/sf_0.8-0.tar.gz' to file '/tmp/TERR_000e6b8b45671/downloaded_packages/sf_0.8-0.tar.gz'
  Downloaded 8607770 bytes
* unpacking *source* package sf from "/tmp/TERR_000e6b8b45671/downloaded_packages/sf_0.8-0.tar.gz" to "/tmp/TERR_000e6b8b45671/source_000e721da3172c"
* checking MD5 checksums
    MD5 checksums ok
* installing *source* package from "/tmp/TERR_000e6b8b45671/source_000e721da3172c/sf" to "/home/docker/tibco/site-library"
Error in source2binary(dir, install_opts = install_opts) : Cannot rename old binaryDir from '/home/docker/tibco/site-library/sf' to '/home/docker/tibco/site-library/00LOCK--sf'
    Cannot install package from /tmp/TERR_000e6b8b45671/source_000e721da3172c/sf
> library("sf")
The following object(s) are masked _from_ 'package:RSQLite':

    dbDataType, dbWriteTable
Linking to GEOS 3.6.2, GDAL 2.2.3, PROJ 4.9.3

[ismailsunni]

For RSQLite I do get a few warnings, but can load the package:

Did you use my Dockerfile where there is already some installed R packages?

For sf, I get an error, but sf is already installed - why do you need to install it again?

Sorry, the main point is not to reinstall sf, but trying to reinstall a package that needs sf. In this case, TERR needs to reinstall sf then it will give the error.

Another example is with RSQLite:

> install.packages('RSQLite')
Trying to download URL 'https://tran.tibco.com/terr50/src/contrib/vctrs_0.1.0.tar.gz' to file '/tmp/TERR_00016b8b45671/downloaded_packages/vctrs_0.1.0.tar.gz'
  Downloaded 412633 bytes
Trying to download URL 'https://cloud.r-project.org/src/contrib/bit_1.1-14.tar.gz' to file '/tmp/TERR_00016b8b45671/downloaded_packages/bit_1.1-14.tar.gz'
  Downloaded 54779 bytes
Trying to download URL 'https://cloud.r-project.org/src/contrib/memoise_1.1.0.tar.gz' to file '/tmp/TERR_00016b8b45671/downloaded_packages/memoise_1.1.0.tar.gz'
  Downloaded 11025 bytes
Trying to download URL 'https://cloud.r-project.org/src/contrib/blob_1.2.0.tar.gz' to file '/tmp/TERR_00016b8b45671/downloaded_packages/blob_1.2.0.tar.gz'
  Downloaded 9355 bytes
Trying to download URL 'https://cloud.r-project.org/src/contrib/bit64_0.9-7.tar.gz' to file '/tmp/TERR_00016b8b45671/downloaded_packages/bit64_0.9-7.tar.gz'
  Downloaded 125539 bytes
Trying to download URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.2.0.tar.gz' to file '/tmp/TERR_00016b8b45671/downloaded_packages/RSQLite_2.2.0.tar.gz'
  Downloaded 2373785 bytes
* unpacking *source* package vctrs from "/tmp/TERR_00016b8b45671/downloaded_packages/vctrs_0.1.0.tar.gz" to "/tmp/TERR_00016b8b45671/source_000174b0dc515"
* checking MD5 checksums
    MD5 checksums ok
* installing *source* package from "/tmp/TERR_00016b8b45671/source_000174b0dc515/vctrs" to "/home/docker/tibco/site-library"
Error in source2binary(dir, install_opts = install_opts) : Cannot rename old binaryDir from '/home/docker/tibco/site-library/vctrs' to '/home/docker/tibco/site-library/00LOCK--vctrs'
    Cannot install package from /tmp/TERR_00016b8b45671/source_000174b0dc515/vctrs
> library('vctrs')
> 

It already has vctrs package, but when I tried to RSQLite (which needs vctrs) it failed because it tried to install vctrs