04 November 2018

R AnalyticFlow

System: Slackware Linux (version 14.0)
CPUs: Intel(R) Atom(TM) CPU N270 @1.60GHz
Deps: jdk-8u192-linux-i586.tar.gz, R-3.1.3.tar.gz,
RAnalyticFlow_Linux_3.1.8.tar.gz

Installation of R AnalyticFlow 3.1.8 (RAF3).

The Download page lists R-3.2.0 and above as a prerequisite.

R-3.1.3, 3.2.2 and 3.5.1, appear to output the similar errors.


On Windows 7 (64 bit) with R-3.2.0, running R AnalyticFlow 3.1.8 using
its bundled JRE, which was taken from JDK 8u172, succeeds in starting
an R process.

https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
jdk-8u192-linux-i586.tar.gz

http://slackbuilds.org/repository/14.2/development/jdk/
jdk.tar.gz

Modify the .SlackBuild as follows.

- VERSION=${VERSION:-8u181}
+ VERSION=${VERSION:-8u192}

bash-4.2# installpkg jdk-8u192-i586-1_SBo.tgz

...

bash-4.2# exit

http://mirrors.dotsrc.org/cran/src/base/R-3/
R-3.1.3.tar.gz

http://slackbuilds.org/repository/14.0/academic/R/
R.tar.gz

Modify the .SlackBuild as follows.

- VERSION=3.0.1
+ VERSION=3.1.3

- cp -a README NEWS $PKG/usr/doc/$PRGNAM-$VERSION
+ cp README $PKG/usr/doc/$PRGNAM-$VERSION
- tar cfJ $PKG/usr/doc/$PRGNAM-$VERSION/OLDER_NEWS.txz ONEWS OONEWS

bash-4.2# installpkg /tmp/R-3.1.3-i486-1_SBo.tgz

...

bash-4.2#

Possibly these files are unnecessary, but I'm in the habit of adding them.

bash-4.2# cat /etc/profile.d/R.csh
#!/bin/csh
setenv R_HOME /usr/lib/R
setenv PATH ${PATH}:/usr/lib/R/bin:/usr/lib/R/bin/exec
bash-4.2# cat /etc/profile.d/R.sh
#!/bin/sh
export R_HOME=/usr/lib/R
export PATH="$PATH:/usr/lib/R/bin:/usr/lib/R/bin/exec"
bash-4.2#

bash-4.2# source /etc/profile.d/R.sh
bash-4.2# echo $R_HOME
/usr/lib/R
bash-4.2#

If you do not want to be queried by the Tk GUI for a CRAN mirror,
you can enter the URL for your local mirror in an .Rprofile file.

bash-4.2# cat .Rprofile
r <- getOption("repos")
r["CRAN"] <- "http://mirrors.dotsrc.org/cran/"
options(repos = r)
rm(r)
bash-4.2#

This command may be unnecessary as no R-3.1.3 files seem to
be altered in /usr/lib/R/etc; on some earlier releases where files
had been changed in /usr/lib/R/etc, backups of the original files
were generated.

bash-4.2# R CMD javareconf

...

bash-4.2#

Launch R and install the current rJava and JavaGD packages (rJava_0.9-10, JavaGD_0.6-1).

bash-4.2# R

...

> install.packages(c("rJava", "JavaGD"))

...

* DONE (rJava)

...

* DONE (JavaGD)

The downloaded source packages are in
'/tmp/Rtmp2eBy45/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> quit()
Save workspace image? [y/n/c]: n
bash-4.2#

http://download.ef-prime.com/ranalyticflow/3.1.8/bin/
RAnalyticFlow_Linux_3.1.8.tar.gz

Extract the above .tar.gz download and move the extracted directory.

bash-4.2# tar xvf RAnalyticFlow_Linux_3.1.8.tar.gz

...

bash-4.2# mv RAnalyticFlow_3 /opt/r-analyticflow
bash-4.2# cd /opt/r-analyticflow
bash-4.2# cp linux/r-analyticflow.desktop /usr/share/applications
bash-4.2# cp img/desktop_32.png /usr/share/pixmaps/r-analyticflow.png
bash-4.2# exit

Reboot.

Login as an ordinary user, start the X Server, and then launch the program.

The "Application Log..." output.

com.ef_prime.rflow.core.app.r.base.RSessionManager lambda$restart$0 Failed to start R process
java.io.IOException: org.apache.thrift.transport.TTransportException: java.net.ConnectException:
Connection refused (Connection refused)
 at com.ef_prime.rflow.core.app.r.base.RSessionManager.startProcess(RSessionManager.java:202)
 at com.ef_prime.rflow.core.app.r.base.RSessionManager.lambda$restart$0(RSessionManager.java:280)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
 at java.lang.Thread.run(Thread.java:748)

Caused by: org.apache.thrift.transport.TTransportException: java.net.ConnectException: Connection refused (Connection refused)
 at org.apache.thrift.transport.TSocket.open(TSocket.java:226)
 at org.apache.thrift.transport.TFramedTransport.open(TFramedTransport.java:81)
 at com.ef_prime.rflow.core.app.r.base.RServerRpcClient.reconnect(RServerRpcClient.java:32)
 at com.ef_prime.rflow.core.app.r.base.RpcRClient.connect(RpcRClient.java:71)
 at com.ef_prime.rflow.core.app.r.base.RSessionManager.startProcess(RSessionManager.java:184)
 ... 4 more

Caused by: java.net.ConnectException: Connection refused (Connection refused)
 at java.net.PlainSocketImpl.socketConnect(Native Method)
 at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
 at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
 at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
 at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
 at java.net.Socket.connect(Socket.java:589)
 at org.apache.thrift.transport.TSocket.open(TSocket.java:221)
 ... 8 more

powerpoint



Ryota Suzuki & Tatsuhiro Nagai

R AnalyticFlow 3 is an open-source GUI for data analysis on top of R. It is
designed to simplify the process of data analysis for both R experts and beginners. It
is written in Java and runs on Windows, OS X and Linux. Interactive GUI modules
are available to perform data analysis without writing code, or you can write R scripts
if you prefer. Then you can connect these modules (or scripts) to build an “analysis
flow”, which is a workflow representing the processes of data analysis. An analysis
flow can be executed by simple mouse operation, which facilitates collaborative
works among people with different fields of expertise. R AnalyticFlow 3 is extensible:
you can easily build custom GUI modules to add functions that you need. Custom
module builder is available for this purpose, which itself is a simple, user-friendly
GUI to design custom modules. Any R function including your original R script can
be converted to a GUI module. It also provides typical tools such as code editor,
object/file browser, graphics device, help browser and R console. There are also
many useful features including code completion, debugger, object-caching, autobackup
and project manager.

NB: Oracle is discontinuing public updates for JDK 8 effective January 2019.

03 November 2018

RStudio

System: Slackware Linux (version 14.0)
CPUs: Intel(R) Atom(TM) CPU N270 @1.60GHz
Deps: apache-ant-1.9.9-bin.tar.bz2,
jdk-8u192-linux-i586.tar.gz, R-2.15.0.tar.gz,
rstudio-0.97.75.tar.gz

This RStudio release uses R_ext/rlocale.h from R-2.xx.

http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
jdk-8u192-linux-i586.tar.gz

http://slackbuilds.org/repository/14.2/development/jdk/
jdk.tar.gz

Upgrade the version number in the .SlackBuild to 192.

bash-4.3# installpkg /tmp/jdk-8u192-i586-1_SBo.tgz

...

bash-4.3# exit

http://slackbuilds.org/repository/14.2/development/apache-ant/
apache-ant-1.9.9-bin.tar.bz2
apache-ant.tar.gz

bash-4.3# installpkg apache-ant-1.9.9-noarch-1_SBo.tgz
...

bash-4.3# exit

http://mirrors.dotsrc.org/cran/src/base/R-2/
R-2.15.0.tar.gz

http://slackbuilds.org/repository/13.37/academic/R/
R.tar.gz

bash-4.2# installpkg /tmp/R-2.15.0-i486-1_SBo.tgz

...

bash-4.2#

Possibly these files are unnecessary, but I'm in the habit of adding them.

bash-4.2# cat /etc/profile.d/R.csh
#!/bin/csh
setenv R_HOME /usr/lib/R
setenv PATH ${PATH}:/usr/lib/R/bin:/usr/lib/R/bin/exec
bash-4.2# cat /etc/profile.d/R.sh
#!/bin/sh
export R_HOME=/usr/lib/R
export PATH="$PATH:/usr/lib/R/bin:/usr/lib/R/bin/exec"
bash-4.2# exit

http://slackbuilds.org/repository/14.1/development/rstudio-desktop/
gin-1.5.zip
core-dictionaries.zip
mathjax-20.zip
junit-4.9b3.jar

https://code.google.com/archive/p/google-web-toolkit/downloads
gwt-2.5.0.rc1.zip

https://github.com/rstudio/rstudio/releases/tag/v0.97.75
rstudio-0.97.75.tar.gz

A SlackBuild for rstudio is located on this log.

bash-4.2# installpkg /tmp/rstudio-0.97.75-i486-1_SBo.tgz

...

bash-4.2# exit



Josh Paulson, JJ Allaire, Joe Cheng

RStudio is a free and open source integrated development environment (IDE) for the R programming
language. RStudio aims to combine the various components of R (console, source, editing, graphics,
history, help, etc.) into one seamless and productive workbench. RStudio also makes it easier to
separate your workflow into projects and utilize other powerful tools such as version control. It is
designed to both ease the learning curve for new R users as well as provide high productivity tools for
more advanced users. Additionally, RStudio can be deployed as a server to enable web access to R
sessions running on remote systems.

NB: Oracle is discontinuing public updates for JDK 8 effective January 2019.

19 October 2018

AutoKey

C. Dekter's code which could be utilised on GNU/Linux to enable Ctrl+Alt+Key
to work the same as AltGr+Key on Danish keyboards; easier typing for a brace,
bracket, caret, forward slash, the pipe symbol, or a tilde, while coding.

https://github.com/autokey/autokey-python2 [v0.91.1]
https://github.com/autokey/autokey (python3) [v0.90.4]

06 October 2018

JDK

System: Slackware Linux (version 14.2)
CPU: Intel(R) Core(TM) i7 @2.20GHz
Deps: jdk-8u192-linux-i586.tar.gz
Updated:  02-11-2018

https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
jdk-8u192-linux-i586.tar.gz

http://slackbuilds.org/repository/14.2/development/jdk/
jdk.tar.gz

Upgrade the version number in the .SlackBuild to 192.

bash-4.3# installpkg jdk-8u192-i586-1_SBo.tgz

...

bash-4.3# exit

NB: For Slackware64 one would download jdk-8u192-linux-x64.tar.gz

The following from the Links Page use Java 8.

Mimer SQL 11.0.2B* (for dbvis 10.0.x)
R AnalyticFlow 3.1.8
SQuirreL SQL Client Version 3.8.1

* The Beta test (Linux) version is only available as a 64-bit release.

TLS

Numerous State run and corporate entities began in the first quarter last year to disable
support on their servers for TLS 1.0/1.1. Slackware linux users may want to review the
patches sub-directory of their respective release number, for relevant software upgrades.

Furthermore it's noted that JDK 8 uses TLS 1.2 as default.

23 September 2018

HOP

The book Higher Order Perl by Mark Dominus was pubished in April of 2005.

The proof for the second edition can be viewed online.

The author writes that Larry Wall, the creator of Perl, Tom Christiansen and
Randal Schwartz, and other early Perl coders, came from the Unix sysadmin
community.

He cites Peter Norvig's PAIP, and alleges Perl shares six of the seven salient
features of Lisp of which Norvig writes.

I am not sure I agree with the author's advocacy of writing Perl in a functional
style, but the book contains a few interesting coding examples.

The importing or calling of subroutines is not addressed, on which see perlsub.

16 September 2018

Software Design

Talk by Prof. John Ousterhout.

ousterhout

61 minutes

A brief retrospect on Tcl/Tk is presented 55:53 minutes into the video.

The language was intially built as more of a textual command language where
one would be typing commands to programs, almost like a shell language. The
Tk extension was good at doing kind of simple interactive GUIs, but over time
with the prevalent use of the Internet people wound up doing more work in the
web.

In an e-mail I received from Paul Haahr this year he wrote me that he believed the
idea of serialising all code to strings was something that he and Byron Rakitzis, the
co-authors of the es shell, had taken inspiration from Tcl on; Paul Haahr had heard
John Ousterhout's Tcl presentation at the USENIX Conference in 1990.

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