Something to watch with the SYSODSESCAPECHAR automatic SAS macro variable

October 10th, 2021

Recently, a client of mine updated one of their systems from SAS 9.4 M5 to SAS 9.4 M7. In spite of performing due diligence regarding changes between the maintenance release, a change in behaviour of the SYSODSESCAPECHAR automatic macro variable surprised them. The macro variable captures the assignment of the ODS escape character used to prefix RTF codes for page numbering and other things. That setting is made using an ODS ESCAPECHAR statement like the following:

ods escapechar="~";

In the M5 release, the tilde character in this example was output by the automatic macro variable but that changed in the M7 release to 7E, the hexadecimal code for the same and this tripped up one of their validated macro programs used in output production. The adopted solution was to use the escape sequence (*ESC*) that gave the same outcome that was there before the change. That was less verbose than alternative code changing the hexadecimal code into the expected ASCII character that follows.

data _null_;
call symput("new",byte(input("&sysodsescapechar.",hex.)));
run;

The above supplies a hexadecimal code to the BYTE function for correct rendering with the SYMPUT routine assigning the resulting value to a macro variable named new. Just using the escape sequence is far more succinct though there is now an added validation need once user pilot testing has completed. In my line of business, the updating of code is the quickest part of many such changes; documentation and testing always take longer.

Limiting Google Drive upload & synchronisation speeds using Trickle

October 9th, 2021

Having had a mishap that lost me some photos in the early days of my dalliance with digital photography, I have been far more careful since then and that now applies to other files as well. Doing regular backups is a must that you find reiterated by many different authors and the current computing climate makes doing that more vital than it ever was.

So, as well as having various local backups, I also have remote ones in the form of OneDrive, Dropbox and Google Drive. These more correctly may be file synchronisation services but disciplined use can make them useful as additional storage facilities in the interests of maintaining added resilience. There also are dedicated backup services that I have seen reviewed in the likes of PC Pro magazine but I have to make use of those.

Insync

Part of my process for dealing with new digital photo files is to back them up to Google Drive and I did that with a Windows client in the early days but then moved to Insync running on Linux Mint. One drawback to the approach is that this hogs the upload bandwidth of an internet connection that has yet to move to fibre from copper cabling. Having fibre connections to a local cabinet helps but a 100 KiB/s upload speed is easily overwhelmed and digital photo file sizes keep increasing. It does not help that I insist on using more flexible raw formats like DNG, CR2 or CR3 either.

Making less images could help to cut the load but I still come away from an excursion with many files because I get so besotted with my surroundings. This means that upload sessions take numerous hours and can extend across calendar days. Ultimately, this makes my internet connection far less usable so I want to throttle upload speed much like what is possible in the Transmission BitTorrent client or in the Dropbox client. Unfortunately, this is not available in Insync so I have tried using the trickle command instead and an example is below:

trickle -d 2000 -u 50 insync

Here, the upload speed is limited to 50 KiB/s while the download speed is limited to 2000 KiB/s. In my case, the latter of these hardly matters while the former leaves me with acceptable internet usability. Insync does not work smoothly with this, however, so occasional restarts are needed to keep file uploads progressing and CPU load also is higher. As rough as the user experience feels, uploads can continue in parallel with other work.

gdrive

One other option that I am exploring is the use of the command line tool gdrive and this appears to work well with trickle. After downloading and installing the tool, getting going is a matter of issuing the following command and following the instructions:

gdrive about

On web servers, I even have the tool backing up things to Google Drive on a scheduled basis. Because of a Google Drive limitation that I have encountered not only with gdrive but also with Insync and the Google’s own Windows Google Drive client, synchronisation only can happen with two new folders, one local and the other remote. Handily, gdrive supports the usual bash style commands for working with remote directories so something like the following will create a directory on Google Drive:

gdrive mkdir ttdc [ID for parent folder]

Here, the ID for the parent folder may be omitted but it can be obtained by going to Google Drive online and getting a link location by right clicking on a folder and choosing the appropriate context menu item. This gets you something like the following and the required identifier is found between the last slash and the first question mark in the address string (so as not to share any real links, I made the address more general below):

https://drive.google.com/drive/folders/[remote folder ID]?usp=sharing

Then, synchronisation uses a command like the following:

gdrive sync upload [local folder or file path] [remote folder ID]

There also is the option to do a one way upload and this is the form of the command used:

gdrive upload [local folder or file path] -p [remote folder ID]

Because every file or folder object has its own ID on Google Drive, it is possible to create two objects on there that appear to have the same name though that is sure to cause confusion even if you know what is happening. It is possible in each of the above to throttle them using trickle as well:

trickle -d 2000 -u 50 gdrive sync upload [local folder or file path] [remote folder ID]
trickle -d 2000 -u 50 gdrive upload [local folder or file path] -p [remote folder ID]

Handily, this works without the added drama seen with Insync and lends itself to scripting as well so it could be something that I will incorporate into my current workflow. One thing that needs to be watched is file upload failures but there may be ways to catch those and retry them so that would another thing that needs doing. This is built into Insync and it would be a learning opportunity if I was to stick with gdrive instead.

When CRON is stalled by incorrect file and folder permissions

October 8th, 2021

During the past week, I rebooted my system only to find that a number of things no longer worked and my Pi-hole DNS server was among them. Having exhausted other possibilities by testing out things on another machine, I did a status check when I spotted a line like the following in my system logs and went investigating further:

cron[322]: (root) INSECURE MODE (mode 0600 expected) (crontabs/root)

It turned out to be more significant than I had expected because this was why every CRON job was failing and that included the network set up needed by Pi-hole; a script is executed using the @reboot directive to accomplish this and I got Pi-hole working again by manually executing it. The evening before, I did make some changes to file permissions under /var/www but I was not expecting it to affect other parts of /var though that may have something to do with some forgotten heavy-handedness. The cure was to issue a command like the following for execution in a terminal session:

sudo chmod -R 600 /var/spool/cron/crontabs/

Then, CRON itself needed starting since it had not not running at all and executing this command did the needful without restarting the system:

sudo systemctl start cron

That outcome was proved by executing the following command to issue some terminal output that include the welcome text “active (running)” highlighted in green:

sudo systemctl status cron

There was newly updated output from a frequently executing job that checked on web servers for me but this was added confirmation. It was a simple solution to a perplexing situation that led up all sorts of blind alleys before I alighted on the right solution to the problem.

Some books and other forms of documentation on R

September 11th, 2021

The thrust of an exhortation from a computing handbook publisher comes to mind here: don’t just look things up on Google, read a book so you really understand what you are doing. Something like those words was used to sell an eBook on Github but the same sentiment applies to R or any other computing language. Using a search engine will get you going or add to existing knowledge but only a book or a training course will help to embed real competence.

In the case of R, there are a myriad of blogs out there that can be consulted as well as function and package documentation on RDocumentation or rrdr.io. For the former, R-bloggers or R Weekly can make good places to start while ones like Stats and R, Statistics Globe, STHDA, PSI’s VIS-SIG and anything from RStudio (including their main blog as well as their AI one) can be worth consulting. Additionally, there is also RStudio Education and the NHS-R Community, who also have a Github repository together with a YouTube channel. Many packages have dedicated websites as well so there is no lack of documentation with all of these so here is a selection:

Tidyverse

forcats

tidyr

Distill for R Markdown

Databases using R

RMariaDB

R Markdown

xaringanExtra

Shiny

formattable

reactable

DT

rhandsontable

thematic

bslib

plumber

ggforce

officeverse

officer

pharmaRTF

COVID-19 Data Hub

To come to the real subject of this post, R is unusual in that books that you can buy also have companions websites that contain the same content with the same structure. Whatever funds this approach (and some appear to be supported by RStudio itself by the looks of things), there certainly are a lot of books available freely online in HTML as you will see from the list below while a few do not have a print counterpart as far as I know:

Big Book of R

R Programming for Data Science

Hands-On Programming with R

Advanced R

Cookbook for R

R Graphics Cookbook

R Markdown: The Definitive Guide

R Markdown Cookbook

RMarkdown for Scientists

bookdown: Authoring Books and Technical Documents with R Markdown

blogdown: Creating Websites with R Markdown

pagedown: Create Paged HTML Documents for Printing from R Markdown

Dynamic Documents with R and knitr

Mastering Shiny

Engineering Production-Grade Shiny Apps

Outstanding User Interfaces with Shiny

R Packages

Mastering Spark with R

Happy Git and GitHub for the useR

JavaScript for R

HTTP Testing in R

Many of the above have counterparts published by O’ Reilly or Chapman & Hall, to name the two publishers that I have found so far. Aside from sharing these with you, there is also the personal of having the collection of links somewhere so I can close tabs in my Firefox session. There are other web articles open in other tabs that I need to retain and share but these will need to do for now and I hope that you find them as useful as I do.

A little bit of abstraction

August 21st, 2021

A little bit of abstraction

Data science has remained in my awareness since 2017 though my work is more on its fringes in clinical research. In fact, I have been involved more in standardisation and automation of more traditional data reporting than in the needs of data modelling such as data engineering or other similar disciplines. Much of this effort has meant the use of SAS, with which I have programmed since 2000 and for which I have a licence (an expensive commodity, it has to be said), but other technologies are being explored with R, Python and Julia being among them.

The change in technological scope does bring an element of excitement and new interest but there is also some sadness when tried and trusted technologies meet with new competition and valued skills are no longer as career securing as they once were. Still, there is plenty of online training out there and I already have collect some of my thoughts on this. The learning continues and the need for repositioning is also clear.

A little bit of abstraction

A little bit of abstraction

The journey also has brought some curios to my notice. One of these is This Person Does Not Exist, a website building photos of non-existent faces using machine learning. Recently, I learned of others like it such as This Artwork Does Not Exist, This Cat Does Not Exist, This Horse Does Not Exist, and This Chemical Does Not Exist. The last of these probably should be entitled “This Molecule Does Not Exist (Yet)” since it is a fictitious molecular structure that has been created and what you get is an actual moving image that spins it around in three-dimensional space. The one with dynamically generated abstract art is the main inspiration for this piece and is of more interest to me while the other two are more explanatory though the horse website is not so successful in its execution and one can ask why we need more cat pictures.

To some, the idea of creating fake pictures may feel a little foreboding and that especially applies to photos of people and the the livelihoods of any content creators. Nevertheless, these sources of imagery have their legitimate uses such as decorating websites or brochures and that is where my interest is piqued. After all, there are some subjects where pictures can be scarce so any form of decoration that enlivens and article has to have some use. Technology websites like this one can feature images too with screenshots and device photos being commonplace but they can all look like each other, hence the need for a little more variety and having pictures often increases the choice of website themes as well since so many need images to make them work or stand out. As ever, being sparing with any new innovations remains in order so that is how I approach this matter as well.