Adventures & experiences in contemporary technology
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 is 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 Posit (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, which 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:
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:
R Programming for Data Science
R Markdown: The Definitive Guide
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
Engineering Production-Grade Shiny Apps
Outstanding User Interfaces with Shiny
Happy Git and GitHub for the useR
Outstanding User Interfaces with Shiny
Engineering Production-Grade Shiny Apps
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 motivation 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.
If the milestone date was to be believed, WordPress 2.5 was due yesterday. However, it has yet to show and a quick look on WordPress Trac reveals why: loads of outstanding tickets relating to bugs. In fact, there seem to be more tickets associated with this than other releases. I suppose that we can expect the new release when we see it then. Interestingly, the administration screen theming references have been removed from the pre-release version so that’s a functionality for a future release and it’s not hard to see why. Otherwise, the style of the screens in the latest Subversion revision looks a bit smarter and my blog themes are not getting broken. For my online blogs, I’ll be sticking with 2.3.3 for now.
Moving from one operating system to another like I have means that a certain amount of migration is in order. I have already talked about migrating my email but there are lesser acts too. One of these is carrying across bookmarks into the new world. This should be an easy thing to achieve and, for the most part, it is. However, the Import… entry on the File menu of the main browser only brings in bookmarks from other applications. To get more flexibility, you need to open up the Bookmarks Manager window from the Bookmarks menu (Organise Bookmarks… is the entry that you need). The File menu of the Bookmarks Manager has entries named Import… and Export…; their functions should be very apparent. The former will read from a file, very useful if you do not want to disrupt what you already have. Another migration option is the potentially disruptive act of copying in an alternative bookmarks.html file into your Firefox profile folder and overwriting the one that’s already there.
In recent months, I have been doing a clear out of paper books in case the recent European Union referendum result in the U.K. affects my ability to stay there since I am an Irish citizen. In my two decades here, I have not felt as much uncertainty and lack of belonging as I do now. It is as if life wants to become difficult for a while.
What made the clearance easier was that there was of making sure that the books were re-used and eBooks replaced anything that I would wanted to keep. However, what I had not realised is that demand for eBooks has flatlined, something that only became apparent in recent article in PC Pro article penned by Stuart Turton. He had all sorts of suggestions about how to liven up the medium but I have some of my own.
Niall Benvie also broached the subject from the point of view of photographic display in an article for Outdoor Photography because most are looking at photos on their smartphones and that often reduces the quality of what they see. Having a partiality to photo books, it remains the one class of books that I am more likely to have in paper form, even I have an Apple iPad Pro (the original 12.9 inch version) and am using it to write these very words. There also is the six year old 24 inch Iiyama screen that I use with my home PC.
The two apps with which I have had experience are Google Play Books and Amazon Kindle, both of which I have used on both iOS and Android while I use the Windows app for the latter too. Both apps are simple and work effectively until you end up with something of a collection. Then, shortcomings become apparent.
Search functionality is something that can be hidden away on menus and that is why I missed it for so long. For example, Amazon’s Kindle supports puts the search box in a prominent place on iOS but hides the same function in menus on its Android or Windows incarnations. Google Play Books consistently does the latter from what I have seen and it would do no harm to have a search box on the library screen since menus and touchscreen devices do not mix as well. The ability to search within a book is similarly afflicted so this also needs moving to a more prominent place and is really handy for guidebooks or other more technical textbooks.
The ability to organise a collection appears to be another missed opportunity. The closest that I have seen so far are the Cloud and Device screens on Amazon’s Kindle app but even this is not ideal. Having the ability to select some books as favourites would help as would hiding others from the library screen would be an improvement. Having the ability to re-sell unwanted eBooks would be another worthwhile addition because you do just that with paper books.
When I started on this piece, I reached the conclusion the eBooks too closely mimicked libraries of paper books. Now, I am not so sure. It appears to me that the format is failing to take full advantage of its digital form and that might have been what Turton was trying to evoke but the examples that he used did not appeal to me. Also, we could do with more organisation functionality in apps and the ability to resell could be another opportunity. Instead, we appear to be getting digital libraries and there are times when a personal collection is best.
All the while, paper books are being packaged in ever more attractive ways and there always will be some that look better in paper form than in digital formats and that still applies to those with glossy appealing photos. Paper books almost feel like gift items these days and you cannot fault the ability to browse them by flicking through the pages with your hands.
There are times when I just need to share some links outside the fleeting environment of Twitter, and this is where they might appear. The practice is very much in the spirit of the original weblog idea when it was about link sharing and not about writing down one’s thoughts as it subsequently became before sharing of photos, videos and other multimedia content became a mainstay of (legal) sharing for some people.
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This may refer to an older Ubuntu version but the advice contained in the article remains relevant to current ones. In fact, I have used it to harden some VPS systems that I have. Now, I only need to see what impact this action might have.
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Archive area of old releases of Java for those who need them.
Having exhausted the trial time on PhotoShop Elements 5, I am now having a look at its big brother PhotoShop CS2. That has got me thinking about PhotoShop books so that I become more of the possibilities and how to use them. Having a Safari subscription as I do, that naturally became my first port of call and I seemed to find two that answered my needs. Both are by Scott Kelby and they now lie on my Safari bookshelf: The Photoshop Elements 5 Book for Digital Photographers and The Photoshop CS2 Book for Digital Photographers. Even so, I am tempted to get a dead tree version of one of them and that presents a chicken and egg dilemma: the books could help choose which software to buy and the software dictates which of them will be the more useful. That said, I suspect price and features will swing it the way of Elements 5; paying over £400 for software whose capabilities I may never need does not sound financially sensible.
Update March 5th, 2007: I have now got my mits on the dead tree edition of Scott Kelby’s The Photoshop Elements 5 Book for Digital Photographers as well as Brad Hinkel’s Focal Easy Guide to Photoshop CS2. Now for some reading…
Though my main home PC runs Linux Mint, I do like to have the facility to use Windows software from time to time and virtualisation has allowed me to continue doing that. For a good while, it was a Windows 7 guest within a VirtualBox virtual machine and, before that, one running Windows XP fulfilled the same role. However, it did feel as if things were running slower in VirtualBox than once might have been the case and I jumped ship to VMware Player. It may be proprietary and closed source but it is free of charge and has been doing what was needed. A subsequent recent upgrade of video driver on the host operating system allowed the enabling of a better graphical environment in the Windows 7 guest.
Instability
However, there were issues with stability and I lost the ability to flit from the VM window to the Linux desktop at will with the system freezing on me and needing a reboot. Working in Windows 7 using full screen mode avoided this but it did feel as I was constrained to working in a Windows machine whenever I did so. The graphics performance was imperfect too with screening refreshing being very blocky with some momentary scrambling whenever I opened the Start menu. Others would not have been as patient with that as I was though there was the matter of an expensive Photoshop licence to be guarded too.
In hindsight, a bit of pruning could have helped. An example would have been driver housekeeping in the form of removing VirtualBox Guest Additions because they could have been conflicting with their VMware counterparts. For some reason, those thoughts entered my mind and I was pondering another more expensive option instead.
Considering NAS & Windows/Linux Networking
That would have taken the form of setting aside a PC for running Windows 7 and having a NAS for sharing files between it and my Linux system. In fact, I did get to exploring what a four bay QNAP TS-412 would offer me and realised that you cannot put normal desktop hard drives into devices like that. For a while, it looked as if it would be a matter of getting drives bundled with the device or acquiring enterprise grade disks so as to main the required continuity of operation. The final edition of PC Plus highlighted another one though: the Western Digital Red range. These are part way been desktop and enterprise classifications and have been developed in association with NAS makers too.
Looking at the NAS option certainly became an education but it has exited any sort of wish list that I have. After all, there is the cost of such a setup and it’s enough to get me asking if I really need such a thing. The purchase of a Netgear FS 605 ethernet switch would have helped incorporate it but there has been no trouble sorting alternative uses for it since it bumps up the number of networked devices that I can have, never a bad capability to have. As I was to find, there was a less expensive alternative that became sufficient for my needs.
In-situ Windows 8 Upgrade
Microsoft have been making available evaluation copies of Windows 8 Enterprise that last for 90 days before expiring. One is in my hands has been running faultlessly in a VMware virtual machine for the past few weeks. That made me wonder if upgrading from Windows 7 to Windows 8 help with my main Windows VM problems. Being a curious risk-taking type I decided to answer the question for myself using the £24.99 Windows Pro upgrade offer that Microsoft have been running for those not needing a disk up front; they need to pay £49.99 but you can get one afterwards for an extra £12.99 and £3.49 postage if you wish, a slightly cheaper option. There also was a time cost in that it occupied a lot of a weekend on me but it seems to have done what was needed so it was worth the outlay.
Given the element of risk, Photoshop was deactivated to be on the safe side. That wasn’t the only pre-upgrade action that was needed because the Windows 8 Pro 32-bit upgrade needs at least 16 GB before it will proceed. Of course, there was the matter of downloading the installer from the Microsoft website too. This took care of system evaluation and paying for the software as well as the actual upgrade itself.
The installation took a few hours with virtual machine reboots along the way. Naturally, the licence key was needed too as well as the selection of a few options though there weren’t many of these. Being able to carry over settings from the pre-exisiting Windows 7 instance certainly helped with this and with making the process smoother too. No software needed reinstatement and it doesn’t feel as if the system has forgotten very much at all, a successful outcome.
Post-upgrade Actions
Just because I had a working Windows 8 instance didn’t mean that there wasn’t more to be done. In fact, it was the post-upgrade sorting that took up more time than the actual installation. For one thing, my digital mapping software wouldn’t work without .Net Framework 3.5 and turning on the operating system feature form the Control Panel fell over at the point where it was being downloaded from the Microsoft Update website. Even removing Avira Internet Security after updating it to the latest version had no effect and it was a finding during the Windows 8 system evaluation process. The solution was to mount the Windows 8 Enterprise ISO installation image that I had and issue the following command from a command prompt running with administrative privileges (it’s all one line though that’s wrapped here):
dism.exe /online /enable-feature /featurename:NetFX3 /Source:d:\sources\sxs /LimitAccess
For sake of assurance regarding compatibility, Avira has been replaced with Trend Micro Titanium Internet Security. The Avira licence won’t go to waste since I have another another home in mind for it. Removing Avira without crashing Windows 8 proved impossible though and necessitating booting Windows 8 into Safe Mode. Because of much faster startup times, that cannot be achieved with a key press at the appropriate moment because the time window is too short now. One solution is to set the Safe Boot tickbox in the Boot tab of Msconfig (or System Configuration as it otherwise calls itself) before the machine is restarted. There may be others but this was the one that I used. With Avira removed, clearing the same setting and rebooting restored normal service.
Dealing with a Dual Personality
One observer has stated that Windows 8 gives you two operating systems for the price of one: the one in the Start screen and the one on the desktop. Having got to wanting to work with one at a time, I decided to make some adjustments. Adding Classic Shell got me back a Start menu and I left out the Windows Explorer (or File Explorer as it is known in Windows 8) and Internet Explorer components. Though Classic Shell will present a desktop like what we have been getting from Windows 7 by sweeping the Start screen out of the way for you, I found that this wasn’t quick enough for my liking so I added Skip Metro Suite to do this and it seemed to do that a little faster. The tool does more than sweeping the Start screen out of the way but I have switched off these functions. Classic Shell also has been configured so the Start screen can be accessed with a press of Windows key but you can have it as you wish. It has updated too so that boot into the desktop should be faster now. As for me, I’ll leave things as they are for now. Even the possibility of using Windows’ own functionality to go directly to the traditional desktop will be left untested while things are left to settle. Tinkering can need a break.
Outcome
After all that effort, I now have a seemingly more stable Windows virtual machine running Windows 8. Flitting between it and other Linux desktop applications has not caused a system freeze so far and that was the result that I wanted. There now is no need to consider having separate Windows and Linux PC’s with a NAS for sharing files between them so that option is well off my wish-list. There are better uses for my money.
Not everyone has had my experience though because I saw a report that one user failed to update a physical machine to Windows 8 and installed Ubuntu instead; they were a Linux user anyway even if they used Fedora more than Ubuntu. It is possible to roll back from Windows 8 to the previous version of Windows because there is a windows.old directory left primarily for that purpose. However, that may not help you if you have a partially operating system that doesn’t allow you to do just that. In time, I’ll remove it using the Disk Clean-up utility by asking it to remove previous Windows installations or running File Explorer with administrator privileges. Somehow, the former approach sounds the safer.
What About Installing Afresh?
While there was a time when I went solely for upgrades when moving from one version of Windows to the next, the annoyance of the process got to me. If I had known that installing the upgrade twice onto a computer with a clean disk would suffice, it would have saved me a lot. Staring from Windows 95 (from the days when you got a full installation disk with a PC and not the rescue media that we get now) and moving through a sequence of successors not only was time consuming but it also revealed the limitations of the first in the series when it came to supporting more recent hardware. It was enough to have me buying the full retailed editions of Windows XP and Windows 7 when they were released; the latter got downloaded directly from Microsoft. These were retail versions that you could move from one computer to another but Windows 8 will not be like that. In fact, you will need to get its System Builder edition from a reseller and that can only be used on one machine. It is the merging of the former retail and OEM product offerings.
What I have been reading is that the market for full retail versions of Windows was not a big one anyway. However, it was how I used to work as you have read above and it does give you a fresh system. Most probably get Windows with a new PC and don’t go building them from scratch like I have done for more than a decade. Maybe the System Builder version would apply to me anyway and it appears to be intended for virtual machine use as well as on physical ones. More care will be needed with those licences by the looks of things and I wonder what needs not to be changed so as not to invalidate a licence. After all, making a mistake might cost between £75 and £120 depending on the edition.
Final Thoughts
So far Windows 8 is treating me well and I have managed to bend to my will too, always a good thing to be able to say. In time, it might be that a System Builder copy could need buying yet but I’ll leave well alone for now. Though I needed new security software, the upgrade still saved me money over a hardware solution to my home computing needs and I have a backup disk on order from Microsoft too. That I have had to spend some time settling things was a means of learning new things for me but others may not be so patient and, with Windows 7 working well enough for most, you have to ask if it’s only curious folk like me who are taking the plunge. Still, the dramatic change has re-energised the PC world in an era when smartphones and tablets have made so much of the running recently. That too is no bad thing because an unchanging technology is one that dies and there are times when big changes are needed, as much as they upset some folk. For Microsoft, this looks like one of them and it’ll be interesting to see where things go from here for PC technology.
In recent times, I have lugged my Toshiba Equium with me while working away from home; I needed a full screen laptop of my own for attending to various things after work hours so it needs to come with me. It’s not the most portable of things with its weight and the lack of battery life. Now that I think of it, I reckon that it’s more of a desktop PC replacement machine than a mobile workhorse. After all, it only lasts an hour on its own battery away from a power socket. Virgin Trains’ tightness with such things on their Pendolinos is another matter…
Unless my BlackBerry is discounted, battery life seems to be something with which I haven’t had much luck because my Asus Eee PC isn’t too brilliant either. Without decent power management, two hours seems to be as good as I get from its battery. However, three to four hours become possible with better power management software on board. That makes the netbook even more usable though there are others out there offering longer battery life. Still, I am not tempted by these because the gadget works well enough for me that I don’t need to wonder about how money I am spending on building a mobile computing collection.
While I am not keen on spending too much cash or having a collection of computers, the battery life situation with my Toshiba is more than giving me pause for thought. The figures quoted for MacBooks had me looking at them though they aren’t at all cheap. Curiosity about the world of the Mac may make them attractive to me but the prices forestalled that and the concept was left on the shelf.
Recently, PC Pro ran a remarkably well-timed review of laptops offering long battery life (in issue 205). The minimum lifetime in this collection was over five hours so the list of reviewed devices is an interesting one for me. In fact, it even may become a shortlist should I decide to spend money on buying a more portable laptop than the Toshiba that I already have. The seventeen hour battery life for a Sony VAIO SB series sounds intriguing even if you need to buy an accessory to gain this. That it does over seven hours without the extra battery slice makes it more than attractive anyway. The review was food for thought and should come in handy if I decide that money needs spending.
Here’s something that I would really appreciate: a book on code cutting for WordPress customisation and extension. Having the Codex is all very fine but having a dead tree compendium that you can peruse at your leisure is a definite bonus. If there was a way to get the Codex on PDF and print it all off for easier reading, that would be progress. I believe that a publisher did plan to bring to the market something like what I want but author and publisher parted company, a pity. It would be great to see something like Apress’ Pro Drupal Development for WordPress. What about it, Automattic folks?
Being a Safari subscriber, I found a pleasant surprise awaiting me in this month’s email newsletter: eBooks from SAS Books are now available on Safari. Having a quick look, I found a small but useful selection. Topics like the SQL procedure, the Macro language and Enterprise Guide caught my eye but there’s more than this on offer. It’ll be interesting to see where this leads…