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Fix a (potential) issue with log paths on Windows? #57
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This is really strange. I asked a colleague with a Windows machine to do a couple of quick checks for me and we don't seem to be able to reproduce the issue. What I thought might be a problem (fixed unix-like path separator in admixr forced on Windows) does not actually seem to be an issue. What's more, I have heard from other people who actually do use Windows with admixr? Of course, hard to tell without having more information. I will leave this open for now. |
Hi, @bodkan , glad to hear some more about this issue. Great thanks for your time and effort.
The related scripts are:
All went well until the "run a test" step, the ERROR message:
I went to this path and only two files were found. The .log file was NOT found. I think "admixr" is a new and very cool R package. It will definitely become popular in population researchers, especially for those with little experiences for Unix environment, me included 😄. Hope to hear more and thanks again. |
Hi, Thanks for reporting back. Can you explain to me what you mean by
Are you running some dual-boot setup or are you running Ubuntu in some virtual machine/emulator within Windows? What is a "subsystem" in this context? It's hard for me to understand what's going on without having access to this particular setup of a combination of Windows & Ubuntu & conda (none of the three I use). I worry the only efficient solution might be to clone the admixr repository with this exact OS/conda setup, add a breakpoint (in RStudio) to the Also, what happens when you run |
Closing for insufficient information. Anyone should feel free to reopen in case similar problems appear again. |
Hi, @bodkan I run this in Windows using Rstudio. Loading admixr package. In I follow your suggestion, run Great thanks for any possible suggestions. Best, |
Hello Xia, Thanks for adding more information to this issue. I have never progressed with Windows support, probably because ADMIXTOOLS itself is officially supported on macOS and Linux (not Windows, AFAIK) and I guess many users who are running Windows are doing analyses on computing clusters (which are almost exclusively Linux, I'd say). It's nice to have more information. I have a couple of follow-up questions before we can proceed:
Cheers, |
Dear Martin, I found ADMIXTOOLS version 7.0.2 6/22/21 (for Linux and Mac). But admixr is R package like other packages that can run on Rstudio in Windows, right? Are ADMIXTOOLS and admixr independent? I followed your questions to check again. It showed warning message when run Here is some information.
When I continue to run command, it shows like following.
Best, |
Hello again Xia, I'm afraid I have some bad news. Also, thanks to the information you've provided, I finally understand the issue that the user above had back then.
Yes, admixr and ADMIXTOOLS are two different pieces of software. Briefly, ADMIXTOOLS is a collection of command-line programs maintained by the Reich group. These are officially distributed for macOS and for Linux (AFAIK there's no official Windows support). The admixr R package that I'm developing serves as an R interface connecting to the underlying ADMIXTOOLS program. Without ADMIXTOOLS present on the system, admixr can never work. This is why you see this message when you first load it:
I know there is one way to run Linux subsystem on Windows called WSL. I suggest you give this a shot. Because this starts essentially a full-featured Linux environment under Windows, you should be able to install ADMIXTOOLS based on instructions from its authors. If you run into issues, I'm sure you can ask them for help. Once you get ADMIXTOOLS itself running, please feel free to let me know here and I'd be more than happy to help you connect admixr from R to ADMIXTOOLS programs running on your system. |
Hello bodkan! has Xia asked you more about connecting admixr and ADMIXTOOLS? I am trying to run admixr through windows R. I have installed the Linux subsystem (runs ubuntu) WSL on windows and have used conda / bioconda to install ADMIXTOOLS. I confirm that admixtools is accessible through WSL. I am running into issues connecting R to admixtools. The previous error that other users also encountered in this thread : What I have tried already: and variations of this. Additionally, when I search 'which qpDstat' on the R terminal, the output is 'no qpDstat in (/c/Users/jahn {list of environments}).' Do you know of any way to access admixtools through R? Thanks in advance for the help |
Hi, I'm afraid I don't remember the exact background to this issue. But I can reopen it to see if we can figure it out. To my knowledge, there aren't many ADMIXTOOLS users on Windows so the feedback (or possibility to debug issues) has been a bit tricky. I don't have access to a Windows machine and don't really know WSL but the first thing to make sure that works (before we even bring admixr to the picture) is to make sure R itself can find the qpDstat et al. binaries. For instance, on my machine, I get this:
And then I can verify this:
So if R can see qpDstat et al. in the $PATH, then admixr can also find it. Can you test this? Before |
I have found a (very suboptimal and slow) way to run Windows in a virtual machine on my Mac but setting up WSL, conda, ADMIXTOOLS from conda, etc. would take me a while as I don't know a thing about Windows. I'm currently swamped with other bugs and issues in my other software, but if you don't find a way to do the |
Hi bodkan,
returns nothing, so I'm guessing that windows R has an issue with the $PATH. I have since installed R on WSL and am running it through the linux terminal. This works well and I am able to work with admixr on my data. However this means that I have to continuously move my data files from the windows environment (where I do most of my data analysis) to the linux environment. This is not very effective in the long run... The problem is not urgent, but if you find the time to work on the |
OK, yes. This:
means that it's a problem with finding the WSL ADMIXTOOLS installation in your Windows system. I think it goes even beyond R, to be honest. My suggestion would be to google around the topic of "access path to a wsl binary on windows". Something like this might be useful? Again, I don't know Windows or WSL, so can't vouch for anything at this point. There must be a way to access files installed via WSL from Windows. Like, even in the Windows command prompt. If you find how to refer to them, then you have your answer. Also, perhaps I'm revealing a bit too much about my ignorance but I would normally write this:
as this:
No idea if this makes any difference though. |
See this post: DReichLab/AdmixTools#63 (comment)
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