[Bug] Unable to install locally

[apn83]

Thanks for using our 3D RNA-seq App. Describe the bug I am unable to install the last step. Is there any specific version of R that needs to be used ? Installation exits with "RUVSeq" not available. I did install it separately but still I end up with error

Screenshots

Warning messages:
1: package ‘BiocVersion’ is not available (for R version 3.4.4) 
2: In install.packages(...) :
  installation of package ‘ShortRead’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘EDASeq’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘RUVSeq’ had non-zero exit status
> if(!requireNamespace("ThreeDRNAseq", quietly = TRUE))
+   devtools::install_github('wyguo/ThreeDRNAseq')
Downloading GitHub repo wyguo/ThreeDRNAseq@master
Skipping 5 packages not available: tximport, limma, edgeR, RUVSeq, ComplexHeatmap
Installing 6 packages: RUVSeq, plotly, tidyr, hexbin, dplyr, tidyselect
Installing packages into ‘/home/nagaraap/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Error: Failed to install 'ThreeDRNAseq' from GitHub:
  (converted from warning) package ‘RUVSeq’ is not available (for R version 3.4.4).

Skipping 5 packages not available: tximport, limma, edgeR, RUVSeq, ComplexHeatmap: I am not sure, why it says package not available. I did see them installed sucessfully. Additional context Add any other context about the problem here.

[wyguo]

Hi, It seems that you are using an old version of R 3.4.4. The old version may cause package conflicts. You could try higher version of R > 3.5.1. In the RUVseq R package web-page, they even requires R 3.6, see: https://bioconductor.org/packages/release/bioc/html/RUVSeq.html.

[apn83]

Hi, It seems that you are using an old version of R 3.4.4. The old version may cause package conflicts. You could try higher version of R > 3.5.1. In the RUVseq R package web-page, they even requires R 3.6, see: https://bioconductor.org/packages/release/bioc/html/RUVSeq.html.

Yes. Now it works after updating R > 3.6. But the problem is, If I start rstudio normally, shiny would crash saying that, 'Permission denied' to create output directories. If I start as sudo QT_XCB_FORCE_SOFTWARE_OPENGL=1 rstudio. It works, but I get a message ,QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-root' and it saves the folder in root path with weird name: /file20522884ffb6. Is there a way to override this and manually set output path later ? Thanks in Advance.

[wyguo]

What system are you working on? Windows, Linux or Mac?

[apn83]

What system are you working on? Windows, Linux or Mac?

I am working on Linux, Ubuntu 18.04.

[wyguo]

Hi The way to create tmp folder in Windows and Linux are different. I have made some changes to allow the App to create tmp folder for data saving in Linux system. You can remove the ThreeDRNAseq R package by remove.packages('ThreeDRNAseq'), then install the updated version by devtools::install_github('wyguo/ThreeDRNAseq') But I use Windows myself and didn't test the updated version on a linux system. If you still have problem, please let me know. I will find a way to test. An alternative is you can use the 3D App hosted by our server: https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/

[apn83]

Hi The way to create tmp folder in Windows and Linux are different. I have made some changes to allow the App to create tmp folder for data saving in Linux system. You can remove the ThreeDRNAseq R package by remove.packages('ThreeDRNAseq'), then install the updated version by devtools::install_github('wyguo/ThreeDRNAseq') But I use Windows myself and didn't test the updated version on a linux system. If you still have problem, please let me know. I will find a way to test. An alternative is you can use the 3D App hosted by our server: https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/

Hi, Now I am able to get the following:

Outputs are saved in: 
/tmp/file5e7646fb450 
/tmp/file5e7646fb450/data 
/tmp/file5e7646fb450/figure 
/tmp/file5e7646fb450/result 
/tmp/file5e7646fb450/report

As i understand, after the analyses I need to locally move the folder to desired name and location. Thanks.

[wyguo]

Hi, Since you are working locally, you can access the tmp folder to get all the results, or in the last step, you can click the button download to download (copy) the results to your default download folder.

[kaylieQian]

Hi, thanks for the nice App!

I have a problem too in install the App locally. when I run the last command : run3DApp(), warning message shows up like this:

when I run debug and it says: the source is not available.

Did I do anything wrong and how can I fix it?