TCGAbiolinksGUI is not stable on windows 7.
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Entering edit mode
@ansarisarabio-17058
Last seen 6.1 years ago

Hi,

I am trying to use TCGAbiolinksGUI on windows 7. I have tried to use docker toolbox and Kitematic software. They did not work and asked me to install stringi packages several times. After all, the chrome TCGAbiolinks was not stable and closed after a few seconds.

Then, I tried to load it via R studio packages. It was not stable, too. I received this message several times. I have tried to update and upgrade every package. It did not work. Unfortunately, I am totally new to R and do not get the warning messages! Could it be possible to interpret this message for me?

Many thanks,

> library("TCGAbiolinksGUI")
> TCGAbiolinksGUI()
Warning: Error in if: argument is of length zero
  48: survivalplotdata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#30]
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#72]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  48: survivalplotdata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#30]
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#84]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  48: survivalplotdata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#30]
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#99]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/volcano.R#99]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  64: <reactive:volcanodata> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/volcano.R#62]
  48: volcanodata
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/volcano.R#106]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  68: eval [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#164]
  67: eval
  66: withProgress
  65: <reactive:heatmapdata> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#161]
  49: heatmapdata
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#98]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#111]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  50: <Anonymous>
Warning: Error in if: argument is of length zero
  50: <Anonymous>
Warning: Error in if: argument is of length zero
  96: eval [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dmr.R#153]
  95: eval
  94: withProgress
  93: <reactive:dmrdata> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dmr.R#150]
  77: dmrdata
  75: observeEventHandler [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dmr.R#29]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  51: <Anonymous>
Warning: Error in if: argument is of length zero
  68: eval [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/meanMet.R#153]
  67: eval
  66: withProgress
  65: <reactive:meandata> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/meanMet.R#150]
  49: meandata
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/meanMet.R#26]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  51: <Anonymous>
Warning: Error in gzfile: invalid 'description' argument
  80: gzfile
  79: load
  77: deadata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#165]
  75: observeEventHandler [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#179]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in gzfile: invalid 'description' argument
  80: gzfile
  79: load
  77: deadata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#165]
  75: observeEventHandler [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#186]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in gzfile: invalid 'description' argument
  52: gzfile
  51: load
  49: deadata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#165]
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#194]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in if: argument is of length zero
  66: <reactive:annotation.maf> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/oncoprint.R#112]
  50: annotation.maf
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/oncoprint.R#90]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in gzfile: invalid 'description' argument
  70: gzfile
  69: load
  64: <reactive:maedata> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#347]
  48: maedata
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#192]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in gzfile: invalid 'description' argument
  78: <Anonymous>
Warning: Error in gzfile: invalid 'description' argument
  78: <Anonymous>
Warning: Error in gzfile: invalid 'description' argument
  70: gzfile
  69: load
  64: <reactive:elmer.results.data> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#334]
  48: elmer.results.data
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#357]
   4: shiny::runApp
   1: TCGAbiolinksGUI
Warning: Error in gzfile: invalid 'description' argument
  78: <Anonymous>
Warning: Error in gzfile: invalid 'description' argument
  51: <Anonymous>
Warning: Error in gzfile: invalid 'description' argument
  51: <Anonymous
tcgabiolinks tcgabiolinksgui • 1.5k views
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@huangtao334334-17102
Last seen 6.3 years ago

TCGAbiolinksGUI is also not stable on windows 10， the same errors.
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Please, could you try the GitHub version?

You can install with:

​devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI")
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Thank you very much! I have tried it. I found a new error :((

 devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI")
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinksGUI@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinksGUI/zipball/master
Installing TCGAbiolinksGUI
"C:/PROGRA~1/R/R-35~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  "C:/Users/Sara  \
  Ansari/AppData/Local/Temp/RtmpQFW6gg/devtools1abc78001994/BioinformaticsFMRP-TCGAbiolinksGUI-711bd09"  \
  --library="C:/Users/Sara Ansari/Documents/R/win-library/3.5" --install-tests 

ERROR: dependency 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19' is not available for package 'TCGAbiolinksGUI'
* removing 'C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI'
In R CMD INSTALL
Installation failed: Command failed (1)

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We added a function to normalized DNA methylation idats that uses that missing package (although we might change to sesame in the future). You should be able to install the missing dependency with: source("https://bioconductor.org/biocLite.R") biocLite("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")
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Hi,

Thank you very much for your prompt reply to the questions! After installing the last package that I mentioned before, TCGAbiolinksGUI loaded perfectly and I managed to download and prepare gene expression data. I didn't change anything and immediately start working with DEA. It was so slow and just let me select the downloaded file. Suddenly, TCGAbiolinksGUI crashed and the chrome closed. I restarted the Rstudio and the laptop. It didn't help. I get this message:

> TCGAbiolinksGUI(run = TRUE)
Warning: Error in readChar: cannot open the connection
  52: readChar
  51: load
  49: deadata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#165]
  47: <observer> [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#197]
   4: shiny::runApp
   1: TCGAbiolinksGUI

Another problem is TCGAbiolinks that was working greatly is not available anymore. I have installed it again form Github and Bioconductor websites. It is a temporary solution and I have to repeat it every time I restart the Rstudio.

> library("TCGAbiolinks")

Error: package or namespace load failed for ‘TCGAbiolinks’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

 there is no package called ‘stringi’

> install.packages("stringi")

Installing package into ‘C:/Users/Sara Ansari/Documents/R/win-library/3.5’

(as ‘lib’ is unspecified)

 

  There is a binary version available but the source version is later:

        binary source needs_compilation

stringi  1.1.7  1.2.4              TRUE

Binaries will be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/stringi_1.1.7.zip'

Content type 'application/zip' length 14368013 bytes (13.7 MB)

downloaded 13.7 MB

package ‘stringi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\Sara Ansari\AppData\Local\Temp\Rtmpam8A8F\downloaded_packages

> library("TCGAbiolinks")

> TCGAbiolinks()

Error in TCGAbiolinks() : could not find function "TCGAbiolinks"

I was wondering if my system (window7/core i3 laptop) isn't compatible with this package? I have searched and found that "stringi" is not stable in windows so I have to download and install it every session that I want to use TCGAbiolinks/GUI.

Thank you very much in advance for your time!

P.S. TCGAbiolinksGUI is stable in another field expect Transcriptome analysis. So strange!

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