TCGAbiolinksGUI is not stable on windows 7.
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Entering edit mode
@ansarisarabio-17058
Last seen 2.5 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,

Warning: Error in if: argument is of length zero
4: shiny::runApp
Warning: Error in if: argument is of length zero
4: shiny::runApp
Warning: Error in if: argument is of length zero
4: shiny::runApp
Warning: Error in if: argument is of length zero
4: shiny::runApp
Warning: Error in if: argument is of length zero
48: volcanodata
4: shiny::runApp
Warning: Error in if: argument is of length zero
67: eval
66: withProgress
49: heatmapdata
4: shiny::runApp
Warning: Error in if: argument is of length zero
4: shiny::runApp
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
95: eval
94: withProgress
77: dmrdata
4: shiny::runApp
Warning: Error in if: argument is of length zero
51: <Anonymous>
Warning: Error in if: argument is of length zero
67: eval
66: withProgress
49: meandata
4: shiny::runApp
Warning: Error in if: argument is of length zero
51: <Anonymous>
Warning: Error in gzfile: invalid 'description' argument
80: gzfile
4: shiny::runApp
Warning: Error in gzfile: invalid 'description' argument
80: gzfile
4: shiny::runApp
Warning: Error in gzfile: invalid 'description' argument
52: gzfile
4: shiny::runApp
Warning: Error in if: argument is of length zero
50: annotation.maf
4: shiny::runApp
Warning: Error in gzfile: invalid 'description' argument
70: gzfile
48: maedata
4: shiny::runApp
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
48: elmer.results.data
4: shiny::runApp
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

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Entering edit mode
@huangtao334334-17102
Last seen 2.8 years ago

TCGAbiolinksGUI is also not stable on windows 10， the same errors.

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Entering edit mode

Please, could you try the GitHub version?

You can install with:

​devtools::install_github("BioinformaticsFMRP/TCGAbiolinksGUI")
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Entering edit mode

Thank you very much! I have tried it. I found a new error :((

"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  \
--library="C:/Users/Sara Ansari/Documents/R/win-library/3.5" --install-tests

ERROR: dependency 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19' is not available for package '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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Entering edit mode

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:

Warning: Error in readChar: cannot open the connection
4: shiny::runApp

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.

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

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

package ‘stringi’ successfully unpacked and MD5 sums checked

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.

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