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I am a beginner in R and I am trying to install arrayQualityMetrics package there's an error though in the 'Hmisc' dependency I get this error :

Error in parse(outFile) :
/tmp/RtmpkFTuHf/R.INSTALLbd637e8c1e92/Hmisc/R/describe.s:1443:63: unexpected '\>'
1442:  
1443:   b \<- gt::gt(a)                                             |\>
^
ERROR: unable to collate and parse R files for package ‘Hmisc’

* removing ‘/home/mariemchatti/R/x86_64-pc-linux-gnu-library/3.6/Hmisc’
  Warning in install.packages :
  installation of package ‘Hmisc’ had non-zero exit status

I searched but couldn't find an answer to this specific error.

I am on Ubuntu 20.04 Rstudio version 3.6.3 (2020-02-29)

THANKS !

Phil
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shatty mariem
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  • How exactly are you trying to install the `arrayQualityMetrics` package? Are you running `install.packages("arrayQualityMetrics")`? What happens if you run `install.packages("Hmisc")` first? – MrFlick Jun 13 '23 at 15:25
  • @MrFlick I initially tried to install it using 'BiocManager::install('arrayQualityMetrics')', also using tried 'install.packages("Hmisc")' and got the same error in both scenarios. Using 'install.packages("arrayQualityMetrics")' also didn't work as it tells me it's not available for this R version. – shatty mariem Jun 13 '23 at 16:43
  • @shattymariem, what do you get when you type `R.Version()$version.string`? Remember that R and RStudio are two separate things. RStudio is the pretty wrapper around R, the programming language. Even if your RStudio is up-to-date, you may still be running an older version of R. You usually get "not available for this R version" errors when your R (the language that you download from CRAN) is too old for the packages. – David Jun 13 '23 at 18:31
  • @David Thank you. When I type that, what I get is the following: R version 3.6.3 (2020-02-29). so the error "ERROR: unable to collate and parse R files for package 'xx' is related to the R version? – shatty mariem Jun 18 '23 at 20:15
  • @shattymariem This post: [https://stackoverflow.com/questions/56471638/error-unable-to-collate-and-parse-r-files-for-package-upload-to-cran] has a problem similar to yours. It is possible that it is a version issue since your R hasn't been updated since 2020. I would suggest updating it even if it doesn't solve your problem. Have you been mixing operating systems, such as editing the program on a PC and then running the code in linux? – David Jun 18 '23 at 22:34

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