Error installing rTASSEL

[massub....@gmail.com]

Dear guys,

I am facing problem installing rTASSEL, I have checked my java and jdk are 64 bit so as my windows 8. But still am facing the error below can someone please take a look and point me to the right direction. Am going round and round but still not getting anywhere, please help me in this regard.

Thanking you in advance.

> remotes::install_github("maize-genetics/rTASSEL")

Downloading GitHub repo maize-genetics/rTASSEL@HEAD

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√  checking for file 'C:\Users\Massub\AppData\Local\Temp\RtmpIdLKV2\remotes8c0640e195d\maize-genetics-rTASSEL-5023d3e/DESCRIPTION' (418ms)

-  preparing 'rTASSEL': (590ms)

√  checking DESCRIPTION meta-information ... 

-  checking for LF line-endings in source and make files and shell scripts

-  checking for empty or unneeded directories

-  building 'rTASSEL_0.9.22.tar.gz'

   

Installing package into ‘C:/Users/Massub/Documents/R/win-library/4.0’

(as ‘lib’ is unspecified)

* installing *source* package 'rTASSEL' ...

** using staged installation

** R

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

  converting help for package 'rTASSEL'

    finding HTML links ... done

    TasselGenotypePhenotype-class           html  

    assocModelFitter                        html  

    distanceMatrix                          html  

    distanceToRMatrix                       html  

    exportGenotypeTable                     html  

    filterGenotypeTableSites                html  

    filterGenotypeTableTaxa                 html  

    genomicPrediction                       html  

    getPhenotypeDF                          html  

    getSumExpFromGenotypeTable              html  

    kinshipMatrix                           html  

    kinshipToRMatrix                        html  

    ldJavaApp                               html  

    ldPlot                                  html  

    linkageDiseq                            html  

    manhattanPlot                           html  

    readGenotypePhenotype                   html  

    readGenotypeTableFromPath               html  

    readPhenotypeFromDataFrame              html  

    readPhenotypeFromPath                   html  

    startLogger                             html  

*** copying figures

** building package indices

** installing vignettes

** testing if installed package can be loaded from temporary location

*** arch - i386

Error: package or namespace load failed for 'rTASSEL':

 .onLoad failed in loadNamespace() for 'rJava', details:

  call: library.dynam("rJava", pkgname, libname)

  error: DLL 'rJava' not found: maybe not installed for this architecture?

Error: loading failed

Execution halted

*** arch - x64

ERROR: loading failed for 'i386'

* removing 'C:/Users/Massub/Documents/R/win-library/4.0/rTASSEL'

Error: Failed to install 'rTASSEL' from GitHub:

  (converted from warning) installation of package ‘C:/Users/Massub/AppData/Local/Temp/RtmpIdLKV2/file8c05f43564a/rTASSEL_0.9.22.tar.gz’ had non-zero exit status

[kpoviessi akovognon]

Please, use an old version of Rstudio, I think it will be okay.

I don't know exactly what version of rstudio, but I think you need to use an old version.

All the Best!

[massub....@gmail.com]

Thank you for your reply but am already using an older version of Rstudio i.e. 1.3.1073.

[Peter Bradbury]

"error: DLL 'rJava' not found: maybe not installed for this architecture?" indicates the problem which is that rJava has not been installed (or properly installed).  That is a prerequisite for installing rTASSEL. There is a link on the rTASSEL wiki near the top with directions for installing rJava with Windows10. Hopefully, that also works for Windows 8. 

[Brandon Monier]

@massub - Can you load rJava outside of RStudio (e.g. in the command line)?

[Brandon Monier]

@massub - what is the architecture of your R installation? 32 or 64 bit? What do you get when you run:

Sys.getenv("R_ARCH")

[Caesarius]

      Hello everyone,

I have tried 

Sys.setenv   in two different ways w/o success as other posted solution:

  Caesarius

[Brandon Monier]

Hi Caesarius,

The error that you are getting in your last screenshot (`%1 is not a valid win32 application`) is indicative of your Java and R architectures not matching (e.g. conflict between 32 and 64-bit installations). Double check to see if the architecture matches (e.g. running 32-bit R - use 32-bit Java JDK and vice-versa).

Regards,

Brandon M.

[Caesarius]

Thank you, Brandon !

 Both Java JDK   and  R are 64 bit versions, as screenshot posted earlier I hope to prove it .

If not , please let me know.

   Regards,

  Caesarius 

[Brandon Monier]

@Caesarius - When you installed R for your Windows OS, what components did you select on installation? Both 32-bit and 64-bit or just 64-bit? See pic for further information:

[Caesarius]

@Brandon ,

Thank you again.

 I am not the one that did the installation, but the system administrator. 

I do not have the admin privileges on the network, but I may suggest the system admin to take a look at your hint.

Hopefully will make rTassel work.

  Regards,

 Caesarius 

[Brandon Monier]

@Caesarius - sounds good. I am curious if both versions are installed and the `devtools` package is trying to build for both of them. If you have the capability, reinstalling the package using the following parameters might help:

devtools::install_bitbucket(

    repo = "bucklerlab/rTASSEL",

    ref = "master",

    build_vignettes = FALSE,

    INSTALL_opts = c("--no-multiarch")

)

Using the `--no-multiarch` option in `INSTALL_opts` will force building the package for your currently running R version.

[Caesarius]

Mr. Brandon Monier,

Thank you !

This instruction solved the problem and maybe should be provided as an alternative installation for the rTassel  tutorial   to maybe help those many without administrative privileges. 

devtools::install_bitbucket(

    repo = "bucklerlab/rTASSEL",

    ref = "master",

    build_vignettes = FALSE,

    INSTALL_opts = c("--no-multiarch")

)

 Regards,

 Caesarius