Problem installing package - "MafH5.gnomAD.r3.0.GRCh38"
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@sbpatel2009-14018
Last seen 3.7 years ago

I am trying to install the package MafH5.gnomAD.r3.0.GRCh38. I have tried to install it on RStudio on my personal computer but got the error message below. To troubleshoot I also tried running the same code on RStudio Cloud but got the error below. I also searched this forum for " Installation path not writeable" but only got to one post that was incomplete. Please advise.

Below is the output on my Personal Computer: R version 4.0.1, RStudio version 1.3.959

    > library(BiocManager) 
    Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
    > install("MafH5.gnomAD.r3.0.GRCh38") 
    Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Installing package(s) 'MafH5.gnomAD.r3.0.GRCh38' 
    installing the source package ‘MafH5.gnomAD.r3.0.GRCh38’

     trying URL
     'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/MafH5.gnomAD.r3.0.GRCh38_3.11.0.tar.gz'
     Content type 'application/x-gzip' length unknown downloaded 3743.9 MB

     Error in untar2(tarfile, files, list, exdir, restore_times) :   
     incomplete block on file

     The downloaded source packages are in
        ‘C:\Users\Owner\AppData\Local\Temp\RtmpcLveSl\downloaded_packages’
     Installation path not writeable, unable to update packages: survival
     Old packages: 'bit64' Update all/some/none? [a/s/n]:  a

       There is a binary version available but the source version is later:
           binary  source needs_compilation bit64  0.9-7 0.9-7.1              TRUE

       Binaries will be installed trying URL
     'https://cran.rstudio.com/bin/windows/contrib/4.0/bit64_0.9-7.zip'
     Content type 'application/zip' length 540636 bytes (527 KB) downloaded
     527 KB

     package ‘bit64’ successfully unpacked and MD5 sums checked

     The downloaded binary packages are in
        C:\Users\Owner\AppData\Local\Temp\RtmpcLveSl\downloaded_packages
     Warning message: In install.packages(...) :   installation of package
     ‘MafH5.gnomAD.r3.0.GRCh38’ had non-zero exit status

Below is the output on RStudio Cloud:

> library(BiocManager)
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
> install("MafH5.gnomAD.r3.0.GRCh38")
Installing package(s) 'MafH5.gnomAD.r3.0.GRCh38'
Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, nlme, nnet, spatial, survival
Warning message:
package ‘MafH5.gnomAD.r3.0.GRCh38’ is not available (for R version 3.6.3) 
> library("MafH5.gnomAD.r3.0.GRCh38")
Error in library("MafH5.gnomAD.r3.0.GRCh38") : 
  there is no package called ‘MafH5.gnomAD.r3.0.GRCh38’
MafH5.gnomAD.r3.0.GRCh38 • 460 views
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@james-w-macdonald-5106
Last seen 20 hours ago
United States

The first error:

Error in untar2(tarfile, files, list, exdir, restore_times) :  incomplete block on file

Looks like you didn't get a complete download, so maybe try again. The message you get from RStudio cloud is due to the fact that this package is only available for the current release version of Bioconductor, and R-3.6.3 uses the previous release.

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Yep. That file is a monster!

trying URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/MafH5.gnomAD.r3.0.GRCh38_3.11.0.tar.gz'
Content type 'application/x-gzip' length unknown
downloaded 4410.7 MB

* installing *source* package 'MafH5.gnomAD.r3.0.GRCh38' ...
** using staged installation
** R
** inst

And note that you only downloaded 3743.9 MB. So please try again

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