Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
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@amalabdel-aziz-23602
Last seen 24 months ago

Dear All, I have a problem downloading the human genome (TxDb.Hsapiens.UCSC.hg38.knownGene). Please see below the code I used and the warning message and let me know how to solve it. Thanks a lot

I have used the following code and my Bioconductor version is 3.6

source("https://bioconductor.org/biocLite.R")
BiocInstaller::biocVersion()
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")

But I receive the following warning message:

The downloaded source packages are in
        ‘C:\Users\Amal Kamal\AppData\Local\Temp\Rtmp2H9M0N\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Amal Kamal\Documents\R\win-library\3.4" C:\Users\AMALKA~1\AppData\Local\Temp\Rtmp2H9M0N/downloaded_packages/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Amal Kamal\Documents\R\win-library\3.4" C:\Users\AMALKA~1\AppData\Local\Temp\Rtmp2H9M0N/downloaded_packages/blob_1.2.1.tar.gz' had status 1 
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘blob’ had non-zero exit status
5: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Amal Kamal\Documents\R\win-library\3.4" C:\Users\AMALKA~1\AppData\Local\Temp\Rtmp2H9M0N/downloaded_packages/lifecycle_0.2.0.tar.gz' had status 1 
6: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘lifecycle’ had non-zero exit status
annotation software TxDb • 243 views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States

You are using a very outdated version of R and Bioconductor. We don't support old versions, particularly versions that are years out of date. Please upgrade to R-4.0.0 and BioC3.11.

Also, it is usually less problematic to use library paths that don't have spaces in them, so you don't have to rely on the formation of a Windows short path to remove the spaces.

AND, if you are telling R that it's OK to install source packages, you have to have RTools installed as well.

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Err. I meant to say if you are telling R to install source packages and those packages have C or C++ or Fortran code that needs to be compiled, which isn't true in this case, but it's still worth it to have the RTools installed.

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