TxDb.Hsapiens.UCSC.hg38.knownGene In install.packages(pkgs = doing, lib = lib, ...) Non-Zero Exit Status
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Entering edit mode
tdfyoder • 0
@tdfyoder-20272
Last seen 6 months ago

Hello,

I've tried installing TxDb.Hsapiens.UCSC.hg38.knownGene on R-Studio-- Windows 10. mgcv has been updated but "doing and lib" continually fail despite different installation methods. Please advise. Thank you so much!

> biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.3 (2019-03-11).
Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
installing the source package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31934087 bytes (30.5 MB)
downloaded 30.5 MB

* installing *source* package 'TxDb.Hsapiens.UCSC.hg38.knownGene' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'rlang'
Error : package 'GenomicFeatures' could not be loaded
ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg38.knownGene'
* removing 'C:/Users/yoderto/Documents/R/win-library/3.5/TxDb.Hsapiens.UCSC.hg38.knownGene'
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\yoderto\AppData\Local\Temp\RtmpgZL3as\downloaded_packages’
Old packages: 'mgcv'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
     binary source needs_compilation
mgcv 1.8-27 1.8-28              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/mgcv_1.8-27.zip'
Content type 'application/zip' length 2922121 bytes (2.8 MB)
downloaded 2.8 MB

package ‘mgcv’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\yoderto\AppData\Local\Temp\RtmpgZL3as\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ had non-zero exit status
annotation UCSC doing lib mgcv • 1.0k views
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Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

You should be using BiocManager to install things, rather than BiocInstaller.

install.packages("BiocManager")

Then do note the error right there in the middle of your output:

Error: package or namespace load failed for 'GenomicFeatures' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'rlang'

Which implies you should install rlang directly

library(BiocManager)
BiocManager::install(c("rlang","TxDb.Hsapiens.UCSC.hg38.knownGene"))

And let us know if that doesn't sort things out.

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