Question: Fail to download package "TxDb.Mmusculus.UCSC.mm10.ensGene"
0
gravatar for 674139534
17 months ago by
6741395340
6741395340 wrote:

Dear all,

I'm a beginner in bioinfomatics and I'm following the workflow of singcell on bioconductor.During the process, I need to download the package"TxDb.Mmusculus.UCSC.mm10.ensGene";however, I failed after three attempts.

Here is my platform information when downloading:

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

And after I run:

source("http://bioconductor.org/biocLite.R")
biocLite("TxDb.Mmusculus.UCSC.mm10.ensGene")

It displays:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocLite("TxDb.Mmusculus.UCSC.mm10.ensGene")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘TxDb.Mmusculus.UCSC.mm10.ensGene’
installing the source package ‘TxDb.Mmusculus.UCSC.mm10.ensGene’

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz'
Content type 'application/x-gzip' length 18183825 bytes (17.3 MB)
downloaded 17.3 MB

* installing *source* package 'TxDb.Mmusculus.UCSC.mm10.ensGene' ...
** 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 'stringi'
Error : package 'GenomicFeatures' could not be loaded
ERROR: lazy loading failed for package 'TxDb.Mmusculus.UCSC.mm10.ensGene'
* removing 'D:/Rstudio/R-3.5.0/library/TxDb.Mmusculus.UCSC.mm10.ensGene'
* restoring previous 'D:/Rstudio/R-3.5.0/library/TxDb.Mmusculus.UCSC.mm10.ensGene'
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\Administrator\AppData\Local\Temp\RtmpSkl0hS\downloaded_packages’
Old packages: 'MASS', 'survival'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
         binary source needs_compilation
MASS     7.3-49 7.3-50              TRUE
survival 2.41-3 2.42-3              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/MASS_7.3-49.zip'
Content type 'application/zip' length 1171437 bytes (1.1 MB)
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/survival_2.41-3.zip'
Content type 'application/zip' length 5428031 bytes (5.2 MB)
downloaded 5.2 MB

package ‘MASS’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Administrator\AppData\Local\Temp\RtmpSkl0hS\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TxDb.Mmusculus.UCSC.mm10.ensGene’ had non-zero exit status

What should I do with this?

Thank you!

ADD COMMENTlink modified 17 months ago by Martin Morgan ♦♦ 24k • written 17 months ago by 6741395340
Answer: Fail to download package "TxDb.Mmusculus.UCSC.mm10.ensGene"
0
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

The first error to occur is

** 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 'stringi'

so you should tackle that. You could treat the symptom by installing stringi

biocLite("stringi")

and then try again with the original command.

A more elaborate attack on the problem would try to discover why stringi is not installed, because usually R would check that packages and their immediate dependencies are available (just as TxDb.* checks that GenomicFeatures is installed before installing TxDb.* itself, GenomicFeatures would have checked that its dependencies were installed, and so on recursively). So at some point, when GenomicFeatures was installed, stringi must have been installed. There are several possibilities, including installing earlier packages in non-standard ways, removing packages once installed, and perhaps installing packages in different 'libraries' (shown with .libPaths()) .

ADD COMMENTlink written 17 months ago by Martin Morgan ♦♦ 24k
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