Unable to download "BSgenome.Hsapiens.UCSC.hg19" package using R 3.6.3 on Windows 10 x64
2
0
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@msteinruecke-24052
Last seen 13 months ago

I have just started the HarvardX Introduction to Bioconductor course on EdX. The course suggests getting started with the following code:

# install Bioconductor and check version
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version="3.10")

# install Bioconductor packages
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
BiocManager::install(c("genefilter","geneplotter"))

# load installed packages
library(BSgenome.Hsapiens.UCSC.hg19)
library(genefilter)
library(geneplotter)

The course suggests using R version 3.6.3 and Bioconductor version 3.10. I have tried running this code but get the following errors:

> BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
Bioconductor version 3.10 (BiocManager 1.30.10), R
  3.6.3 (2020-02-29)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg19'
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
downloaded 10.9 MB

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

The downloaded source packages are in
    ‘C:\Users\44771\AppData\Local\Temp\RtmpyeA7bo\downloaded_packages’
Installation path not writeable, unable to update
  packages: boot, class, KernSmooth, lattice, MASS,
  mgcv, nlme, nnet, spatial, survival
Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 11427840 != reported length 688190187

> library(BSgenome.Hsapiens.UCSC.hg19)
Error in library(BSgenome.Hsapiens.UCSC.hg19) : 
  there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
2: In install.packages(...) :
  installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status

When I run sessionInfo(), I get the following:

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_Europe.1252 
[2] LC_CTYPE=English_Europe.1252   
[3] LC_MONETARY=English_Europe.1252
[4] LC_NUMERIC=C                   
[5] LC_TIME=English_Europe.1252    

attached base packages:
[1] stats4    parallel  stats     graphics 
[5] grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] AnnotationDbi_1.48.0 IRanges_2.20.2      
[3] S4Vectors_0.24.4     lattice_0.20-38     
[5] Biobase_2.46.0       BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5             XVector_0.26.0        
 [3] zlibbioc_1.32.0        GenomicRanges_1.38.0  
 [5] BiocParallel_1.20.1    bit_4.0.4             
 [7] xtable_1.8-4           rlang_0.4.7           
 [9] blob_1.2.1             GenomeInfoDb_1.22.1   
[11] tools_3.6.3            grid_3.6.3            
[13] DBI_1.1.0              bit64_4.0.2           
[15] digest_0.6.25          GenomeInfoDbData_1.2.2
[17] BiocManager_1.30.10    vctrs_0.3.2           
[19] bitops_1.0-6           RCurl_1.98-1.2        
[21] memoise_1.1.0          RSQLite_2.2.0         
[23] compiler_3.6.3         Rsamtools_2.2.3       
[25] Biostrings_2.54.0

Many thanks for your help.

BSgenome.Hsapiens.UCSC.hg19 HarvardX Introduction to Bioconductor • 912 views
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2
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@martin-morgan-1513
Last seen 10 weeks ago
United States

This

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
downloaded 10.9 MB

indicates that only 10.9 MB of 656.3 MB were downloaded. Do you have a reliable internet connection?

You could try again, or perhaps download https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz through other means (e.g., via your browser) and try to install locally

install.packages("path/to/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz", repos = NULL, type = "source")
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0
Entering edit mode

Great, that works. Thanks for your help

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1
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@herve-pages-1542
Last seen 5 hours ago
Seattle, WA, United States

Looks like you ran out of disk space.

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