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.
Great, that works. Thanks for your help
not working for me and showing this :
https://cran.rstudio.com/bin/windows/Rtools/ Warning: invalid package 'path/to/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz' Error: ERROR: no packages specified Warning in install.packages : installation of package ‘path/to/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz’ had non-zero exit status
Please don't add new questions as comments to 2-year old posts. If you have a question, make a new post. In addition, showing one line of output is not helpful. You need to show your function call and all the R output.