Dear all, would you please let me know how I could fix the error that I am getting when I do install some packages such as BSgenome.Hsapiens.UCSC.hg19 ? Thank you !

> BiocManager::install("BSgenome.Hsapiens.UCSC.hg19", force=TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://ftp.osuosl.org/pub/cran

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg19'
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz'
Content type 'application/x-gzip' length 710245413 bytes (677.3 MB)
=======
downloaded 94.9 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz' failed
In addition: Warning messages:
1: In .inet_warning(msg) :
  downloaded length 99493868 != reported length 710245413
2: In .inet_warning(msg) :
  URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz': Timeout of 300 seconds was reached
Old packages: 'Matrix', 'Rfast2'

```

Hi,

Big pakages can take a long time to download, depending on the quality of your internet connection. Unfortunately download.file(), the R function in charge of the download, will stop the download after 300 seconds (5 min) by default. A terrible feature!

The good news is that you can change this by putting something like:

R_DEFAULT_INTERNET_TIMEOUT=600

in your .Renviron file. This will give download.file() up to 10 min to complete a download.

Best,

H.