Error in BSgenome.Hsapiens.UCSC.hg19

[EmanAbda]

BiocManager::install('BSgenome.Hsapiens.UCSC.hg19')
every step i did to download this package , when i call it with library
error :
there is no package

[matthew-paul-2006]

Can you try running the code directly from the BSgenome page:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
library(BSgenome.Hsapiens.UCSC.hg19)

Let me know if that works. That should ensure you have Bioconductor properly installed, and the BSgenome properly installed. Let me know if you're still having issues or if you get it fixed.

[EmanAbda]

i already did this but i am still having that issue

library(BSgenome.Hsapiens.UCSC.hg19)
Error in library(BSgenome.Hsapiens.UCSC.hg19) :
there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’

[matthew-paul-2006]

I'm going to need some additional information then. It is likely that it is not installing correctly. Do you get an error message when you run the install?

It may also be useful to know your setup. Can you run sessionInfo() and copy the result?

[EmanAbda]

it is the code of the install..

if (!require("BiocManager", quietly = TRUE))

• install.packages("BiocManager")
  Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31 ucrt)

BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31 ucrt)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg19'
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.18/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 486.1 MB

Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 0 != reported length 0
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz': Timeout of 300 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘BSgenome.Hsapiens.UCSC.hg19’ failed
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.3.2/library
packages:
cluster, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart
Old packages: 'gplots'
Update all/some/none? [a/s/n]:
a

There is a binary version available but the source version is later:
binary source needs_compilation
gplots 3.1.3 3.1.3.1 FALSE

installing the source package ‘gplots’

trying URL 'https://cran.rstudio.com/src/contrib/gplots_3.1.3.1.tar.gz'
Content type 'application/x-gzip' length 520586 bytes (508 KB)
downloaded 508 KB

• installing source package 'gplots' ...
  ** package 'gplots' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** data
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (gplots)

The downloaded source packages are in
‘C:\Users\mylab\AppData\Local\Temp\Rtmp4GQ4AG\downloaded_packages’

library(BSgenome.Hsapiens.UCSC.hg19)
Error in library(BSgenome.Hsapiens.UCSC.hg19) :
there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’

> sessionInfo() R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 time zone: Africa/Cairo tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocManager_1.30.22 loaded via a namespace (and not attached): [1] compiler_4.3.2 tools_4.3.2 rstudioapi_0.15.0 --     |    

[matthew-paul-2006]

Seems like you have an issue with your download. You have two errors that are sticking out and they could be related.

1. Timeout of 300 seconds was reached.
This means that you do not have a stable download. This is likely down to connectivity issues or something with your network setup making the download trickier like firewalls. You can try increasing your timeout limit to see if this helps using the code below. You can then rerun the install. Or if you can increase your stability with better wi-fi/plugging your laptop in directly.

options(timeout=600)

2. Installation paths not writeable, unable to update packages
I think this can manifest as a result of local permission issues or maybe more likely network issues. If the above does not work, you may need to reach out to IT support wherever you are. If it's a personal laptop on a personal network you should not be restricted in what you install/download. If this is not the case you may need administrator permissions.

[EmanAbda]

Thanks alot for helping me, it works

[matthew-paul-2006]

Great! Good luck with getting stuck into the ATACseq.