Question

problem withDESeq2

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fnu.chelsea • 0

@947f0210

Last seen 2.5 years ago

Germany

I am trying to load library (DESeq2) and I get the following message


library(DESeq2)
Loading required package: GenomicRanges
Error: package or namespace load failed for ‘GenomicRanges’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘XVector’
Error: package ‘GenomicRanges’ could not be loaded

sessionInfo( )

DESeq2 • 1.1k views

ADD COMMENT • link updated 2.5 years ago by jennifer.wokaty ▴ 70 • written 2.5 years ago by fnu.chelsea • 0

shepherl · Answer 1 · 2022-06-13

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shepherl 4.1k

@lshep

Last seen 4 hours ago

United States

install XVector with BiocManager::install("XVector") and try again. If you continue to have trouble, please also include your sessionInfo()

ADD COMMENT • link 2.5 years ago shepherl 4.1k

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So, XVector didn't get install with this command also. Code:

if (!require("BiocManager", quietly = TRUE))
 BiocManager::install("XVextor")

Error: 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
Installing package(s) 'XVextor'
Warning message:
package ‘XVextor’ is not available for Bioconductor version '3.14'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 

SessionInfo() R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] GenomeInfoDb_1.30.1 IRanges_2.28.0      S4Vectors_0.32.4    BiocGenerics_0.40.0 BiocManager_1.30.18

loaded via a namespace (and not attached):
[1] compiler_4.1.2         tools_4.1.2            GenomeInfoDbData_1.2.7 RCurl_1.98-1.7         bitops_1.0-7

ADD REPLY • link updated 2.5 years ago by shepherl 4.1k • written 2.5 years ago by fnu.chelsea • 0

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You mis-spelled XVector in the above. BiocManager::install("XVextor") should be BiocManager::install("XVector")

ADD REPLY • link 2.5 years ago shepherl 4.1k

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Ok, Thanks. I tried again but I still get error:

Code: if (!require("BiocManager", quietly = TRUE))
 BiocManager::install("XVector")
----------------------------------------------------------------------------
Error::   'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01)
Installing package(s) 'XVector'
also installing the dependency ‘zlibbioc’

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/zlibbioc_1.40.0.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/zlibbioc_1.40.0.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/zlibbioc_1.40.0.zip': HTTP status was '403 Forbidden'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘zlibbioc’ failed
trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/XVector_0.34.0.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/XVector_0.34.0.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/XVector_0.34.0.zip': HTTP status was '403 Forbidden'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘XVector’ failed
-----------------------------------------------------------------------
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] GenomeInfoDb_1.30.1 IRanges_2.28.0      S4Vectors_0.32.4    BiocGenerics_0.40.0 BiocManager_1.30.18

loaded via a namespace (and not attached):
[1] compiler_4.1.2         tools_4.1.2            GenomeInfoDbData_1.2.7 RCurl_1.98-1.7         bitops_1.0-7

ADD REPLY • link updated 2.5 years ago by shepherl 4.1k • written 2.5 years ago by fnu.chelsea • 0

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I was able to install XVector on a windows 10 VM with Bioc 3.14. The errors suggest that you're having problems downloading. Could you first try visiting https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/zlibbioc_1.40.0.zip in a browser? If that works, in R try to download it with download.file. If you're not able to download the file via download.file, try setting a proxy. See Setting Proxies in ?download.file.

ADD REPLY • link 2.5 years ago jennifer.wokaty ▴ 70