Question: package DESeqDataSet is not available for R version 3.6.1
0
gravatar for HAILYTR
27 days ago by
HAILYTR0
HAILYTR0 wrote:

Hi, I have used Deseq2 packages for months but today when I tried to install the package, using BiocManager::install("DESeqDataSet")

I received:

Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1
  (2019-07-05)
Installing package(s) 'DESeqDataSet'
Update old packages: 'sys'
Update all/some/none? [a/s/n]: 
a
  There is a binary version available but the source
  version is later:
    binary source needs_compilation
sys    3.2    3.3              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/sys_3.2.zip'
Content type 'application/zip' length 59724 bytes (58 KB)
downloaded 58 KB

package ‘sys’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\tranl\AppData\Local\Temp\RtmpItqrwM\downloaded_packages

****Warning message:
package ‘DESeqDataSet’ is not available (for R version 3.6.1)**

Why doesn't R think that the package is available?

sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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

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

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.4  compiler_3.6.1      Matrix_1.2-17      
 [4] tools_3.6.1         parallel_3.6.1      curl_4.0           
 [7] remotes_2.1.0       grid_3.6.1          data.table_1.12.2  
[10] BiocParallel_1.18.1 lattice_0.20-38

Thanks for your help.

deseq2 • 87 views
ADD COMMENTlink modified 27 days ago by Martin Morgan ♦♦ 23k • written 27 days ago by HAILYTR0
Answer: package DESeqDataSet is not available for R version 3.6.1
0
gravatar for Martin Morgan
27 days ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Do you mean to BiocManager::install("DESeq2") instead of DEseqDataSet (which has never existed, I think?).

ADD COMMENTlink written 27 days ago by Martin Morgan ♦♦ 23k
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