Answers.Body: <p><a href="https://bioconductor.org/" rel="nofollow noreferrer">Bioconductor</a> is a package management tool for R that allows you to install the appropriate package versions for your R version.</p>
  <p>For R 3.6.3 you'll need Bioconductor 3.10:</p>
  <pre><code>if (!requireNamespace(&quot;BiocManager&quot;, quietly = TRUE))
      install.packages(&quot;BiocManager&quot;)
  BiocManager::install(version = &quot;3.10&quot;)
  </code></pre>
  <p>Then you install  DESeq2:</p>
  <pre><code>BiocManager::install(&quot;DESeq2&quot;)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-24T15:40:56.900Z
Answers.LastActivityDate: 2020-07-24T15:40:56.900Z
Answers.UserDisplayName: PPK
Answers.Body: <p>these errors are generated when I am doing what PPK suggested:
  Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3
  (2020-02-29)
  Installation path not writeable, unable to update packages: nlme,
  spatial, survival</p>
  <blockquote>
  <p>BiocManager::install(&quot;DESeq2&quot;)
  Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3
  (2020-02-29)
  Installing package(s) 'DESeq2'
  Warning: dependency ‘XML’ is not available
  also installing the dependencies ‘annotate’, ‘genefilter’, ‘geneplotter’</p>
  </blockquote>
  <h1>trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz'
  Content type 'application/x-gzip' length 1873132 bytes (1.8 MB)</h1>
  <p>downloaded 1.8 MB</p>
  <h1>trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz'
  Content type 'application/x-gzip' length 1421076 bytes (1.4 MB)</h1>
  <p>downloaded 1.4 MB</p>
  <h1>trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz'
  Content type 'application/x-gzip' length 1431450 bytes (1.4 MB)</h1>
  <p>downloaded 1.4 MB</p>
  <h1>trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz'
  Content type 'application/x-gzip' length 2060061 bytes (2.0 MB)</h1>
  <p>downloaded 2.0 MB</p>
  <p>ERROR: dependency ‘XML’ is not available for package ‘annotate’</p>
  <ul>
  <li>removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/annotate’
  ERROR: dependency ‘annotate’ is not available for package ‘genefilter’</li>
  <li>removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
  ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’</li>
  <li>removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
  ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’</li>
  <li>removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’</li>
  </ul>
  <p>The downloaded source packages are in
  ‘/tmp/RtmphLXrZb/downloaded_packages’
  Installation path not writeable, unable to update packages: nlme,
  spatial, survival
  Warning messages:
  1: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status
  2: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status
  3: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
  4: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status</p>
  <p>I have tried to instal XML and the other dependencies without success..</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-24T15:52:43.073Z
Answers.LastActivityDate: 2020-07-24T15:52:43.073Z
Answers.UserDisplayName: marilu
Body: <p>I am trying to download DESeq2 in R 3.6.3. Is it possible?
  This is printed when I am trying: Warning in install.packages : package ‘DESeq2’ is not available (for R version 3.6.3)
  Thank you!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-24T15:11:29.440Z
Comments.Text: You might have more luck using conda to look for older versions of the DESeq2 package that are compatible with R 3.6.3. If not, you can use conda to install compatible versions of R and DESeq2 in a new environment and use that environment for your analyses.
Comments.UserDisplayName: Ram RS
Tags: <r><rna-seq>
Title: can I download DESeq2 in R 3.6.3 in Linux MInt?
ThreadText: # can I download DESeq2 in R 3.6.3 in Linux MInt?
  
  (Asked by: username_0 on 2020-07-24)
  
  I am trying to download DESeq2 in R 3.6.3. Is it possible?
  This is printed when I am trying: Warning in install.packages : package ‘DESeq2’ is not available (for R version 3.6.3)
  Thank you!
  
  **Tags:** r, rna-seq
  
  > **Comments:**
  > **username_1**: You might have more luck using conda to look for older versions of the DESeq2 package that are compatible with R 3.6.3. If not, you can use conda to install compatible versions of R and DESeq2 in a new environment and use that environment for your analyses.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2020-07-24. Score: 1
  
  [Bioconductor](https://bioconductor.org/) is a package management tool for R that allows you to install the appropriate package versions for your R version.
  
  For R 3.6.3 you'll need Bioconductor 3.10:
  
  ```
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install(version = "3.10")
  
  ```
  
  Then you install DESeq2:
  
  ```
  BiocManager::install("DESeq2")
  
  ```
  
  
  ---
  
  ### Answer by username_0 on 2020-07-24. Score: 0
  
  these errors are generated when I am doing what PPK suggested:
  Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3
  (2020-02-29)
  Installation path not writeable, unable to update packages: nlme,
  spatial, survival
  
  > BiocManager::install("DESeq2")
  > Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3
  > (2020-02-29)
  > Installing package(s) 'DESeq2'
  > Warning: dependency ‘XML’ is not available
  > also installing the dependencies ‘annotate’, ‘genefilter’, ‘geneplotter’
  
  # trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate\_1.64.0.tar.gz' Content type 'application/x-gzip' length 1873132 bytes (1.8 MB)
  
  downloaded 1.8 MB
  
  # trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter\_1.68.0.tar.gz' Content type 'application/x-gzip' length 1421076 bytes (1.4 MB)
  
  downloaded 1.4 MB
  
  # trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter\_1.64.0.tar.gz' Content type 'application/x-gzip' length 1431450 bytes (1.4 MB)
  
  downloaded 1.4 MB
  
  # trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2\_1.26.0.tar.gz' Content type 'application/x-gzip' length 2060061 bytes (2.0 MB)
  
  downloaded 2.0 MB
  
  ERROR: dependency ‘XML’ is not available for package ‘annotate’
  
  * removing ‘/home/nikolena/R/x86\_64-pc-linux-gnu-library/3.6/annotate’
    ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
  * removing ‘/home/nikolena/R/x86\_64-pc-linux-gnu-library/3.6/genefilter’
    ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
  * removing ‘/home/nikolena/R/x86\_64-pc-linux-gnu-library/3.6/geneplotter’
    ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
  * removing ‘/home/nikolena/R/x86\_64-pc-linux-gnu-library/3.6/DESeq2’
  
  The downloaded source packages are in
  ‘/tmp/RtmphLXrZb/downloaded\_packages’
  Installation path not writeable, unable to update packages: nlme,
  spatial, survival
  Warning messages:
  1: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status
  2: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status
  3: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
  4: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status
  
  I have tried to instal XML and the other dependencies without success..
  
  
  ---
  
  