<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>

CC BY-SA 4.0
2020-07-24T15:40:56.900Z
2020-07-24T15:40:56.900Z
PPK
<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>

CC BY-SA 4.0
2020-07-24T15:52:43.073Z
2020-07-24T15:52:43.073Z
marilu
<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>

CC BY-SA 4.0
2020-07-24T15:11:29.440Z
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.
Ram RS
<r><rna-seq>
can I download DESeq2 in R 3.6.3 in Linux MInt?
# 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 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..


---

