Answers.Body: <p>As @terdon mentioned in the comments, you need to <code>sudo yum install libicu</code> on the relevant nodes (or have your admin do that for you). Alternatively, seurat can be installed via conda, which means you don't need root access.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-25T22:15:20.807Z
Answers.Text: Actually I tried installing `Seurat` using `conda install -c bioconda r-seurat ` and it is not working. It is giving `PackageNotFoundError`.
Answers.UserDisplayName: Nikita Vlasenko
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-26T06:50:10.683Z
Answers.Text: You need `-c conda-forge` too. You might then need to fix readline with `conda upgrade -c conda-forge readline`.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-26T08:25:09.080Z
Answers.Text: If you don't wish to use conda as your r package manager (because, for a start, it will install a new copy of R with its own library), you can install just ICU with conda `conda install -c conda-forge icu`, and then install seurat in R
Answers.UserDisplayName: Ian Sudbery
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-25T22:03:25.490Z
Answers.LastActivityDate: 2018-04-25T22:03:25.490Z
Answers.UserDisplayName: Devon Ryan
Body: <p>When I am trying to install <code>Seurat</code> in <code>R markdown file</code>:</p>
  
  <pre><code>install.packages("Seurat")
  </code></pre>
  
  <p>it fails with the following errors:</p>
  
  <pre><code>Installing package into ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3’
  (as ‘lib’ is unspecified)
  Warning in install.packages :
    dependency ‘proxy’ is not available
  also installing the dependencies ‘igraph’, ‘dtw’, ‘diffusionMap’
  
  trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.2.1.tar.gz'
  
  Content type 'unknown' length 2703426 bytes (2.6 MB)
  
  downloaded 2.6 MB
  
  trying URL 'https://cran.rstudio.com/src/contrib/dtw_1.18-1.tar.gz'
  
  Content type 'unknown' length 849256 bytes (829 KB) downloaded 829 KB trying URL 'https://cran.rstudio.com/src/contrib/diffusionMap_1.1-0.tar.gz'
  
  Content type 'unknown' length 39130 bytes (38 KB)
  downloaded 38 KB
  
  trying URL 'https://cran.rstudio.com/src/contrib/Seurat_2.3.0.tar.gz'
  
  Content type 'unknown' length 846065 bytes (826 KB)
  
  downloaded 826 KB
  * installing *source* package ‘igraph’ ...
  ** package ‘igraph’ successfully unpacked and MD5 sums checked
  installing to /sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph/libs
  ** R
  ** demo
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  
  Error in dyn.load(file, DLLpath = DLLpath, ...) :    unable to load shared object '/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph/libs/igraph.so': libicui18n.so.58: cannot open shared object file: No such file or directory
  
  Error: loading failed Execution halted ERROR: loading failed
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph’ Warning in install.packages :   installation of package ‘igraph’ had non-zero exit status
  
  ERROR: dependency ‘proxy’ is not available for package ‘dtw’
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/dtw’ Warning in install.packages :   installation of package ‘dtw’ had non-zero exit status
  
  ERROR: dependency ‘igraph’ is not available for package ‘diffusionMap’
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/diffusionMap’ Warning in install.packages :   installation of package ‘diffusionMap’ had non-zero exit status
  
  ERROR: dependencies ‘igraph’, ‘dtw’, ‘diffusionMap’ are not available for package ‘Seurat’
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/Seurat’ Warning in install.packages :   installation of package ‘Seurat’ had non-zero exit status
  </code></pre>
  
  <p>How could it be fixed? What to try?</p>
  
  <p>Operating system is <code>CentOS Linux release 7.3.1611 (Core)</code></p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>I also tried development version of <code>Seurat</code> but it failed too:
  <a href="http://satijalab.org/seurat/devinstall.html" rel="nofollow noreferrer">http://satijalab.org/seurat/devinstall.html</a></p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>I tried installing <code>Seurat</code> using <code>conda install -c bioconda r-seurat</code> and it is not working. It is giving the error:</p>
  
  <blockquote>
    <p>-bash-4.2$ conda install -c bioconda r-seurat 
    Fetching package metadata .............
    Solving package specifications: </p>
    
    <p>PackageNotFoundError: Packages missing in current channels:</p>
  </blockquote>
  
  <ul>
  <li>r-seurat -> r-cowplot</li>
  <li>r-seurat -> r-diffusionmap</li>
  <li>r-seurat -> r-dtw</li>
  <li>r-seurat -> r-ggridges</li>
  <li>r-seurat -> r-ica</li>
  <li>r-seurat -> r-pbapply</li>
  <li>r-seurat -> r-ranger</li>
  <li>r-seurat -> r-rcppprogress</li>
  <li>r-seurat -> r-sdmtools</li>
  <li>r-seurat -> r-tclust</li>
  </ul>
  
  <blockquote>
    <p>We have searched for the packages in the following channels:</p>
  </blockquote>
  
  <ul>
  <li><a href="https://conda.anaconda.org/bioconda/linux-64" rel="nofollow noreferrer">https://conda.anaconda.org/bioconda/linux-64</a></li>
  <li><a href="https://conda.anaconda.org/bioconda/noarch" rel="nofollow noreferrer">https://conda.anaconda.org/bioconda/noarch</a></li>
  <li><a href="https://repo.continuum.io/pkgs/main/linux-64" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/main/linux-64</a></li>
  <li><a href="https://repo.continuum.io/pkgs/main/noarch" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/main/noarch</a></li>
  <li><a href="https://repo.continuum.io/pkgs/free/linux-64" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/free/linux-64</a></li>
  <li><a href="https://repo.continuum.io/pkgs/free/noarch" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/free/noarch</a></li>
  <li><a href="https://repo.continuum.io/pkgs/r/linux-64" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/r/linux-64</a></li>
  <li><a href="https://repo.continuum.io/pkgs/r/noarch" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/r/noarch</a></li>
  <li><a href="https://repo.continuum.io/pkgs/pro/linux-64" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/pro/linux-64</a></li>
  <li><a href="https://repo.continuum.io/pkgs/pro/noarch" rel="nofollow noreferrer">https://repo.continuum.io/pkgs/pro/noarch</a></li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-25T18:26:07.340Z
Comments.Text: You seem to be missing the `libicui18n.so` library. Please [edit] your question and tell us what operating system you are using. If Linux, tell us what distribution.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-25T18:49:21.197Z
Comments.Text: I just updated. It is `CentOS`. I am working with `rstudio` on the cluster.
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-25T18:57:39.177Z
Comments.Text: Ah, thanks. So what is the output of `yum search libicui18n` (if that returns nothing, try `yum search libicui` or even `yum search icui` until you get a result). Then, install the package. If that works, let me know and I can post answer (or just post it yourself, up to you).
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-25T19:40:56.397Z
Comments.Text: The output in all the three cases is `No matches found`. Also, I do not have `root` privileges obviously, so maybe I should download this `libicui18n.so` library and install it locally somehow?
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-25T19:56:08.240Z
Comments.Text: Hmm, I haven't used an rpm-based system in ages. You might need to search for `libicui*` or something. I did check CentOS's repository, and there is such a package. I don't remember how to install rpms locally though and I'm on mobile, so I can't help much. You could try asking how to find and install the relevant package on [unix.se].
Comments.UserDisplayName: terdon
Tags: <r><seurat>
Title: Seurat installation fails
ThreadText: # Seurat installation fails
  
  (Asked by: username_0 on 2018-04-25)
  
  When I am trying to install `Seurat` in `R markdown file`:
  
  ```
  install.packages("Seurat")
  
  ```
  
  it fails with the following errors:
  
  ```
  Installing package into ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3’
  (as ‘lib’ is unspecified)
  Warning in install.packages :
    dependency ‘proxy’ is not available
  also installing the dependencies ‘igraph’, ‘dtw’, ‘diffusionMap’
  
  trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.2.1.tar.gz'
  
  Content type 'unknown' length 2703426 bytes (2.6 MB)
  
  downloaded 2.6 MB
  
  trying URL 'https://cran.rstudio.com/src/contrib/dtw_1.18-1.tar.gz'
  
  Content type 'unknown' length 849256 bytes (829 KB) downloaded 829 KB trying URL 'https://cran.rstudio.com/src/contrib/diffusionMap_1.1-0.tar.gz'
  
  Content type 'unknown' length 39130 bytes (38 KB)
  downloaded 38 KB
  
  trying URL 'https://cran.rstudio.com/src/contrib/Seurat_2.3.0.tar.gz'
  
  Content type 'unknown' length 846065 bytes (826 KB)
  
  downloaded 826 KB
  * installing *source* package ‘igraph’ ...
  ** package ‘igraph’ successfully unpacked and MD5 sums checked
  installing to /sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph/libs
  ** R
  ** demo
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  
  Error in dyn.load(file, DLLpath = DLLpath, ...) :    unable to load shared object '/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph/libs/igraph.so': libicui18n.so.58: cannot open shared object file: No such file or directory
  
  Error: loading failed Execution halted ERROR: loading failed
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph’ Warning in install.packages :   installation of package ‘igraph’ had non-zero exit status
  
  ERROR: dependency ‘proxy’ is not available for package ‘dtw’
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/dtw’ Warning in install.packages :   installation of package ‘dtw’ had non-zero exit status
  
  ERROR: dependency ‘igraph’ is not available for package ‘diffusionMap’
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/diffusionMap’ Warning in install.packages :   installation of package ‘diffusionMap’ had non-zero exit status
  
  ERROR: dependencies ‘igraph’, ‘dtw’, ‘diffusionMap’ are not available for package ‘Seurat’
  * removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/Seurat’ Warning in install.packages :   installation of package ‘Seurat’ had non-zero exit status
  
  ```
  
  How could it be fixed? What to try?
  
  Operating system is `CentOS Linux release 7.3.1611 (Core)`
  
  > Update
  
  I also tried development version of `Seurat` but it failed too:
  <http://satijalab.org/seurat/devinstall.html>
  
  > Update
  
  I tried installing `Seurat` using `conda install -c bioconda r-seurat` and it is not working. It is giving the error:
  
  > -bash-4.2$ conda install -c bioconda r-seurat
  > Fetching package metadata .............
  > Solving package specifications:
  >
  > PackageNotFoundError: Packages missing in current channels:
  
  * r-seurat -> r-cowplot
  * r-seurat -> r-diffusionmap
  * r-seurat -> r-dtw
  * r-seurat -> r-ggridges
  * r-seurat -> r-ica
  * r-seurat -> r-pbapply
  * r-seurat -> r-ranger
  * r-seurat -> r-rcppprogress
  * r-seurat -> r-sdmtools
  * r-seurat -> r-tclust
  
  > We have searched for the packages in the following channels:
  
  * <https://conda.anaconda.org/bioconda/linux-64>
  * <https://conda.anaconda.org/bioconda/noarch>
  * <https://repo.continuum.io/pkgs/main/linux-64>
  * <https://repo.continuum.io/pkgs/main/noarch>
  * <https://repo.continuum.io/pkgs/free/linux-64>
  * <https://repo.continuum.io/pkgs/free/noarch>
  * <https://repo.continuum.io/pkgs/r/linux-64>
  * <https://repo.continuum.io/pkgs/r/noarch>
  * <https://repo.continuum.io/pkgs/pro/linux-64>
  * <https://repo.continuum.io/pkgs/pro/noarch>
  
  **Tags:** r, seurat
  
  > **Comments:**
  > **username_1**: You seem to be missing the `libicui18n.so` library. Please [edit] your question and tell us what operating system you are using. If Linux, tell us what distribution.  
  > **username_0**: I just updated. It is `CentOS`. I am working with `rstudio` on the cluster.  
  > **username_1**: Ah, thanks. So what is the output of `yum search libicui18n` (if that returns nothing, try `yum search libicui` or even `yum search icui` until you get a result). Then, install the package. If that works, let me know and I can post answer (or just post it yourself, up to you).  
  > **username_0**: The output in all the three cases is `No matches found`. Also, I do not have `root` privileges obviously, so maybe I should download this `libicui18n.so` library and install it locally somehow?  
  > **username_1**: Hmm, I haven't used an rpm-based system in ages. You might need to search for `libicui*` or something. I did check CentOS's repository, and there is such a package. I don't remember how to install rpms locally though and I'm on mobile, so I can't help much. You could try asking how to find and install the relevant package on [unix.se].  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-04-25. Score: 2 | Accepted answer
  
  As @username_1 mentioned in the comments, you need to `sudo yum install libicu` on the relevant nodes (or have your admin do that for you). Alternatively, seurat can be installed via conda, which means you don't need root access.
  
  > **Comments:**
  > **username_0**: Actually I tried installing `Seurat` using `conda install -c bioconda r-seurat ` and it is not working. It is giving `PackageNotFoundError`.  
  > **username_2**: You need `-c conda-forge` too. You might then need to fix readline with `conda upgrade -c conda-forge readline`.  
  > **username_3**: If you don't wish to use conda as your r package manager (because, for a start, it will install a new copy of R with its own library), you can install just ICU with conda `conda install -c conda-forge icu`, and then install seurat in R  
  
  ---
  
  