Answers.Body: <p>If you do <code>?devtools::install</code>, you will see that the <code>install()</code> function from the <code>devtools</code> package, not surprisingly, requires a package to be specified:</p>
  
  <pre><code>install(pkg = ".", reload = TRUE, quick = FALSE, build = !quick,
    args = getOption("devtools.install.args"), quiet = FALSE,
    dependencies = NA, upgrade = "ask", build_vignettes = FALSE,
    keep_source = getOption("keep.source.pkgs"), force = FALSE, ...)
  </code></pre>
  
  <p>So it is absolutely normal that <code>devtools::install()</code> does not install anything. Just specify the packages(s) with the <code>pkg</code> argument.</p>
  
  <p>And this is how you install <code>Signature Tools</code>:</p>
  
  <pre><code>install.packages("remotes")
  remotes::install_github("Nik-Zainal-Group/signature.tools.lib")
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-11T00:35:22.097Z
Answers.Text: Thank you but your solution gives ERROR: dependency ‘NNLM’ is not available for package ‘signature.tools.lib’
  * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/signature.tools.lib’
  Error: Failed to install 'signature.tools.lib' from GitHub:
    (converted from warning) installation of package ‘/var/folders/wk/qwgr9yqs6ts0czx__y_w8gch0000gq/T//RtmpA8PudK/filec5bcb188c2b/signature.tools.lib_0.0.0.9000.tar.gz’ had non-zero exit status
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-16T12:23:58.857Z
Answers.LastActivityDate: 2020-03-16T12:23:58.857Z
Answers.UserDisplayName: haci
Body: <p>I want to install <code>Signature Tools Lib R package</code></p>
  
  <p>I typed</p>
  
  <pre><code>&gt; devtools::install()
  Error: Could not find package root, is your working directory inside a package?
  &gt;
  </code></pre>
  
  <p>Packages does need this list of sotware</p>
  
  <pre><code>R package dependencies:
      VariantAnnotation,
      BSgenome.Hsapiens.UCSC.hg38,
      BSgenome.Hsapiens.1000genomes.hs37d5,
      BSgenome.Mmusculus.UCSC.mm10,
      BSgenome.Cfamiliaris.UCSC.canFam3,
      SummarizedExperiment,
      BiocGenerics,
      GenomeInfoDb,
      NMF,
      foreach,
      doParallel,
      doMC,
      lpSolve,
      ggplot2,
      methods,
      cluster,
      stats,
      NNLM,
      nnls,
      GenSA,
      gmp,
      plyr,
      RCircos,
      scales,
      GenomicRanges,
      IRanges,
      BSgenome
  </code></pre>
  
  <p>I have installed all of these one by one but again when trying things like the below, I get error</p>
  
  <pre><code>Error in tabToSNVcatalogue(subs = tmpSNVtab, genome.v = "hg19") : 
    could not find function "tabToSNVcatalogue"
  &gt; devtools::test()
  Error: Could not find package root, is your working directory inside a package?
  &gt; 
  &gt; library(signature.tools.lib)
  Error in library(signature.tools.lib) : 
    there is no package called ‘signature.tools.lib’
  &gt; 
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-16T10:45:18.163Z
Comments.Text: First, we would need to know which is the package you want to install. Second this is related to Bioinformatics? it doesn't seem so, could you edit the question to include this details?
Comments.UserDisplayName: llrs
Tags: <r>
Title: Error in ruuning a package in R
ThreadText: # Error in ruuning a package in R
  
  (Asked by: username_0 on 2020-03-16)
  
  I want to install `Signature Tools Lib R package`
  
  I typed
  
  ```
  > devtools::install()
  Error: Could not find package root, is your working directory inside a package?
  >
  
  ```
  
  Packages does need this list of sotware
  
  ```
  R package dependencies:
      VariantAnnotation,
      BSgenome.Hsapiens.UCSC.hg38,
      BSgenome.Hsapiens.1000genomes.hs37d5,
      BSgenome.Mmusculus.UCSC.mm10,
      BSgenome.Cfamiliaris.UCSC.canFam3,
      SummarizedExperiment,
      BiocGenerics,
      GenomeInfoDb,
      NMF,
      foreach,
      doParallel,
      doMC,
      lpSolve,
      ggplot2,
      methods,
      cluster,
      stats,
      NNLM,
      nnls,
      GenSA,
      gmp,
      plyr,
      RCircos,
      scales,
      GenomicRanges,
      IRanges,
      BSgenome
  
  ```
  
  I have installed all of these one by one but again when trying things like the below, I get error
  
  ```
  Error in tabToSNVcatalogue(subs = tmpSNVtab, genome.v = "hg19") : 
    could not find function "tabToSNVcatalogue"
  > devtools::test()
  Error: Could not find package root, is your working directory inside a package?
  > 
  > library(signature.tools.lib)
  Error in library(signature.tools.lib) : 
    there is no package called ‘signature.tools.lib’
  > 
  
  ```
  
  **Tags:** r
  
  > **Comments:**
  > **username_1**: First, we would need to know which is the package you want to install. Second this is related to Bioinformatics? it doesn't seem so, could you edit the question to include this details?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-03-16. Score: 4
  
  If you do `?devtools::install`, you will see that the `install()` function from the `devtools` package, not surprisingly, requires a package to be specified:
  
  ```
  install(pkg = ".", reload = TRUE, quick = FALSE, build = !quick,
    args = getOption("devtools.install.args"), quiet = FALSE,
    dependencies = NA, upgrade = "ask", build_vignettes = FALSE,
    keep_source = getOption("keep.source.pkgs"), force = FALSE, ...)
  
  ```
  
  So it is absolutely normal that `devtools::install()` does not install anything. Just specify the packages(s) with the `pkg` argument.
  
  And this is how you install `Signature Tools`:
  
  ```
  install.packages("remotes")
  remotes::install_github("Nik-Zainal-Group/signature.tools.lib")
  
  ```
  
  > **Comments:**
  > **username_0**: Thank you but your solution gives ERROR: dependency ‘NNLM’ is not available for package ‘signature.tools.lib’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/signature.tools.lib’ Error: Failed to install 'signature.tools.lib' from GitHub:   (converted from warning) installation of package ‘/var/folders/wk/qwgr9yqs6ts0czx__y_w8gch0000gq/T//RtmpA8PudK/filec5bcb188c2b/signature.tools.lib_0.0.0.9000.tar.gz’ had non-zero exit status  
  
  ---
  
  