Answers.Body: <p>I am able to successfully install these packages using:</p>
  <pre><code>BiocManager::install(c(&quot;Homo.sapiens&quot;, &quot;EnsDb.Hsapiens.v75&quot;, &quot;TxDb.Hsapiens.UCSC.hg19.knownGene&quot;))
  </code></pre>
  <p>This completes without any errors / warnings (R v4.0.3 / macOS 10.16), so I don't believe the packages themselves/Bioconductor are 'broken', but I suspect you are having compiler issues due to the Big Sur update.</p>
  <p>These are the steps I used to solve the problem:</p>
  <ol>
  <li>Reinstall xcode command line tools (even if it says &quot;up to date&quot;)</li>
  </ol>
  <pre><code>sudo rm -rf /Library/Developer/CommandLineTools
  sudo xcode-select --install
  </code></pre>
  <ol start="2">
  <li>Install gcc &amp; llvm via Homebrew (<a href="https://docs.brew.sh/Installation" rel="nofollow noreferrer">instructions for installing Homebrew</a>) or, if you already have gcc/llvm installed via Homebrew, skip to the next step</li>
  </ol>
  <pre><code># This can take several hours
  brew install gcc
  brew install llvm
  </code></pre>
  <ol start="3">
  <li>Once you have gcc &amp; llvm installed via Homebrew:</li>
  </ol>
  <pre><code>brew cleanup
  brew update
  brew upgrade
  brew reinstall gcc
  brew reinstall llvm
  </code></pre>
  <ol start="4">
  <li>Link some headers into /usr/local/include</li>
  </ol>
  <pre><code>sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/
  
  # You can safely ignore warnings like this:
  #ln: /usr/local/include//tcl.h: File exists
  #ln: /usr/local/include//tclDecls.h: File exists
  #ln: /usr/local/include//tclPlatDecls.h: File exists
  #ln: /usr/local/include//tclTomMath.h: File exists
  #ln: /usr/local/include//tclTomMathDecls.h: File exists
  #ln: /usr/local/include//tk.h: File exists
  #ln: /usr/local/include//tkDecls.h: File exists
  #ln: /usr/local/include//tkPlatDecls.h: File exists
  </code></pre>
  <ol start="5">
  <li>Create a new <code>~/.R/Makevars</code> file (if you already have a <code>~/.R/Makevars</code> file, save it in a different directory (away from <code>~/.R/</code>)) and include only these lines in the file:</li>
  </ol>
  <pre><code>FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
  CXX1X=/usr/local/gfortran/bin/g++
  CXX98=/usr/local/gfortran/bin/g++
  CXX11=/usr/local/gfortran/bin/g++
  CXX14=/usr/local/gfortran/bin/g++
  CXX17=/usr/local/gfortran/bin/g++
  
  LLVM_LOC = /usr/local/opt/llvm
  CC=/usr/local/gfortran/bin/gcc -fopenmp
  CXX=/usr/local/gfortran/bin/g++ -fopenmp
  CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
  CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
  LDFLAGS=-L/usr/local/opt/gettext/lib -L<span class="math-container">$(LLVM_LOC)/lib -Wl,-rpath,$</span>(LLVM_LOC)/lib
  CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
  </code></pre>
  <ol start="6">
  <li>Compile a package from source in R/Rstudio</li>
  </ol>
  <pre><code># To check whether openmp is enabled, compile data.table:
  install.packages(&quot;data.table&quot;, type = &quot;source&quot;)
  </code></pre>
  <ol start="7">
  <li>If your package fails to compile, a couple of SO users have had to install a fresh gfortran (re: <a href="https://stackoverflow.com/a/65334247/12957340">https://stackoverflow.com/a/65334247/12957340</a>), which you can download from <a href="https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/10.2-bigsur-intel" rel="nofollow noreferrer">https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/10.2-bigsur-intel</a></li>
  </ol>
  <p>Once you can install packages from source without error/issue, update Bioconductor</p>
  <pre><code>BiocManager::install(version = &quot;3.12&quot;)
  </code></pre>
  <p>Then, finally, you should be able to install your packages using</p>
  <pre><code>BiocManager::install(c(&quot;Homo.sapiens&quot;, &quot;EnsDb.Hsapiens.v75&quot;, &quot;TxDb.Hsapiens.UCSC.hg19.knownGene&quot;))
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-07T19:46:21.037Z
Answers.Text: You are amazing Jared, I'll go through the steps right now to see if it works, fingers crossed.
Answers.UserDisplayName: Sam
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-16T02:12:50.107Z
Answers.Text: Awesome, it is working now. Thank you so much, Jared :)
Answers.UserDisplayName: Sam
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-07T04:11:25.000Z
Answers.LastActivityDate: 2021-01-07T22:12:14.380Z
Answers.LastEditDate: 2021-01-07T22:12:14.380Z
Answers.UserDisplayName: jared_mamrot
Body: <p>I think there is a problem with <code>TxDb.Hsapiens.UCSC.hg19.knownGene</code> and  <code>EnsDb.Hsapiens.v75</code>.  I'm struggling to install all of these packages as they pause at  <code>byte-compile and prepare package for lazy loading </code>. Can anyone try to re-install them in their local machine because am not the only one who is having the problem, please? They used to work fine until a week ago!</p>
  <p>As usual, I install the packages by:</p>
  <pre><code>BiocManager::install(c(&quot;Homo.sapiens&quot;, &quot;EnsDb.Hsapiens.v75&quot;, &quot;TxDb.Hsapiens.UCSC.hg19.knownGene&quot;))
  
  </code></pre>
  <p>I also tried installing them individually:</p>
  <pre><code>BiocManager::install(&quot;EnsDb.Hsapiens.v75&quot;)
  BiocManager::install(&quot;TxDb.Hsapiens.UCSC.hg19.knownGene&quot;)
  </code></pre>
  <p>It pause at:</p>
  <pre class="lang-r prettyprint-override"><code>* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  </code></pre>
  <p>sessionInfo( )</p>
  <pre><code>R version 4.0.3 (2020-10-10)
  Platform: x86_64-apple-darwin17.0 (64-bit)
  Running under: macOS Big Sur 10.16
  
  Matrix products: default
  BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
  LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
  
  locale:
  [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  loaded via a namespace (and not attached):
  [1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3    
  </code></pre>
  <p>I've tried with and without RStudio.
  I'd be grateful if someone can try to replicate the error, please?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-01T13:18:41.953Z
Comments.Text: Can you edit your question to include how you are trying to install the packages? thanks.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-01T13:27:56.937Z
Comments.Text: Sorry @user438383, I forgot to add how I installed the pacakges. I edited the question now and added more details.
Comments.UserDisplayName: Sam
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-01T13:33:19.693Z
Comments.Text: Thanks. Just tried it on macOs 10.15 and it seems to have installed OK. Does the same problem occur if you try and install a different package via bioconductor, or a package using ``install.packages()``?
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-01T13:37:03.110Z
Comments.Text: Oh, thank you. This is extremely strange because I tried it on my friend's computer and had the same problem. I can install any other package via Bioconductor without problem except for these three. Can I ask if you installed all three of them?
Comments.UserDisplayName: Sam
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-01T13:39:28.180Z
Comments.Text: It's been a week and I've tried uninstalling R, RStudio and `RFrameworks ` countless times but still not working. I'm sorry but can I ask if if you used `BiocManager::install(c("Homo.sapiens", "EnsDb.Hsapiens.v75", "TxDb.Hsapiens.UCSC.hg19.knownGene"))` to install them?
Comments.UserDisplayName: Sam
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-01T18:27:06.537Z
Comments.Text: This sounds like a system issue of some sort possibly having to do with Big Sur. Have you tried to install any of these with conda?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-02T16:47:47.020Z
Comments.Text: Sorry, I only wanted to see if someone can replicate the error because am having it in two machines. My apologies again and feel free to close the question.
Comments.UserDisplayName: Sam
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-03T01:26:34.470Z
Comments.Text: It just paused indefinitely?
Comments.UserDisplayName: Phoenix Mu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-01-03T17:53:39.430Z
Comments.Text: Did you mean it also paused indefinitely in your local machine when you installed it? Thank you so much.
Comments.UserDisplayName: Sam
Tags: <bioconductor><software-installation>
Title: `TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed
ThreadText: # `TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed
  
  (Asked by: username_0 on 2021-01-01)
  
  I think there is a problem with `TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75`. I'm struggling to install all of these packages as they pause at `byte-compile and prepare package for lazy loading` . Can anyone try to re-install them in their local machine because am not the only one who is having the problem, please? They used to work fine until a week ago!
  
  As usual, I install the packages by:
  
  ```
  BiocManager::install(c("Homo.sapiens", "EnsDb.Hsapiens.v75", "TxDb.Hsapiens.UCSC.hg19.knownGene"))
  
  ```
  
  I also tried installing them individually:
  
  ```
  BiocManager::install("EnsDb.Hsapiens.v75")
  BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
  
  ```
  
  It pause at:
  
  ```r
  * installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  
  ```
  
  sessionInfo( )
  
  ```
  R version 4.0.3 (2020-10-10)
  Platform: x86_64-apple-darwin17.0 (64-bit)
  Running under: macOS Big Sur 10.16
  
  Matrix products: default
  BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
  LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
  
  locale:
  [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  loaded via a namespace (and not attached):
  [1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3    
  
  ```
  
  I've tried with and without RStudio.
  I'd be grateful if someone can try to replicate the error, please?
  
  **Tags:** bioconductor, software-installation
  
  > **Comments:**
  > **username_1**: Can you edit your question to include how you are trying to install the packages? thanks.  
  > **username_0**: Sorry @username_1, I forgot to add how I installed the pacakges. I edited the question now and added more details.  
  > **username_1**: Thanks. Just tried it on macOs 10.15 and it seems to have installed OK. Does the same problem occur if you try and install a different package via bioconductor, or a package using ``install.packages()``?  
  > **username_0**: Oh, thank you. This is extremely strange because I tried it on my friend's computer and had the same problem. I can install any other package via Bioconductor without problem except for these three. Can I ask if you installed all three of them?  
  > **username_0**: It's been a week and I've tried uninstalling R, RStudio and `RFrameworks ` countless times but still not working. I'm sorry but can I ask if if you used `BiocManager::install(c("Homo.sapiens", "EnsDb.Hsapiens.v75", "TxDb.Hsapiens.UCSC.hg19.knownGene"))` to install them?  
  > **username_2**: This sounds like a system issue of some sort possibly having to do with Big Sur. Have you tried to install any of these with conda?  
  > **username_0**: Sorry, I only wanted to see if someone can replicate the error because am having it in two machines. My apologies again and feel free to close the question.  
  > **username_3**: It just paused indefinitely?  
  > **username_0**: Did you mean it also paused indefinitely in your local machine when you installed it? Thank you so much.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2021-01-07. Score: 1 | Accepted answer
  
  I am able to successfully install these packages using:
  
  ```
  BiocManager::install(c("Homo.sapiens", "EnsDb.Hsapiens.v75", "TxDb.Hsapiens.UCSC.hg19.knownGene"))
  
  ```
  
  This completes without any errors / warnings (R v4.0.3 / macOS 10.16), so I don't believe the packages themselves/Bioconductor are 'broken', but I suspect you are having compiler issues due to the Big Sur update.
  
  These are the steps I used to solve the problem:
  
  1. Reinstall xcode command line tools (even if it says "up to date")
  
  ```
  sudo rm -rf /Library/Developer/CommandLineTools
  sudo xcode-select --install
  
  ```
  
  2. Install gcc & llvm via Homebrew ([instructions for installing Homebrew](https://docs.brew.sh/Installation)) or, if you already have gcc/llvm installed via Homebrew, skip to the next step
  
  ```
  # This can take several hours
  brew install gcc
  brew install llvm
  
  ```
  
  3. Once you have gcc & llvm installed via Homebrew:
  
  ```
  brew cleanup
  brew update
  brew upgrade
  brew reinstall gcc
  brew reinstall llvm
  
  ```
  
  4. Link some headers into /usr/local/include
  
  ```
  sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/
  
  # You can safely ignore warnings like this:
  #ln: /usr/local/include//tcl.h: File exists
  #ln: /usr/local/include//tclDecls.h: File exists
  #ln: /usr/local/include//tclPlatDecls.h: File exists
  #ln: /usr/local/include//tclTomMath.h: File exists
  #ln: /usr/local/include//tclTomMathDecls.h: File exists
  #ln: /usr/local/include//tk.h: File exists
  #ln: /usr/local/include//tkDecls.h: File exists
  #ln: /usr/local/include//tkPlatDecls.h: File exists
  
  ```
  
  5. Create a new `~/.R/Makevars` file (if you already have a `~/.R/Makevars` file, save it in a different directory (away from `~/.R/`)) and include only these lines in the file:
  
  ```
  FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
  CXX1X=/usr/local/gfortran/bin/g++
  CXX98=/usr/local/gfortran/bin/g++
  CXX11=/usr/local/gfortran/bin/g++
  CXX14=/usr/local/gfortran/bin/g++
  CXX17=/usr/local/gfortran/bin/g++
  
  LLVM_LOC = /usr/local/opt/llvm
  CC=/usr/local/gfortran/bin/gcc -fopenmp
  CXX=/usr/local/gfortran/bin/g++ -fopenmp
  CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
  CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
  LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
  CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
  
  ```
  
  6. Compile a package from source in R/Rstudio
  
  ```
  # To check whether openmp is enabled, compile data.table:
  install.packages("data.table", type = "source")
  
  ```
  
  7. If your package fails to compile, a couple of SO users have had to install a fresh gfortran (re: <https://stackoverflow.com/a/65334247/12957340>), which you can download from <https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/10.2-bigsur-intel>
  
  Once you can install packages from source without error/issue, update Bioconductor
  
  ```
  BiocManager::install(version = "3.12")
  
  ```
  
  Then, finally, you should be able to install your packages using
  
  ```
  BiocManager::install(c("Homo.sapiens", "EnsDb.Hsapiens.v75", "TxDb.Hsapiens.UCSC.hg19.knownGene"))
  
  ```
  
  > **Comments:**
  > **username_0**: You are amazing Jared, I'll go through the steps right now to see if it works, fingers crossed.  
  > **username_0**: Awesome, it is working now. Thank you so much, Jared :)  
  
  ---
  
  