text: user10179: 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:
  * 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?
  
  user9098: 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:
  
  Reinstall xcode command line tools (even if it says "up to date")
  
  sudo rm -rf /Library/Developer/CommandLineTools
  sudo xcode-select --install
  
  
  Install gcc & llvm via Homebrew (instructions for installing Homebrew) 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
  
  
  Once you have gcc & llvm installed via Homebrew:
  
  brew cleanup
  brew update
  brew upgrade
  brew reinstall gcc
  brew reinstall llvm
  
  
  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
  
  
  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
  
  
  Compile a package from source in R/Rstudio
  
  # To check whether openmp is enabled, compile data.table:
  install.packages("data.table", type = "source")
  
  
  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"))
  
  
original_text: 10179: <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>
   9098: <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>
  