<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>

CC BY-SA 4.0
2021-01-07T19:46:21.037Z
You are amazing Jared, I'll go through the steps right now to see if it works, fingers crossed.
Sam
CC BY-SA 4.0
2021-01-16T02:12:50.107Z
Awesome, it is working now. Thank you so much, Jared :)
Sam
CC BY-SA 4.0
2021-01-07T04:11:25.000Z
2021-01-07T22:12:14.380Z
2021-01-07T22:12:14.380Z
jared_mamrot
<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>

CC BY-SA 4.0
2021-01-01T13:18:41.953Z
Can you edit your question to include how you are trying to install the packages? thanks.
user438383
CC BY-SA 4.0
2021-01-01T13:27:56.937Z
Sorry @user438383, I forgot to add how I installed the pacakges. I edited the question now and added more details.
Sam
CC BY-SA 4.0
2021-01-01T13:33:19.693Z
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()``?
user438383
CC BY-SA 4.0
2021-01-01T13:37:03.110Z
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?
Sam
CC BY-SA 4.0
2021-01-01T13:39:28.180Z
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?
Sam
CC BY-SA 4.0
2021-01-01T18:27:06.537Z
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?
Devon Ryan
CC BY-SA 4.0
2021-01-02T16:47:47.020Z
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.
Sam
CC BY-SA 4.0
2021-01-03T01:26:34.470Z
It just paused indefinitely?
Phoenix Mu
CC BY-SA 4.0
2021-01-03T17:53:39.430Z
Did you mean it also paused indefinitely in your local machine when you installed it? Thank you so much.
Sam
<bioconductor><software-installation>
`TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed
# `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:
* 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 @user438383, 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:

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"))

> **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 :)  

---

