<p>I have reported the <a href="https://support.bioconductor.org/p/104488/" rel="nofollow noreferrer">error on support.bioconductor.org</a> but we were not able to solve the problem. It seems that some dependencies are making problems, but as reinstalling my home R folder did not resolve the issue, I have come up with the following workaround:</p>
<p>I downloaded the latest R version from my favorite CRAN mirror, opened an R session with <code>pathToNewR/bin/R</code> from my terminal and installed <code>RnBeads</code> there. This works fine.</p>
<p>Note: I had to make sure that <code>pathToNewR/library</code> is the only entry in <code>.libPaths()</code>, as per default, my home R folder was also contained in <code>.libPaths()</code>.</p>
<p>As a consequence, I am independent from the (maybe broken) R version and packages on my server and can finally work with <code>RnBeads</code> :)</p>

CC BY-SA 3.0
2018-01-03T13:23:42.113Z
If I come up with another solution that works fine with my server R version, I will post an update here.
Bluescreen
CC BY-SA 3.0
2018-01-03T13:22:03.760Z
2018-01-03T13:22:03.760Z
2020-06-18T08:30:41.743Z
Bluescreen
<p>I am trying to install <code>RnBeads</code> from bioconductor but the installation of its dependancy <code>TxDb.Hsapiens.UCSC.hg19.knownGene</code> fails. The error is:</p>

<pre><code>biocLite("RnBeads")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘RnBeads’
also installing the dependencies ‘FDb.InfiniumMethylation.hg19’, ‘methylumi’

trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz'
Content type 'application/x-gzip' length 38996322 bytes (37.2 MB)
==================================================
downloaded 37.2 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/methylumi_2.24.1.tar.gz'
Content type 'application/x-gzip' length 6178909 bytes (5.9 MB)
==================================================
downloaded 5.9 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/RnBeads_1.10.2.tar.gz'
Content type 'application/x-gzip' length 6437974 bytes (6.1 MB)
==================================================
downloaded 6.1 MB

* installing *source* package ‘FDb.InfiniumMethylation.hg19’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Error: package or namespace load failed for ‘TxDb.Hsapiens.UCSC.hg19.knownGene’:
 .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
  call: NULL
  error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Error : package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ could not be loaded
ERROR: lazy loading failed for package ‘FDb.InfiniumMethylation.hg19’

The downloaded source packages are in
    ‘/tmp/RtmpY8Yf4l/downloaded_packages’
installation path not writeable, unable to update packages: doMC, doSNOW,
  foreach, iterators, snow, boot, class, cluster, codetools, foreign,
  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
</code></pre>

<p>As suggested by the error message, I tried setting <code>options(expressions=500000)</code>, which unfortunately did not change the error message. An important note may be that I am under network mount and don't have administrative access rights.</p>

<p><strong>Edit</strong></p>

<p>I don't have a .Rprofile file.</p>

<p>Note about <code>installation path not writeable</code>:
Typing .libPaths() reveals that my home R folder is at the first position (and it is writable). The other paths (<code>"/usr/local/lib/R/site-library"</code>                          , <code>"/usr/lib/R/site-library"</code> and <code>"/usr/lib/R/library"</code>) are not writable without sudo.</p>

<p>I also tried to delete my home R folder and to reinstall it. The reinstallation of all packages worked for all packages except for the three listed above (same error message). I also tried <code>biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene", lib.loc=.libPaths()[1], lib=.libPaths()[1])</code> to specifically address my home R directory, but the same error is showing up (but without the <code>installation path not writeable</code> part).</p>

<p>Here is my sessionInfo():</p>

<pre><code>R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libopenblas.so.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3
</code></pre>

<p>Thank you very much!</p>

CC BY-SA 3.0
2017-12-22T08:06:38.517Z
It  might be better then to raise the error to support.bioconductor.org to let the maintainers know about it.
llrs
CC BY-SA 3.0
2017-12-22T08:09:43.647Z
Ok, I will do. If the error is fixable from user side, I will report the answer here.
Bluescreen
<r><bioconductor>
Installing RnBeads via bioconductor - .onLoad failed in loadNamespace(), call: NULL
# Installing RnBeads via bioconductor - .onLoad failed in loadNamespace(), call: NULL

(Asked by: username_0 on 2017-12-21)

I am trying to install RnBeads from bioconductor but the installation of its dependancy TxDb.Hsapiens.UCSC.hg19.knownGene fails. The error is:
biocLite("RnBeads")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘RnBeads’
also installing the dependencies ‘FDb.InfiniumMethylation.hg19’, ‘methylumi’

trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz'
Content type 'application/x-gzip' length 38996322 bytes (37.2 MB)
==================================================
downloaded 37.2 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/methylumi_2.24.1.tar.gz'
Content type 'application/x-gzip' length 6178909 bytes (5.9 MB)
==================================================
downloaded 5.9 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/RnBeads_1.10.2.tar.gz'
Content type 'application/x-gzip' length 6437974 bytes (6.1 MB)
==================================================
downloaded 6.1 MB

* installing *source* package ‘FDb.InfiniumMethylation.hg19’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Error: package or namespace load failed for ‘TxDb.Hsapiens.UCSC.hg19.knownGene’:
 .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
  call: NULL
  error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Error : package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ could not be loaded
ERROR: lazy loading failed for package ‘FDb.InfiniumMethylation.hg19’

The downloaded source packages are in
    ‘/tmp/RtmpY8Yf4l/downloaded_packages’
installation path not writeable, unable to update packages: doMC, doSNOW,
  foreach, iterators, snow, boot, class, cluster, codetools, foreign,
  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival

As suggested by the error message, I tried setting options(expressions=500000), which unfortunately did not change the error message. An important note may be that I am under network mount and don't have administrative access rights.
Edit
I don't have a .Rprofile file.
Note about installation path not writeable:
Typing .libPaths() reveals that my home R folder is at the first position (and it is writable). The other paths ("/usr/local/lib/R/site-library"                          , "/usr/lib/R/site-library" and "/usr/lib/R/library") are not writable without sudo.
I also tried to delete my home R folder and to reinstall it. The reinstallation of all packages worked for all packages except for the three listed above (same error message). I also tried biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene", lib.loc=.libPaths()[1], lib=.libPaths()[1]) to specifically address my home R directory, but the same error is showing up (but without the installation path not writeable part).
Here is my sessionInfo():
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libopenblas.so.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3

Thank you very much!

**Tags:** r, bioconductor
> **Comments:**
> **username_1**: It  might be better then to raise the error to support.bioconductor.org to let the maintainers know about it.  
> **username_0**: Ok, I will do. If the error is fixable from user side, I will report the answer here.  

---

## 1 answers

### Answer by username_0 on 2018-01-03. Score: 2 | Accepted answer

I have reported the [error on support.bioconductor.org](https://support.bioconductor.org/p/104488/) but we were not able to solve the problem. It seems that some dependencies are making problems, but as reinstalling my home R folder did not resolve the issue, I have come up with the following workaround:

I downloaded the latest R version from my favorite CRAN mirror, opened an R session with `pathToNewR/bin/R` from my terminal and installed `RnBeads` there. This works fine.

Note: I had to make sure that `pathToNewR/library` is the only entry in `.libPaths()`, as per default, my home R folder was also contained in `.libPaths()`.

As a consequence, I am independent from the (maybe broken) R version and packages on my server and can finally work with `RnBeads` :)

> **Comments:**
> **username_0**: If I come up with another solution that works fine with my server R version, I will post an update here.  

---

