Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-03T13:23:42.113Z
Answers.Text: If I come up with another solution that works fine with my server R version, I will post an update here.
Answers.UserDisplayName: Bluescreen
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-03T13:22:03.760Z
Answers.LastActivityDate: 2018-01-03T13:22:03.760Z
Answers.LastEditDate: 2020-06-18T08:30:41.743Z
Answers.UserDisplayName: Bluescreen
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-22T08:06:38.517Z
Comments.Text: It  might be better then to raise the error to support.bioconductor.org to let the maintainers know about it.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-22T08:09:43.647Z
Comments.Text: Ok, I will do. If the error is fixable from user side, I will report the answer here.
Comments.UserDisplayName: Bluescreen
Tags: <r><bioconductor>
Title: Installing RnBeads via bioconductor - .onLoad failed in loadNamespace(), call: NULL
ThreadText: # 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.  
  
  ---
  
  