Answers.Body: <p>Simple, use the latest version of R and Bioconductor, now on version 3.6.1 and Bioconductor 3.9. Those are the versions that are supported. If you can't upgrade R, check that <code>BiocManager::valid()</code> is true, you might have ended in some inconsistency between Bioconductor versions. </p>
  
  <p>Looking at your <code>sessionInfo</code>, you seem to have some problems with the installed libraries, check and correct those too if possible</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-08T15:42:39.103Z
Answers.Text: @IIrs: `BiocManager::valid()` gives the `Warning message:
  10 packages out-of-date; 1 packages too new.`  How can I know the package which is too new?
Answers.UserDisplayName: Charles
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-08T15:45:29.963Z
Answers.Text: It also printed some more messages. Please edit the original question and post the full comment. If it didn't (I don't know how that could be) use `BiocManager::install()` (without any package), it should update the out-of-date packages. But the problem might be that this too-new is the one you have problems with. Store the result of `a <- BiocManager::valid()` and explore the `a$toonew`(or something alike).
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-08T15:34:24.403Z
Answers.LastActivityDate: 2019-07-08T15:34:24.403Z
Answers.UserDisplayName: llrs
Body: <p>How do I solve the problem of loading the  bioconductor <strong>Chipseeker</strong> package? I have installed in the following way and I having an error while loading it and I do not know why.</p>
  
  <pre><code>BiocManager::install("ChIPseeker")
  BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
  BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
  
  library(ChIPseeker) # produces and error
  
  Error: package or namespace load failed for 'ChIPseeker': 
    'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg19.knownGene'
  </code></pre>
  
  <p>Thank you in advance for any help on how to go about this.</p>
  
  <pre><code>session info:
  
  R version 3.5.1 (2018-07-02)
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 7 x64 (build 7601) Service Pack 1
  
  Matrix products: default
  
  locale:
  [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
  [4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    
  
  attached base packages:
  [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
   [1] BiocInstaller_1.32.1                    TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
   [3] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 GenomicFeatures_1.34.8                 
   [5] AnnotationDbi_1.44.0                    GenomicRanges_1.34.0                   
   [7] GenomeInfoDb_1.18.2                     IRanges_2.16.0                         
   [9] S4Vectors_0.20.1                        cellrangerRkit_1.1.0                   
  [11] Rmisc_1.5                               plyr_1.8.4                             
  [13] lattice_0.20-35                         bit64_0.9-7                            
  [15] bit_1.1-14                              ggplot2_3.1.1                          
  [17] RColorBrewer_1.1-2                      Biobase_2.42.0                         
  [19] BiocGenerics_0.28.0                     Matrix_1.2-14                          
  
  loaded via a namespace (and not attached):
  Error in x[["Version"]] : subscript out of bounds
  In addition: Warning message:
  In FUN(X[[i]], ...) : DESCRIPTION von Paket 'digest' fehlt oder zerstört
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-08T13:37:52.300Z
Comments.Text: There might be a problem with your current R session if `sessionInfo()` gives you an error. Try restarting the R session (if you're using RStudio) or just exiting and starting a new R session (if you're on the command line).
Comments.UserDisplayName: Ram RS
Tags: <r><bioconductor><chip-seq>
Title: Error: package or namespace load failed for 'ChIPseeker'
ThreadText: # Error: package or namespace load failed for 'ChIPseeker'
  
  (Asked by: username_0 on 2019-07-08)
  
  How do I solve the problem of loading the bioconductor **Chipseeker** package? I have installed in the following way and I having an error while loading it and I do not know why.
  
  ```
  BiocManager::install("ChIPseeker")
  BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
  BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
  
  library(ChIPseeker) # produces and error
  
  Error: package or namespace load failed for 'ChIPseeker': 
    'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg19.knownGene'
  
  ```
  
  Thank you in advance for any help on how to go about this.
  
  ```
  session info:
  
  R version 3.5.1 (2018-07-02)
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 7 x64 (build 7601) Service Pack 1
  
  Matrix products: default
  
  locale:
  [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
  [4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    
  
  attached base packages:
  [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
   [1] BiocInstaller_1.32.1                    TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
   [3] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 GenomicFeatures_1.34.8                 
   [5] AnnotationDbi_1.44.0                    GenomicRanges_1.34.0                   
   [7] GenomeInfoDb_1.18.2                     IRanges_2.16.0                         
   [9] S4Vectors_0.20.1                        cellrangerRkit_1.1.0                   
  [11] Rmisc_1.5                               plyr_1.8.4                             
  [13] lattice_0.20-35                         bit64_0.9-7                            
  [15] bit_1.1-14                              ggplot2_3.1.1                          
  [17] RColorBrewer_1.1-2                      Biobase_2.42.0                         
  [19] BiocGenerics_0.28.0                     Matrix_1.2-14                          
  
  loaded via a namespace (and not attached):
  Error in x[["Version"]] : subscript out of bounds
  In addition: Warning message:
  In FUN(X[[i]], ...) : DESCRIPTION von Paket 'digest' fehlt oder zerstört
  
  ```
  
  **Tags:** r, bioconductor, chip-seq
  
  > **Comments:**
  > **username_1**: There might be a problem with your current R session if `sessionInfo()` gives you an error. Try restarting the R session (if you're using RStudio) or just exiting and starting a new R session (if you're on the command line).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-07-08. Score: 1
  
  Simple, use the latest version of R and Bioconductor, now on version 3.6.1 and Bioconductor 3.9. Those are the versions that are supported. If you can't upgrade R, check that `BiocManager::valid()` is true, you might have ended in some inconsistency between Bioconductor versions.
  
  Looking at your `sessionInfo`, you seem to have some problems with the installed libraries, check and correct those too if possible
  
  > **Comments:**
  > **username_0**: @IIrs: `BiocManager::valid()` gives the `Warning message: 10 packages out-of-date; 1 packages too new.`  How can I know the package which is too new?  
  > **username_2**: It also printed some more messages. Please edit the original question and post the full comment. If it didn't (I don't know how that could be) use `BiocManager::install()` (without any package), it should update the out-of-date packages. But the problem might be that this too-new is the one you have problems with. Store the result of `a <- BiocManager::valid()` and explore the `a$toonew`(or something alike).  
  
  ---
  
  