<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>

CC BY-SA 4.0
2019-07-08T15:42:39.103Z
@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10 packages out-of-date; 1 packages too new.`  How can I know the package which is too new?
Charles
CC BY-SA 4.0
2019-07-08T15:45:29.963Z
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If it didn't (I don't know how that could be) use `BiocManager::install()` (without any package), it should update the out-of-date packages.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).
llrs
CC BY-SA 4.0
2019-07-08T15:34:24.403Z
2019-07-08T15:34:24.403Z
llrs
<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>

CC BY-SA 4.0
2019-07-08T13:37:52.300Z
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).
Ram RS
<r><bioconductor><chip-seq>
Error: package or namespace load failed for 'ChIPseeker'
# 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).  

---

