minfi, lumi, methylumi, DMRcate installation error
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@poojithastemcell-11859
Last seen 13 days ago
United Kingdom

I have been trying to load minfi, lumi, methylumi and DMRcate packages in Rstudio. These packages are already installed and I have been using it for a while now. However, when I try to load them this past week I have been encountering errors stating - "Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘data.table". 

In addition, I have also been encountering problems with DMRcate functions due to error in loading the annotation packages - IlluminaHumanMethylationEPICanno.ilm10b2.hg19 and IlluminaHumanMethylation450kanno.ilmn12.hg19. 

I have tried uninstalling and reinstalling packages followed by restarting Rstudio. I am unable to resolve this issue. 

Is anyone else facing the same problem or can suggest a solution? Please help me out here.

Regards,

Poojitha Rajasekar

minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19 • 1.4k views
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@james-w-macdonald-5106
Last seen 22 hours ago
United States

The error has nothing to do with any of the packages you mention! Have you tried re-installing the data.table package?

You have to be more clear about the errors you get with the annotation packages. Unless you show code and output as well as the results from sessionInfo(), nobody will be able to help you.

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@poojithastemcell-11859
Last seen 13 days ago
United Kingdom

Hello James,

I uninstalled and reinstalled the most updated version of R and RStudio. I am able to install the packages minfi, methylumi, lumi and DMRcate without any errors. However, I am still unable to run functions in DMRcate. Please see below the codes and the error message I received.

> library(DMRcate)
> library(minfi)
> library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
> type<-factor(targets.controlvs3D7D$groups1)
> design<- model.matrix(~type)
> myannotation <- cpg.annotate("array", M.controlvs3D7D, what="M", arraytype = "450K",
+                              analysis.type="differential", design=design, coef=2)
Error in get(ann) : 
  cannot open file '~/R/win-library/3.3/IlluminaHumanMethylation450kanno.ilmn12.hg19/data/Rdata.rdb': No such file or directory
In addition: Warning message:
In get(results[[i]], pos = which(search() == packages[[i]])) :
  restarting interrupted promise evaluation

I tried uninstalling and reinstalling 'IlluminaHumanMethylation450kanno.ilmn12.hg19'. Again it seems to install properly, but DMRcate does not seem to recognise it. Do you have any suggestions?

Regards,

Poojitha

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If you want to respond to an answer, please use the ADD COMMENT button and type in the box that appears. The Add your answer box below is for adding answers, not additional questions.

In addition, I requested your sessionInfo() output, which you did not supply. The reason we ask for sessionInfo output is because mis-matched package versions are a major reason for people getting errors. If you want help you have to actually read and respond to my requests!

It's also helpful if you give a small, reproducible example that people can use to test. An example of what I mean follows. As you can see, this works for me, so it's possible you have mis-matched packages.

> library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
> library(minfi)
> library(DMRcate)
> library("CopyNumber450kData")
> data(RGcontrolSetEx)

> z <- preprocessFunnorm(RGcontrolSetEx)
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization

> zz <- cpg.annotate("array",z, "M", "450K", "differential", model.matrix(~factor(rep(1:2, each=26))), coef=2)
Your contrast returned 37708 individually significant probes. We recommend the default setting of pcutoff in dmrcate().

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] splines   stats4    parallel  stats     graphics  grDevices utils   
[8] datasets  methods   base     

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I had too many characters, so here's the rest of my sessionInfo()

other attached packages:
 [1] CopyNumber450kData_1.10.0                         
 [2] IlluminaHumanMethylation450kmanifest_0.4.0        
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
 [4] DMRcate_1.10.7                                    
 [5] DMRcatedata_1.10.1                                
 [6] DSS_2.14.0                                        
 [7] bsseq_1.10.0                                      
 [8] limma_3.30.8                                      
 [9] BiocInstaller_1.24.0                              
[10] minfi_1.20.2                                      
[11] bumphunter_1.14.0                                 
[12] locfit_1.5-9.1                                    
[13] iterators_1.0.8                                   
[14] foreach_1.4.3                                     
[15] Biostrings_2.42.1                                 
[16] XVector_0.14.0                                    
[17] SummarizedExperiment_1.4.0                        
[18] GenomicRanges_1.26.2                              
[19] GenomeInfoDb_1.10.2                               
[20] IRanges_2.8.1                                     
[21] S4Vectors_0.12.1                                  
[22] Biobase_2.34.0                                    
[23] BiocGenerics_0.20.0                   
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Sorry about that ! I compared my sessionInfo() with yours. The versions of DMRcate and annotation packages for 450K are the same. However, I have installed R3.3.3. Please see the sessionInfo() on my RStudio in the next comment. However, without making any changes, DMRcate worked for 450K data today. But, it still does not work for EPIC data. This is a bit strange. It still gives the same error.

library(DMRcate)
> library(minfi)
> library(IlluminaHumanMethylationEPICanno.ilm10b2.hg19))
> type<-factor(targets.controlvs3D7D$groups1)
> design<- model.matrix(~type)
myannotation <- cpg.annotate("array", M.controlvs3D7D, what="M", arraytype = "EPIC",
+                              analysis.type="differential", design=design, coef=2)
Error in get(ann) : 
  cannot open file '~/R/win-library/3.3/IlluminaHumanMethylationEPICanno.ilm10b2.hg19
.ilmn12.hg19/data/Rdata.rdb': No such file or directory
In addition: Warning message:
In get(results[[i]], pos = which(search() == packages[[i]])) :
  restarting interrupted promise evaluation

Regards,

Poojitha

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Here is my session Info:

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
 [1] splines   parallel  stats4    stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
 [2] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
 [3] DMRcate_1.10.7                                     
 [4] DMRcatedata_1.10.1                                 
 [5] DSS_2.14.0                                         
 [6] bsseq_1.10.0                                       
 [7] limma_3.30.12                                      
 [8] minfi_1.20.2                                       
 [9] bumphunter_1.14.0                                  
[10] locfit_1.5-9.1                                     
[11] iterators_1.0.8                                    
[12] foreach_1.4.3                                      
[13] Biostrings_2.42.1                                  
[14] XVector_0.14.0                                     
[15] SummarizedExperiment_1.4.0                         
[16] Biobase_2.34.0                                     
[17] GenomicRanges_1.26.3                               
[18] GenomeInfoDb_1.10.3                                
[19] IRanges_2.8.1                                      
[20] S4Vectors_0.12.1                                   
[21] BiocGenerics_0.20.0                                

 

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loaded via a namespace (and not attached):
  [1] colorspace_1.3-2                           siggenes_1.48.0                           
  [3] mclust_5.2.3                               biovizBase_1.22.0                         
  [5] htmlTable_1.9                              base64enc_0.1-3                           
  [7] dichromat_2.0-0                            base64_2.0                                
  [9] interactiveDisplayBase_1.12.0              AnnotationDbi_1.36.2                      
 [11] codetools_0.2-15                           R.methodsS3_1.7.1                         
 [13] methylumi_2.20.0                           knitr_1.15.1                              
 [15] Formula_1.2-1                              Rsamtools_1.26.1                          
 [17] annotate_1.52.1                            GO.db_3.4.0                               
 [19] cluster_2.0.5                              R.oo_1.21.0                               
 [21] shiny_1.0.0                                httr_1.2.1                                
 [23] backports_1.0.5                            assertthat_0.1                            
 [25] Matrix_1.2-8                               lazyeval_0.2.0                            
 [27] acepack_1.4.1                              htmltools_0.3.5                           
 [29] tools_3.3.3                                gtable_0.2.0                              
 [31] doRNG_1.6                                  Rcpp_0.12.9                               
 [33] multtest_2.30.0                            preprocessCore_1.36.0                     
 [35] nlme_3.1-131                               rtracklayer_1.34.2                        
 [37] stringr_1.2.0                              mime_0.5                                  
 [39] ensembldb_1.6.2                            rngtools_1.2.4                            
  

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 [41] gtools_3.5.0                               statmod_1.4.29                            
 [43] XML_3.98-1.5                               beanplot_1.2                              
 [45] org.Hs.eg.db_3.4.0                         AnnotationHub_2.6.4                       
 [47] zlibbioc_1.20.0                            MASS_7.3-45                               
 [49] scales_0.4.1                               BSgenome_1.42.0                           
 [51] VariantAnnotation_1.20.2                   BiocInstaller_1.24.0                      
 [53] GEOquery_2.40.0                            RColorBrewer_1.1-2                        
 [55] missMethyl_1.8.0                           yaml_2.1.14                               
 

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There must be something wrong with the annotation slot for your M.controlvs3D7D object, because cpg.annotate is looking in the wrong place:

Error in get(ann) : 
  cannot open file '~/R/win-library/3.3/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.ilmn12.hg19/data/Rdata.rdb': No such file or directory

If you do

path.package("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")

it should return something like

~/R/win-library/3.3/IlluminaHumanMethylationEPICanno.ilm10b2.hg19

Which is the name of the package. You seem to have some concatenation of the two Illumina methylation annotation packages, which is messing everything up.

 

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Tim Peters ▴ 120
@tim-peters-7579
Last seen 6 weeks ago
Australia

Hi Poojitha,

To further James' comment, I would remove these two lines from your workflow

> library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
> library(minfi)

since DMRcate already attaches minfi when you load it, and then cpg.annotate (via minfi) will attach the annotation package when it is called.

Best,

Tim

 

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