Question: "> example(coMET)" returns error in genesENSEMBL() call
0
gravatar for h.draisma
16 months ago by
h.draisma0
h.draisma0 wrote:

Trying to run the examples as in the "Examples" section on the coMET() help page reproducibly returns the following error:

Error in genesENSEMBL(gen, chrom, start, end, showId = TRUE):
  could not find function "genesENSEMBL"

 

By "reproducibly" I mean that the same error was returned before and after removing the 'coMET' package from my <R> installation and reinstalling then loading it, allowing "all" dependencies (packages) to be updated when prompted.

 

The sequence of commands that I followed in <R> for this was:

> require(coMET)
> example(coMET)
> remove.packages("coMET", lib="~/R/x86_64-pc-linux-gnu-library/3.4")
> require(coMET)   #<-- Apparently allowed me to load the package still indeed, hence closed <R>, then restarted <R>. After that, issuing the same command produced an error stating that the package 'coMET' was not available indeed, as we want.
> source("https://bioconductor.org/biocLite.R")
> biocLite("coMET")
> require(coMET)
> example("coMET")

 

The outputs of '> example("coMET", verbose = TRUE)', "> sessionInfo()" and "> traceback()" are as follows:

> example("coMET", verbose = TRUE)
'envir' chosen:<environment: R_GlobalEnv>
encoding = "UTF-8" chosen
--> parsed 10 expressions; now eval(.)ing them:
has srcrefs:
List of 10
$ :Class 'srcref'  atomic [1:8] 10 1 10 64 1 64 10 10
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 11 1 11 65 1 65 11 11
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 12 1 12 55 1 55 12 12
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 13 1 13 74 1 74 13 13
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 14 1 14 65 1 65 14 14
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 16 1 16 15 1 15 16 16
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 17 1 17 17 1 17 17 17
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 18 1 18 15 1 15 18 18
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 19 1 19 13 1 13 19 19
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>
$ :Class 'srcref'  atomic [1:8] 21 1 57 1 1 1 21 57
  .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x205b39a0>

>>>> eval(expression_nr. 1 )
         =================

coMET> extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
curr.fun: symbol <-
 .. after 'expression(extdata <- system.file("extdata", package="coMET",mustWork=TRUE))'

>>>> eval(expression_nr. 2 )
         =================

coMET> configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
curr.fun: symbol <-
 .. after 'expression(configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt"))'

>>>> eval(expression_nr. 3 )
         =================

coMET> myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
curr.fun: symbol <-
 .. after 'expression(myinfofile <- file.path(extdata, "cyp1b1_infofile.txt"))'

>>>> eval(expression_nr. 4 )
         =================

coMET> myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
curr.fun: symbol <-
 .. after 'expression(myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt"))'

>>>> eval(expression_nr. 5 )
         =================

coMET> mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
curr.fun: symbol <-
 .. after 'expression(mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt"))'

>>>> eval(expression_nr. 6 )
         =================

coMET> chrom <- "chr2"
curr.fun: symbol <-
 .. after 'expression(chrom <- "chr2")'

>>>> eval(expression_nr. 7 )
         =================

coMET> start <- 38290160
curr.fun: symbol <-
 .. after 'expression(start <- 38290160)'

>>>> eval(expression_nr. 8 )
         =================

coMET> end <- 38303219
curr.fun: symbol <-
 .. after 'expression(end <- 38303219)'

>>>> eval(expression_nr. 9 )
         =================

coMET> gen <- "hg38"
curr.fun: symbol <-
 .. after 'expression(gen <- "hg38")'

>>>> eval(expression_nr. 10 )
         =================

coMET> if(interactive()){
coMET+     genetrack <-genesENSEMBL(gen,chrom,start,end,showId=TRUE)
coMET+     snptrack <- snpBiomart(chrom, start, end,
coMET+                     dataset="hsapiens_snp_som",showId=FALSE)
coMET+     strutrack <- structureBiomart(chrom, start, end,
coMET+                     strand, dataset="hsapiens_structvar_som")
coMET+     clinVariant<-ClinVarMainTrack(gen,chrom,start,end)
coMET+     clinCNV<-ClinVarCnvTrack(gen,chrom,start,end)
coMET+     gwastrack <-GWASTrack(gen,chrom,start,end)
coMET+     geneRtrack <-GeneReviewsTrack(gen,chrom,start,end)
coMET+
coMET+     listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
coMET+                     clinCNV,gwastrack,geneRtrack)
coMET+
coMET+     comet(config.file=configfile, mydata.file=myinfofile,  mydata.type="listfile",
coMET+          cormatrix.file=mycorrelation, cormatrix.type="listfile",
coMET+          mydata.file=myexpressfile, mydata.large.type="listfile",
coMET+          tracks.gviz=listgviz,
coMET+          verbose=FALSE, print.image=FALSE,disp.pvalueplot=TRUE)
coMET+ } else {
coMET+     data(geneENSEMBLtrack)
coMET+     data(snpBiomarttrack)
coMET+     data(ISCAtrack)
coMET+     data(strucBiomarttrack)
coMET+     data(ClinVarCnvTrack)
coMET+     data(clinVarMaintrack)
coMET+     data(GWASTrack)
coMET+     data(GeneReviewTrack)
coMET+
coMET+     listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
coMET+                     clinCNV,gwastrack,geneRtrack)
coMET+     comet(config.file=configfile, mydata.file=myinfofile, mydata.type="listfile",
coMET+         cormatrix.file=mycorrelation, cormatrix.type="listfile",
coMET+         mydata.large.file=myexpressfile, mydata.large.type="listfile",
coMET+         tracks.gviz=listgviz,
coMET+         verbose=FALSE, print.image=FALSE,disp.pvalueplot=TRUE)
coMET+ }
Error in genesENSEMBL(gen, chrom, start, end, showId = TRUE) :
  could not find function "genesENSEMBL"
> traceback()
5: eval(ei, envir)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
       getOption("prompt")), continue.echo = paste0(prompt.prefix,
       getOption("continue")), verbose = verbose, max.deparse.length = Inf,
       encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
1: example("coMET", verbose = TRUE)
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
 [1] coMET_1.10.2         trackViewer_1.14.1   ggbio_1.26.0       
 [4] ggplot2_2.2.1        psych_1.7.8          Gviz_1.22.3        
 [7] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0  IRanges_2.12.0     
[10] S4Vectors_0.16.0     BiocGenerics_0.24.0  biomaRt_2.34.2     
[13] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] nlme_3.1-131                  ProtGenerics_1.10.0         
 [3] bitops_1.0-6                  matrixStats_0.53.1          
 [5] bit64_0.9-7                   RColorBrewer_1.1-2          
 [7] progress_1.1.2                httr_1.3.1                  
 [9] tools_3.4.3                   backports_1.1.2             
[11] R6_2.2.2                      rpart_4.1-13                
[13] Hmisc_4.1-1                   DBI_0.8                     
[15] lazyeval_0.2.1                colorspace_1.3-2            
[17] nnet_7.3-12                   gridExtra_2.3               
[19] prettyunits_1.0.2             GGally_1.3.2                
[21] mnormt_1.5-5                  RMySQL_0.10.14              
[23] bit_1.1-12                    curl_3.1                    
[25] compiler_3.4.3                graph_1.56.0                
[27] Biobase_2.38.0                htmlTable_1.11.2            
[29] grImport_0.9-0                DelayedArray_0.4.1          
[31] rtracklayer_1.38.3            scales_0.5.0                
[33] checkmate_1.8.5               pbapply_1.3-4               
[35] RBGL_1.54.0                   stringr_1.3.0               
[37] digest_0.6.15                 Rsamtools_1.30.0            
[39] foreign_0.8-69                XVector_0.18.0              
[41] base64enc_0.1-3               dichromat_2.0-0             
[43] htmltools_0.3.6               ensembldb_2.2.2             
[45] BSgenome_1.46.0               htmlwidgets_1.0             
[47] rlang_0.2.0                   rstudioapi_0.7              
[49] RSQLite_2.0                   shiny_1.0.5                 
[51] BiocParallel_1.12.0           acepack_1.4.1               
[53] VariantAnnotation_1.24.5      RCurl_1.95-4.10             
[55] magrittr_1.5                  GenomeInfoDbData_1.0.0      
[57] Formula_1.2-2                 Matrix_1.2-11               
[59] Rcpp_0.12.15                  munsell_0.4.3               
[61] stringi_1.1.6                 yaml_2.1.17                 
[63] SummarizedExperiment_1.8.1    zlibbioc_1.24.0             
[65] plyr_1.8.4                    AnnotationHub_2.10.1        
[67] blob_1.1.0                    lattice_0.20-35             
[69] Biostrings_2.46.0             splines_3.4.3               
[71] hash_2.2.6                    GenomicFeatures_1.30.3      
[73] knitr_1.20                    pillar_1.2.1                
[75] reshape2_1.4.3                XML_3.98-1.10               
[77] biovizBase_1.26.0             latticeExtra_0.6-28         
[79] data.table_1.10.4-3           httpuv_1.3.6.2              
[81] gtable_0.2.0                  reshape_0.8.7               
[83] assertthat_0.2.0              mime_0.5                    
[85] xtable_1.8-2                  AnnotationFilter_1.2.0      
[87] colortools_0.1.5              survival_2.41-3             
[89] OrganismDbi_1.20.0            tibble_1.4.2                
[91] GenomicAlignments_1.14.1      AnnotationDbi_1.40.0        
[93] memoise_1.1.0                 corrplot_0.84               
[95] cluster_2.0.6                 interactiveDisplayBase_1.16.0
>

 

comet • 188 views
ADD COMMENTlink modified 16 months ago by Tiphaine Martin40 • written 16 months ago by h.draisma0
Answer: "> example(coMET)" returns error in genesENSEMBL() call
0
gravatar for Tiphaine Martin
16 months ago by
France
Tiphaine Martin40 wrote:

Hi,

Sorry, I forgot to update this section too.As you see in the manual 

genesENSEMBL has been replaced by genes_ENSEMBL. 

So please, use genes_ENSEMBL and not genesENSEMBL. I will update the manual.

 

Best,

Tiphaine 

 

ADD COMMENTlink written 16 months ago by Tiphaine Martin40
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