[Bioc-devel] Non-ASCII in datase from Biomart EMBL via Gviz package

[Martin, Tiphaine]

Hi,


I need to create dataset BiomartGeneRegionTrack via Gviz package to run examples in my packages. But when I run

"R CMD check coMET", i have warning message for the checking :


 checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII strings
  '[alpha cell,acidophil cell,acinar cell,adipoblast,adipocyte,amacrine cell,beta cell,capsular cell,cementocyte,chief cell,chondroblast,chondrocyte,chromaffin cell,chromophobic cell,corticotroph,delta cell,dendritic cell,enterochromaffin cell,ependymocyte,epithelium,erythroblast,erythrocyte,fibroblast,fibrocyte,follicular cell,germ cell,germinal epithelium,giant cell,glial cell,glioblast,goblet cell,gonadotroph,granulosa cell,haemocytoblast,hair cell,hepatoblast,hepatocyte,hyalocyte,interstitial cell,juxtaglomerular cell,keratinocyte,keratocyte,lemmal cell,leukocyte,luteal cell,lymphocytic stem cell,lymphoid cell,lymphoid stem cell,macroglial cell,mammotroph,mast cell,medulloblast,megakaryoblast,megakaryocyte,melanoblast,melanocyte,mesangial cell,mesothelium,metamyelocyte,monoblast,monocyte,mucous neck cell,muscle cell,myelocyte,myeloid cell,myeloid stem cell,myoblast,myoepithelial cell,myofibrobast,neuroblast,neuroepithelium,neuron,odontoblast,osteoblast,osteoclast,osteocyte,oxyntic cell,parafollicular cell,paraluteal cell,peptic cell,pericyte,phaeochromocyte,phalangeal cell,pinealocyte,pituicyte,plasma cell,platelet,podocyte,proerythroblast,promonocyte,promyeloblast,promyelocyte,pronormoblast,reticulocyte,retinal pigment epithelium,retinoblast,somatotroph,stem cell,sustentacular cell,teloglial cell,zymogenic cell,small cell,Th1,Cell Type,M<c3><bc>ller cell,primary oocyte,Claudius' cell,Th2,follicular dendritic cell,astrocyte,white,T-lymphoblast,basal cell,T-lymphocyte,helper induced T-lymphocyte:Th2,B-lymphocyte,neutrophil,oocyte,unclassifiable (Cell Type),natural killer cell,helper induced T-lymphocyte,brown,CD4+,Hensen cell,lymphocyte,cardiac muscle cell,lymphoblast,Paneth cell,alveolar macrophage,macrophage,squamous cell,oligodendrocyte,smooth muscle cell,gamete,spermatid,Schwann cell,CD34+,spermatocyte,helper induced T-lymphocyte:Th1,astroblast,eosinophil,oligodendroblast,basophil,peripheral blood mononuclear cell,histiocyte,Sertoli cell,endothelium,granulocyte,spermatozoon,Merkel cell,skeletal muscle cell,thymocyte,foam cell,ovum,secondary spermatocyte,Langerhans cell,primary spermatocyte,transitional,Purkinje cell,Kupffer cell,secondary oocyte,B-lymphoblast]' in object 'biomTrack'


chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"

  biomTrack <- BiomartGeneRegionTrack(genome = gen,
                                      chromosome = chr, start = start,
                                      end = end,  name = "ENSEMBL",
                                      fontcolor="black", groupAnnotation = "group",
                                      just.group = "above",showId=showId )


Do you have an idea to correct this error? I think that we need to discuss with EMBL to correct that, do we ?


Tiphaine


----------------------------
Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.martin at kcl.ac.uk
Fax: +44 (0) 207 188 6761

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