org.Hs.eg.db errors out and stops R (independent of RSQLite v1.0.0 or v0.11.4)
1
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@dietmarpils-7082
Last seen 8.2 years ago
Austria

hello,

loading library org.Hs.eg.db raises following error:

Error: org.Hs.egPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions.

and R stops.

i know there were some problems with the new version of RSQLite 1.0.0. but this error comes with both versons of RSQLite 1.0.0 and 0.11.4.

sessionInfo:

R version 3.1.1 (2014-07-10)
Platform: x86_64-redhat-linux-gnu (64-bit)

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

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

other attached packages:
 [1] org.Hs.eg.db_3.0.0   RSQLite_1.0.0        DBI_0.3.1           
 [4] AnnotationDbi_1.28.1 GenomeInfoDb_1.2.3   IRanges_2.0.0       
 [7] S4Vectors_0.4.0      Biobase_2.26.0       BiocGenerics_0.12.1
[10] rj_1.1.3-1          

loaded via a namespace (and not attached):
[1] rj.gd_1.1.3-1 tools_3.1.1

 

org.Hs.eg.db • 2.2k views
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@vincent-j-carey-jr-4
Last seen 15 days ago
United States

Please do read the posting guide.  You have not given a reproducible example.  I can generate the message you've reported

by referring to org.Hs.egPFAM.  There is a hint as to how to proceed.  First, do not make references to org.Hs.egPFAM.  Second, consider how to replace old code that uses org.Hs.egPFAM with code that will succeed.  Read about "select()", which is in AnnotationDbi package.

You'll need to get familiar with organismDb operations

> sort(columns(org.Hs.eg.db))

 [1] "ACCNUM"       "ALIAS"        "CHR"          "CHRLOC"       "CHRLOCEND"   

 [6] "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS" "ENTREZID"     "ENZYME"      

[11] "EVIDENCE"     "EVIDENCEALL"  "GENENAME"     "GO"           "GOALL"       

[16] "IPI"          "MAP"          "OMIM"         "ONTOLOGY"     "ONTOLOGYALL" 

[21] "PATH"         "PFAM"         "PMID"         "PROSITE"      "REFSEQ"      

[26] "SYMBOL"       "UCSCKG"       "UNIGENE"      "UNIPROT"    

 

> select(org.Hs.eg.db, columns="PFAM", keys="1001", keytype="ENTREZID")

  ENTREZID    PFAM

1     1001 PF01049

2     1001 PF00028

Warning message:

In .generateExtraRows(tab, keys, jointype) :

  'select' resulted in 1:many mapping between keys and return rows

> sessionInfo()

R version 3.1.1 (2014-07-10)

Platform: x86_64-apple-darwin13.1.0 (64-bit)


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

 [1] parallel  stats4    stats     graphics  grDevices datasets  utils    

 [8] tools     methods   base     


other attached packages:

 [1] org.Hs.eg.db_3.0.0   RSQLite_1.0.0        DBI_0.3.1.9000      

 [4] AnnotationDbi_1.28.1 GenomeInfoDb_1.2.2   IRanges_2.0.0       

 [7] S4Vectors_0.4.0      Biobase_2.26.0       BiocGenerics_0.12.0 

[10] rmarkdown_0.3.8      knitr_1.7            weaver_1.32.0       

[13] codetools_0.2-9      digest_0.6.4         BiocInstaller_1.16.1


loaded via a namespace (and not attached):

[1] evaluate_0.5.5  formatR_1.0     htmltools_0.2.6 stringr_0.6.2  

 

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Entering edit mode

okay, you are right. the problem is only in the StatET plugin (http://www.walware.de/goto/statet) for eclipse.

if loading the library "org.Hs.eg.db " in an R console makes no problems, but loading the library inside eclipse stops R raising the above mentioned error. it has to do how eclipse/statet runs R ...

 

the reproducible example is only to load the library inside eclipse/statet.

require(org.Hs.eg.db )

 

Eclipse SDK

Version: 3.8.2
Build id: M20130131-0800

StatET 3.2.2
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Entering edit mode

I got this information from Tobias Verbeke of OpenAnalytics:

This has been fixed some time ago in
http://download.walware.de/rj-2.0/src/contrib/rj_2.0.3-1.tar.gz

 

I did test and it actually fixes this problem (I mean the crash of the statET console).

Hope it helps.

 

 

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