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

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