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Question: Error: hgu95av2PFAM is defunct
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gravatar for Aditya B.
2.4 years ago by
Aditya B.40
Belgium
Aditya B.40 wrote:

Has anyone found a way to properly deal with these errors/warnings from org.Hs.eg.db? One could suggest to ignore them, which is fine when you are using the package org.Hs.eg.db interactively. However, I often import the package in my own packages and these warnings/errors are propagating into my functions. Is there any easy way to deal with this?

 

require(org.Hs.eg.db)

Error: hgu95av2PFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions.
In addition: Warning messages:
1: In (function ()  :
  hgu95av2CHR is deprecated. Please use an appropriate TxDb object or package for this kind of data.
2: In (function ()  :
  hgu95av2CHRLENGTHS is deprecated. Please use an appropriate TxDb object or package for this kind of data.
3: In (function ()  :
  hgu95av2CHRLOC is deprecated. Please use an appropriate TxDb object or package for this kind of data.
4: In (function ()  :
  hgu95av2CHRLOCEND is deprecated. Please use an appropriate TxDb object or package for this kind of data.
Error: hgu95av2PROSITE is defunct. Please use select() if you need access to PFAM or PROSITE accessions.
Error: org.Hs.egPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions.
In addition: Warning messages:
1: In (function ()  :
  org.Hs.egCHR is deprecated. Please use an appropriate TxDb object or package for this kind of data.
2: In (function ()  :
  org.Hs.egCHRLENGTHS is deprecated. Please use an appropriate TxDb object or package for this kind of data.
3: In (function ()  :
  org.Hs.egCHRLOC is deprecated. Please use an appropriate TxDb object or package for this kind of data.
4: In (function ()  :
  org.Hs.egCHRLOCEND is deprecated. Please use an appropriate TxDb object or package for this kind of data.
Error: org.Hs.egPROSITE is defunct. Please use select() if you need access to PFAM or PROSITE accessions.

 

ADD COMMENTlink modified 2.3 years ago • written 2.4 years ago by Aditya B.40

I do not see any such errors using the release version of Bioconductor (3.1). Could you give details on the system where your package is installed (i.e. give the output of sessionInfo()). This way someone may be able to suggest a solution.

ADD REPLYlink written 2.4 years ago by Diego Diez700

Thanks for the suggestion Diego.

 

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
 [1] comics_0.8.0           tidyr_0.2.0            rJava_0.9-6            reshape2_1.4.1         RDAVIDWebService_1.6.0 GOstats_2.34.0         Category_2.34.2        GO.db_3.1.2            Matrix_1.2-1           graph_1.46.0          
[11] multipanelfigure_0.5.2 mpm_1.0-22             KernSmooth_2.23-14     MASS_7.3-41            magrittr_1.5           limma_3.24.10          hgu95av2.db_3.1.3      org.Hs.eg.db_3.1.2     ggplot2_1.0.1          dplyr_0.4.2           
[21] AnnotationDbi_1.30.1   GenomeInfoDb_1.4.1     IRanges_2.2.4          S4Vectors_0.6.0        ALL_1.10.0             Biobase_2.28.0         BiocGenerics_0.14.0    RSQLite_1.0.0          DBI_0.3.1              roxygen2_4.1.1        
[31] devtools_1.8.0         BiocInstaller_1.18.3   rj_2.0.3-2            

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6            rj.gd_2.0.0-1          lattice_0.20-31        png_0.1-7              assertthat_0.1         digest_0.6.8           R6_2.1.0               tiff_0.1-5             plyr_1.8.3             lazyeval_0.1.10       
[11] curl_0.9               annotate_1.46.0        assertive_0.2-5        labeling_0.3           proto_0.3-10           splines_3.2.0          stringr_1.0.0          munsell_0.4.2          rversions_1.0.1        XML_3.98-1.2          
[21] AnnotationForge_1.10.1 grid_3.2.0             RBGL_1.44.0            xtable_1.7-4           GSEABase_1.30.2        gtable_0.1.2           git2r_0.10.1           scales_0.2.5           stringi_0.5-5          genefilter_1.50.0     
[31] xml2_0.1.1             tools_3.2.0            jpeg_0.1-8             survival_2.38-2        colorspace_1.2-6       memoise_0.2.1          knitr_1.10.5          
ADD REPLYlink written 2.4 years ago by Aditya B.40

Does your error occur in a new R session, with no packages loaded, and typing only require(org.Hs.eg.db) ? If not, then the issue is with one of the other packages you have loaded, or other commands that you are running. In any case, after the error occurs you could try the command traceback() to see how it was triggered. Somewhere in your code or the code you are using is a reference to, e.g., org.Hs.egPFAM, and it should be replaced by a reference to select(org.Hs.eg.db, <some additional arguments).

ADD REPLYlink written 2.4 years ago by Martin Morgan ♦♦ 20k

Thanks Martin, I keep having the error after loading R in a fresh session. Traceback tells me:

> traceback()
3: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
2: .Defunct(msg = msg)
1: (function () 
   {
       if (grepl("PFAM", x)) {
           bimapName <- paste0(prefix, "PFAM")
       }
       else {
           bimapName <- paste0(prefix, "PROSITE")
       }
       x <- dc[[bimapName]]
       msg = wmsg(paste0(bimapName, " is defunct. ", "Please use select() if you need access to PFAM or PROSITE accessions. \n"))
       if (interactive()) {
           .Defunct(msg = msg)
       }
   })()

My sessionInfo is:

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.1.2   RSQLite_1.0.0        DBI_0.3.1           
 [4] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.1   IRanges_2.2.4       
 [7] S4Vectors_0.6.0      Biobase_2.28.0       BiocGenerics_0.14.0 
[10] rj_2.0.3-2          

loaded via a namespace (and not attached):
[1] tools_3.2.0   rj.gd_2.0.0-1

 

My IDE platform is Architect. I did just realize that my Architect version is outdated. I will upgrade to the latest version, check whether the problem still occurs, and then report my findings here.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Aditya B.40

Probably Architect is trying to do something with each symbol in a namespace, so somehow this is Architect's problem. Technically, I think 'org.Hs.egPFAM' is an 'active binding', 

> bindingIsActive("org.Hs.egPFAM", getNamespace("org.Hs.eg.db"))
[1] TRUE

and its value is determined when it is evaluated, and evaluation triggers (by design) the .Defunct message.

 

ADD REPLYlink modified 2.3 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.4 years ago by Martin Morgan ♦♦ 20k
2
gravatar for Aditya B.
2.3 years ago by
Aditya B.40
Belgium
Aditya B.40 wrote:

The issue has been fixed in the latest version of Architect.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Aditya B.40
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