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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.
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.Thanks for the suggestion Diego.
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 toselect(org.Hs.eg.db, <some additional arguments).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:
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.
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] TRUEand its value is determined when it is evaluated, and evaluation triggers (by design) the .Defunct message.