On 04/06/2010 06:17 AM, Martin Morgan wrote: > On 04/06/2010 04:37 AM, Erik Wright wrote: >> Hi Martin, >> >> In Writing R Extensions it says that "the import directive imports >> all exported variables from the specified package(s).": >> >> http://cran.r-project.org/doc/manuals/R-exts.html#Specifying- imports-and-exports >> >> Since my NAMESPACE file already says import(Biostrings), do I also >> need to use importFrom(Biostrings, x, y, z) for each x, y, z function >> I want to use? > > import() is sufficient. IMHO import() defeats the developer-side purpose > of carefully controlling what functions the package sees. maybe connecting the dots a little with your other email. Perhaps you are missing importFrom(IRanges, unique)? Martin >> >> Also, where do I get the username/password that I need to access >> svn? > > username: readonly > password: readonly > > (they're on the wiki page, but made more prominent now). > > Martin >> >> Authentication realm: <https: hedgehog.fhcrc.org:443=""> The >> bioconductor Subversion Repository Password for 'me': Authentication >> realm: <https: hedgehog.fhcrc.org:443=""> The bioconductor Subversion >> Repository Username: svn: OPTIONS of >> 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codeto olsBioC': >> authorization failed: Could not authenticate to server: rejected >> Basic challenge (https://hedgehog.fhcrc.org) >> >> Thanks!, Erik >> >> >> On Apr 5, 2010, at 10:01 PM, Martin Morgan wrote: >> >>> On 04/05/2010 07:23 PM, Erik Wright wrote: >>>> Hi Sean, >>>> >>>> Here is a simple function that creates the problem: doUnique <- >>>> function(myDNAStringSet) { myDNAStringSet <- >>>> unique(myDNAStringSet) } >>>> >>>> Here is the output in the R Console: >>>>> doUnique(myDNAStringSet) >>>> Error in unique.default(myDNAStringSet) : unique() applies only >>>> to vectors >>> >>> Likely it is a NAMESPACE issue. Either doUnique is defined in >>> GoneFISHing but the NAMESPACE of GoneFISHing does not have >>> >>> importFrom(Biostrings, unique) >>> >>> or GoneFISHing defines and/or exports its own unique that masks the >>> one exported by Biostrings. If these were packages written by >>> people who didn't talk with one another then you could specify >>> >>> Biostrings::unique(myDNAStringSet) >>> >>> but likely the solution is to develop an appropriate NAMESPACE in >>> GoneFISHing. The codetoolsBioC package at >>> >>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codeto olsBioC >>> >>> >>> > accessible using svn, see >>> >>> http://wiki.fhcrc.org/bioc/SvnHowTo >>> >>> might be helpful. >>> >>> Martin >>> >>>>> sessionInfo() >>>> R version 2.10.1 (2009-12-14) i386-apple-darwin9.8.0 >>>> >>>> locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: [1] stats graphics grDevices utils >>>> datasets methods [7] base >>>> >>>> other attached packages: [1] GoneFISHing_1.0.5 RSQLite_0.8-3 >>>> DBI_0.2-5 [4] Biostrings_2.14.12 IRanges_1.4.11 >>>> >>>> loaded via a namespace (and not attached): [1] Biobase_2.6.1 >>>> >>>> Thanks again!, Erik >>>> >>>> >>>> On Apr 5, 2010, at 8:55 PM, Sean Davis wrote: >>>> >>>>> On Mon, Apr 5, 2010 at 9:51 PM, Erik Wright <eswright at="" wisc.edu=""> >>>>> wrote: >>>>>> Hi all, >>>>>> >>>>>> I am using the unique(x) function with a DNAStringSet in one >>>>>> of my own functions. Recently my function has started >>>>>> returning an error, and I am not sure what changed. The same >>>>>> line of code works fine in the R Console, just not in my >>>>>> function. I am using the function as: >>>>>> >>>>>> myDNAStringSet <- unique(myDNAStringSet) >>>>>> >>>>>> When I run my function the error returned is: >>>>>> >>>>>> Error in unique.default(myDNAStringSet) : unique() applies >>>>>> only to vectors >>>>>> >>>>>> I am guessing that the R is trying to apply the unique >>>>>> function in the base package to the DNAStringSet rather than >>>>>> using the unique function in the Biostrings package. Is >>>>>> there a solution to this? >>>>>> >>>>> >>>>> Hi, Erik. A reproducible example and sessionInfo() would be >>>>> helpful. >>>>> >>>>> Sean >>>> >>>> _______________________________________________ Bioconductor >>>> mailing list Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >>>> archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >>>> -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

On 04/06/2010 04:43 AM, Erik Wright wrote: > Hi Martin, > > When I tried using "Biostrings::unique(myDNAStringSet)", I got this error instead: > Error: 'unique' is not an exported object from 'namespace:Biostrings' > > Any ideas? My bad, sorry. IRanges::unique(). The generic is defined in IRanges, the method for DNAStringSet attached to that generic. Martin > > Thanks!, > Erik > > > On Apr 6, 2010, at 6:37 AM, Erik Wright wrote: > >> Hi Martin, >> >> In Writing R Extensions it says that "the import directive imports all exported variables from the specified package(s).": >> >> http://cran.r-project.org/doc/manuals/R-exts.html#Specifying- imports-and-exports >> >> Since my NAMESPACE file already says import(Biostrings), do I also need to use importFrom(Biostrings, x, y, z) for each x, y, z function I want to use? >> >> Also, where do I get the username/password that I need to access svn? >> >> Authentication realm: <https: hedgehog.fhcrc.org:443=""> The bioconductor Subversion Repository >> Password for 'me': >> Authentication realm: <https: hedgehog.fhcrc.org:443=""> The bioconductor Subversion Repository >> Username: svn: OPTIONS of 'https://hedgehog.fhcrc.org/bioconductor/ trunk/madman/Rpacks/codetoolsBioC': authorization failed: Could not authenticate to server: rejected Basic challenge (https://hedgehog.fhcrc.org) >> >> Thanks!, >> Erik >> >> >> On Apr 5, 2010, at 10:01 PM, Martin Morgan wrote: >> >>> On 04/05/2010 07:23 PM, Erik Wright wrote: >>>> Hi Sean, >>>> >>>> Here is a simple function that creates the problem: >>>> doUnique <- function(myDNAStringSet) { >>>> myDNAStringSet <- unique(myDNAStringSet) >>>> } >>>> >>>> Here is the output in the R Console: >>>>> doUnique(myDNAStringSet) >>>> Error in unique.default(myDNAStringSet) : >>>> unique() applies only to vectors >>> >>> Likely it is a NAMESPACE issue. Either doUnique is defined in >>> GoneFISHing but the NAMESPACE of GoneFISHing does not have >>> >>> importFrom(Biostrings, unique) >>> >>> or GoneFISHing defines and/or exports its own unique that masks the one >>> exported by Biostrings. If these were packages written by people who >>> didn't talk with one another then you could specify >>> >>> Biostrings::unique(myDNAStringSet) >>> >>> but likely the solution is to develop an appropriate NAMESPACE in >>> GoneFISHing. The codetoolsBioC package at >>> >>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codeto olsBioC >>> >>> accessible using svn, see >>> >>> http://wiki.fhcrc.org/bioc/SvnHowTo >>> >>> might be helpful. >>> >>> Martin >>> >>>>> sessionInfo() >>>> R version 2.10.1 (2009-12-14) >>>> i386-apple-darwin9.8.0 >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods >>>> [7] base >>>> >>>> other attached packages: >>>> [1] GoneFISHing_1.0.5 RSQLite_0.8-3 DBI_0.2-5 >>>> [4] Biostrings_2.14.12 IRanges_1.4.11 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.6.1 >>>> >>>> Thanks again!, >>>> Erik >>>> >>>> >>>> On Apr 5, 2010, at 8:55 PM, Sean Davis wrote: >>>> >>>>> On Mon, Apr 5, 2010 at 9:51 PM, Erik Wright <eswright at="" wisc.edu=""> wrote: >>>>>> Hi all, >>>>>> >>>>>> I am using the unique(x) function with a DNAStringSet in one of my own functions. Recently my function has started returning an error, and I am not sure what changed. The same line of code works fine in the R Console, just not in my function. I am using the function as: >>>>>> >>>>>> myDNAStringSet <- unique(myDNAStringSet) >>>>>> >>>>>> When I run my function the error returned is: >>>>>> >>>>>> Error in unique.default(myDNAStringSet) : >>>>>> unique() applies only to vectors >>>>>> >>>>>> I am guessing that the R is trying to apply the unique function in the base package to the DNAStringSet rather than using the unique function in the Biostrings package. Is there a solution to this? >>>>>> >>>>> >>>>> Hi, Erik. A reproducible example and sessionInfo() would be helpful. >>>>> >>>>> Sean >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> Martin Morgan >>> Computational Biology / Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. >>> PO Box 19024 Seattle, WA 98109 >>> >>> Location: Arnold Building M1 B861 >>> Phone: (206) 667-2793 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793