[Bioc-devel] Changes not applied in bioc source

[James W. MacDonald]

The changes you made seem to be reflected in the version of PhyloProfile
that I get:

> sortInputTaxa
function (taxonIDs = NULL, rankName, refTaxon = NULL, taxaTree = NULL)
{
    ncbiID <- fullName <- abbrName <- NULL
    if (missing(rankName))
        return("No taxonomy rank name given!")
    allMainRanks <- getTaxonomyRanks()
    if (!(rankName[1] %in% allMainRanks))
        return("Invalid taxonomy rank given!")
    if (is.null(refTaxon))
        refTaxon <- taxonNames$fullName[1]
    fullnameList <- getNameList()
    taxonNames <- getInputTaxaName(rankName, taxonIDs)
    rankNameTMP <- taxonNames$rank[taxonNames$fullName == refTaxon]


*if (rankName == "strain") {        superID <-
fullnameList$ncbiID[fullnameList$fullName]    }*
    else superID <- fullnameList$ncbiID[fullnameList$fullName ==
        refTaxon & fullnameList$rank == rankNameTMP[1]]
    Dt <- getTaxonomyMatrix()

Best,

Jim



On Thu, Dec 5, 2019 at 12:23 PM Vinh Tran <tran using bio.uni-frankfurt.de> wrote:

> Dear Bioc Team,
>
> I am maintainer of the PhyloProfile package. Last week I made a bug fixed
> for the package and push it into both release_3_10 as well as the master
> (development) branch. The build and check for both PR were successful and I
> can see the new source files with the correct version numbers in the
> corresponding bioc sites. But, it seems that, the bug is still there. I
> checked with BiocManager::install() as well as installed from the source
> files downloaded from both Bioc 3.10 and 3.11. However, the code run
> correctly when I installed the package from the github repo (with both dev
> and release branches), which is linked to the bioc git.
>
> Could you explain me what is happening? Many thanks!
>
> Best regards,
> Vinh
>
> --------------------------------
> Dr. Vinh Tran
>
> Dept. for Applied Bioinformatics
> Inst. for Cell Biology and Neuroscience
> Goethe University Frankfurt
>
> Biologicum, Room 3.209
> Phone +49 (0)69/798-42118
>
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>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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