[Bioc-devel] Citation info still not displayed correctly for some packages

Martin,

Won't it be easier to include actually installation for each package in
the build script, but into a separate temp folder? Thus every package
will be isntalled and citation() should work fine.

Best,
Alexey

On Tue, Aug 30, 2016 at 1:17 AM, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>
wrote:

    On 08/29/2016 05:40 PM, Ramon Diaz-Uriarte wrote:


        Dear All,

        At least for some packages
        (http://bioconductor.org/packages/devel/bioc/html/OncoSimulR.html <http://bioconductor.org/packages/devel/bioc/html/OncoSimulR.html>)
        the
        citation info is still not displayed correctly. I double checked
        installing
        from BioC just now, and the citation is not the one shown in the
        landing
        page on BioC;  the vignette
        (http://www.bioconductor.org/packages/3.4/bioc/vignettes/OncoSimulR/inst/doc/OncoSimulR.html#15_citing_oncosimulr_and_other_documentation
        <http://www.bioconductor.org/packages/3.4/bioc/vignettes/OncoSimulR/inst/doc/OncoSimulR.html#15_citing_oncosimulr_and_other_documentation>)
        also shows the output from citation("OncoSimulR"), which again
        is not the
        same as in the BioC page.

        I think that at least in this case the citation info has not
        been updated
        in the last two builds.


    biocViews (which processes the citations) was updated in the last
    build, it should be used in the next build. I'll keep an eye on it.

    OncoSimulR seems to have a valid CITATION file.

    For a little more information, there are a number of outstanding
    problems with citation processing. Citation information is added
    using readCitationFile() applied to the package _source_, rather
    than the installed package. This is because some packages (those
    without any reverse dependencies) are never actually installed on
    the build system -- they are built into a tar ball and checked, and
    the built tarball is used to generate citation information.

    This means that CITATION files that do things like
    packageDescription("foo") fail, because "foo" is not installed. The
    current solution is to rely on the 'meta' argument to
    readCitationFile(), so CITATION files can replace lines like

        version <- packageDescription("foo")$Version

    with

        version <- meta$Version

    or more flexibly

        if (!exists("meta") || is.null(meta))
            meta <- packageDescription("nlme")

    and one can test that one has a valid CITATION file with

        descr = packageDescription("pkg-name", "/path/to/pkg")
        readCitationFile("/path/to/pkg/pkg-name/inst/CITATION", descr)

    There are related problems, e.g., with use of the knitrcitation or
    omitting the required field 'textVersion', and a bug (generating a
    warning, but apparently not compromising the citation) when a url or
    doi field contains an encoded url, as

    > xx <<- "\\url{http://foo%3Fbar}"; con <- textConnection(xx);

    parse_Rd(con, fragment=TRUE, permissive=TRUE)
    Warning in withCallingHandlers(.External2(C_parseRd, tcon, srcfile,
    "UTF-8",  :
      <connection>:2: unexpected END_OF_INPUT '
    '
    \url{http://foo%3Fbar}
    }

    Here is a summary of the issues I know about; the 'err' and 'warn'
    labels refer to how R reports the initial error; the
    packageDescription 'warnings' actually mean that the CITATION file
    may not be parsed by the build system.

    ## > names(err)
    ## [1] "bioassayR"    # knitcitations()
    ## [2] "ChemmineR"    # knitcitations()
    ## [3] "clippda"      # missing textVersion
    ## [4] "eiR"          # knitcitations()
    ## [5] "fmcsR"        # knitcitations()
    ## [6] "metagenomeSeq"# packageVersion()
    ## [7] "SomatiCA"     # missing textVersion
    ## > names(warn)
    ##  [1] "ALDEx2"      # url encoding '10.1371%2'
    ##  [2] "aroma.light" # print(citn, style="html"); trailing } in title
    ##  [3] "birte"       # packageDescription()
    ##  [4] "BRAIN"       # packageDescription()
    ##  [5] "ChAMP"       # doi encoding %2F
    ##  [6] "ChIPpeakAnno"# url encoding %2F
    ##  [7] "CoGAPS"      # packageDescription()
    ##  [8] "derfinderHelper"  # packageDescription()
    ##  [9] "derfinderPlot"
    ## [10] "destiny"     # packageDescription()
    ## [11] "fabia"       # packageDescription()
    ## [12] "flowFP"      # packageDescription()
    ## [13] "GenomicAlignments"# url encoding
    ## [14] "GenomicFeatures"  # url encoding
    ## [15] "GenomicRanges"    # url encoding
    ## [16] "Genominator" # packageDescription()
    ## [17] "GOSim"       # packageDescription()
    ## [18] "GSRI"        # packageDescription()
    ## [19] "hapFabia"    # packageDescription()
    ## [20] "kebabs"      # packageDescription()
    ## [21] "manta"       # packageDescription()
    ## [22] "mdgsa"       # url encoding
    ## [23] "MEDME"       # packageDescription()
    ## [24] "miRLAB"      # url encoding
    ## [25] "networkBMA"  # packageDescription()
    ## [26] "pcaGoPromoter" # url encoding
    ## [27] "podkat"      # packageDescription()
    ## [28] "procoil"     # packageDescription()
    ## [29] "Rbowtie"     # packageDescription()
    ## [30] "Rcade"       # packageDescription()
    ## [31] "Rchemcpp"    # packageDescription()
    ## [32] "rfPred"      # packageDescription()
    ## [33] "sigaR"       # packageDescription()
    ## [34] "SIM"         # packageDescription()
    ## [35] "SWATH2stats" # url encoding
    ## [36] "TEQC"        # packageDescription()



        Best,


        R.




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