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

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) 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/Onc
oSimulR/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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