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

[Martin Morgan]

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/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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