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

[Alexey Sergushichev]

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> 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) 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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