[Bioc-devel] Citation info still not displayed correctly for some packages
Martin Morgan
martin.morgan at roswellpark.org
Tue Aug 30 14:08:24 CEST 2016
On 08/30/2016 06:56 AM, Alexey Sergushichev wrote:
> 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.
installation is computationally costly and the the build system is taxed
for resources. We do have new hardware in the works and if that loosens
the bottleneck then yes, we would install all packages.
It is convenient to be able to get citation information from packages
that are not installed, and the 'meta' argument to readCitationFile()
seems to have been introduced for exactly this reason. As a developer I
would choose to write my CITATION file in a way that did not require the
package to be installed.
Martin
>
> 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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