[Bioc-devel] Citation info still not displayed correctly for some packages
Alexey Sergushichev
alsergbox at gmail.com
Tue Aug 30 14:15:03 CEST 2016
I see.
> As a developer I would choose to write my CITATION file in a way that did
not require the package to be installed.
I agree. I would suggest then to include this into BiocCheck, so that a
warning or at least a note could be generated, when citation is not working
properly.
--
Alexey
On Tue, Aug 30, 2016 at 3:08 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
> 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/Onc
>> oSimulR/inst/doc/OncoSimulR.html#15_citing_oncosimulr_and_
>> other_documentation
>> <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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