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.mor...@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.mor...@roswellpark.org <mailto:martin.mor...@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. >> >> >> >> >> This email message may contain legally privileged >> and/or...{{dropped:2}} >> >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing >> list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> >> >> > > This email message may contain legally privileged and/or confidential > information. 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