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 < [email protected]> 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. >> >> >> > > This email message may contain legally privileged and/or...{{dropped:2}} > > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
