Martin, thanks a lot and thanks too for the details and the workaround for packageDescription.
best, R. On Tue, 30-08-2016, at 00:17, Martin Morgan <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) 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) >> 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 confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
