Create a folder \inst and place the REFERENCES.bib in it. (see attached) Then in the R function add: #’ @references \insertRef{ENCODE_1}{PkgA}. You have to have the Rdpack installed.
-- Ioannis Vardaxis Stipendiat IMF NTNU On 07/11/16 13:49, "Ioannis Vardaxis" <ioannis.varda...@math.ntnu.no> wrote: > > > > > >On 07/11/16 13:43, "Martin Morgan" <martin.mor...@roswellpark.org> wrote: > >>On 11/07/2016 07:35 AM, Ioannis Vardaxis wrote: >>> Ok, >>> >>> Consider an R.script with a function and roxygen entries above the >>> function out the author etc. One of the entries there is the following: >>>#' >>> @references \insertRef{key}{pkg}. >>> This macro is given by the Rdpack R package for using references in the >>> help pages. Where I have created a REFERENCES.bib file placed in the >>>/inst >>> folder containing the references I want to use. >>> ³key² is the references key from the bib file and ³pkg² is my package >>>name. >> >>what minimal changes do I need to make to this package to be able to >>reproduce the warnings below? >> >>https://github.com/mtmorgan/PkgA/tree/parse-Rd-insertRef >> >>Martin >> >>> >>> Roxygen produces the expected output when I use the above macro. >>> >>> Now when I run: >>> system("R CMD build pkg²)#runs ok >>> system("R CMD BiocCheck pkg_0.99.0.tar.gz²)# gives the following : >>> >>> * This is BiocCheck, version 1.11.0. >>> * BiocCheck is a work in progress. Output and severity of issues may >>> change. >>> * Installing package... >>> * Checking for version number mismatch... >>> * Checking vignette directory... >>> * This is a software package, checking vignette directories... >>> # of chunks: 40, # of eval=FALSE: 0 (0%) >>> * Checking version number... >>> * Checking version number validity... >>> * Checking R Version dependency... >>> * Checking biocViews... >>> * Checking that biocViews are present... >>> * Checking for non-trivial biocViews... >>> * Checking that biocViews come from the same category... >>> * Checking biocViews validity... >>> * Checking for recommended biocViews... >>> * Checking build system compatibility... >>> * Checking for blank lines in DESCRIPTION... >>> * Checking for whitespace in DESCRIPTION field names... >>> * Checking that Package field matches dir/tarball name... >>> * Checking for Version field... >>> * Checking for valid maintainer... >>> * Checking unit tests... >>> * NOTE: Consider adding unit tests. We strongly encourage them. See >>> >>>http://bioconductor.org/developers/how-to/unitTesting-guidelines/. >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>A >>>na >>> lysisStatistics.Rd:106: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>e >>>xp >>> ortBS.Rd:77: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>I >>>nt >>> erPETs-class.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>I >>>nt >>> raPETs-class.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>M >>>AC >>> PET.Rd:53: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kCallerUlt.Rd:186: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kCallerUlt.Rd:188: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kFinder.Rd:97: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> ksToGRanges.Rd:68: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ET >>> Classification.Rd:138: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ET >>> sToGRanges.Rd:73: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>p >>>lo >>> t.Rd:168: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>R >>>eg >>> ionSegmentation.Rd:80: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>am >>> pleChIAPETData.bam.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETs-class.Rd:32: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsBS-class.Rd:42: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsSegm-class.Rd:37: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsSign-class.Rd:27: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>ig >>> nificanceCall.Rd:100: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>ig >>> nificanceCall.Rd:102: unknown macro '\insertRef' >>> Warning in parse_Rd(infile) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>s >>>um >>> mary.Rd:78: unknown macro '\insertRef' >>> * Checking native routine registration... >>> * Checking for deprecated package usage... >>> * Checking parsed R code in R directory, examples, vignettes... >>> * Checking for direct slot access... >>> * Checking for T... >>> Found T in R/PeakFinder.R (line 148, column 85) >>> * WARNING: Use TRUE instead of T (found in 1 files) >>> * Checking for F... >>> * Checking for browser()... >>> * Checking for <<-... >>> * Checking for library/require of MACPET... >>> * Checking DESCRIPTION/NAMESPACE consistency... >>> * Checking function lengths............................... >>> The longest function is 326 lines long >>> The longest 5 functions are: >>> ObsInfMatrix() (R/PeakFinderSubFunctions.R, line 779): 326 lines >>> AnalysisStatistics() (R/AnalysisStatistics.R, line 103): 174 >>>lines >>> FitPeaks() (R/PeakFinderSubFunctions.R, line 235): 167 lines >>> InputCheckPeakCallerUlt() (R/InputChecks.R, line 284): 152 lines >>> MergingOverlaps() (R/PeakFinderSubFunctions.R, line 460): 121 >>>lines >>> * Checking man pages... >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>A >>>na >>> lysisStatistics.Rd:106: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>e >>>xp >>> ortBS.Rd:77: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>I >>>nt >>> erPETs-class.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>I >>>nt >>> raPETs-class.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>M >>>AC >>> PET.Rd:53: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kCallerUlt.Rd:186: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kCallerUlt.Rd:188: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kFinder.Rd:97: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> ksToGRanges.Rd:68: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ET >>> Classification.Rd:138: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ET >>> sToGRanges.Rd:73: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>p >>>lo >>> t.Rd:168: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>R >>>eg >>> ionSegmentation.Rd:80: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>am >>> pleChIAPETData.bam.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETs-class.Rd:32: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsBS-class.Rd:42: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsSegm-class.Rd:37: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsSign-class.Rd:27: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>ig >>> nificanceCall.Rd:100: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>ig >>> nificanceCall.Rd:102: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>s >>>um >>> mary.Rd:78: unknown macro '\insertRef' >>> * Checking exported objects have runnable examples... >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>A >>>na >>> lysisStatistics.Rd:106: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>e >>>xp >>> ortBS.Rd:77: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>I >>>nt >>> erPETs-class.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>I >>>nt >>> raPETs-class.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>M >>>AC >>> PET.Rd:53: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kCallerUlt.Rd:186: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kCallerUlt.Rd:188: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> kFinder.Rd:97: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ea >>> ksToGRanges.Rd:68: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ET >>> Classification.Rd:138: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>P >>>ET >>> sToGRanges.Rd:73: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>p >>>lo >>> t.Rd:168: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>R >>>eg >>> ionSegmentation.Rd:80: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>am >>> pleChIAPETData.bam.Rd:23: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETs-class.Rd:32: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsBS-class.Rd:42: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsSegm-class.Rd:37: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>el >>> fPETsSign-class.Rd:27: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>ig >>> nificanceCall.Rd:100: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>S >>>ig >>> nificanceCall.Rd:102: unknown macro '\insertRef' >>> Warning in parse_Rd(manpage) : >>> >>> >>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/ >>>s >>>um >>> mary.Rd:78: unknown macro '\insertRef' >>> * Checking package NEWS... >>> * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, >>> and vignette source... >>> * NOTE: Consider shorter lines; 76 lines (0%) are > 80 characters >>> long. >>> * NOTE: Consider indenting lines with a multiple of 4 spaces; 525 >>> lines (6%) are not. >>> See http://bioconductor.org/developers/how-to/coding-style/ >>> * Checking for canned comments in man pages... >>> * Checking if package already exists in CRAN... >>> * Checking for support site registration... >>> * Maintainer is registered at support site! >>> >>> >>> Summary: >>> ERROR count: 0 >>> WARNING count: 1 >>> NOTE count: 3 >>> For detailed information about these checks, see the BiocCheck >>> vignette, available at >>> >>>http://bioconductor.org/packages/3.5/bioc/vignettes/BiocCheck/inst/doc/B >>>i >>>oc >>> Check.html#interpreting-bioccheck-output >>> >>> >>> >>> >>> >>> >> >> >>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. >
@article{ENCODE_1, Annote = {10.1038/nature11247}, Author = {ENCODE Project Consortium}, Date = {2012/09/06/print}, Date-Added = {2016-08-16 20:03:13 +0000}, Date-Modified = {2016-10-14 11:06:05 +0000}, Day = {06}, Isbn = {0028-0836}, Journal = {Nature}, L3 = {http://www.nature.com/nature/journal/v489/n7414/abs/nature11247.html#supplementary-information}, M3 = {10.1038/nature11247}, Month = {09}, Number = {7414}, Pages = {57--74}, Publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, Title = {An integrated encyclopedia of DNA elements in the human genome}, Ty = {JOUR}, Url = {http://dx.doi.org/10.1038/nature11247}, Volume = {489}, Year = {2012}, Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature11247}}
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