[Bioc-devel] Question about sumbition process and biocviews

Mon Nov 7 13:43:17 CET 2016

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/Ana
> lysisStatistics.Rd:106: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/exp
> ortBS.Rd:77: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Int
> erPETs-class.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Int
> raPETs-class.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/MAC
> PET.Rd:53: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kCallerUlt.Rd:186: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kCallerUlt.Rd:188: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kFinder.Rd:97: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> ksToGRanges.Rd:68: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/PET
> Classification.Rd:138: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/PET
> sToGRanges.Rd:73: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/plo
> t.Rd:168: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Reg
> ionSegmentation.Rd:80: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sam
> pleChIAPETData.bam.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETs-class.Rd:32: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsBS-class.Rd:42: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsSegm-class.Rd:37: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsSign-class.Rd:27: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sig
> nificanceCall.Rd:100: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sig
> nificanceCall.Rd:102: unknown macro '\insertRef'
> Warning in parse_Rd(infile) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/sum
> 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/Ana
> lysisStatistics.Rd:106: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/exp
> ortBS.Rd:77: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Int
> erPETs-class.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Int
> raPETs-class.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/MAC
> PET.Rd:53: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kCallerUlt.Rd:186: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kCallerUlt.Rd:188: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kFinder.Rd:97: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> ksToGRanges.Rd:68: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/PET
> Classification.Rd:138: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/PET
> sToGRanges.Rd:73: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/plo
> t.Rd:168: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Reg
> ionSegmentation.Rd:80: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sam
> pleChIAPETData.bam.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETs-class.Rd:32: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsBS-class.Rd:42: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsSegm-class.Rd:37: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsSign-class.Rd:27: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sig
> nificanceCall.Rd:100: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sig
> nificanceCall.Rd:102: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/sum
> 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/Ana
> lysisStatistics.Rd:106: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/exp
> ortBS.Rd:77: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Int
> erPETs-class.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Int
> raPETs-class.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/MAC
> PET.Rd:53: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kCallerUlt.Rd:186: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kCallerUlt.Rd:188: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> kFinder.Rd:97: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Pea
> ksToGRanges.Rd:68: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/PET
> Classification.Rd:138: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/PET
> sToGRanges.Rd:73: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/plo
> t.Rd:168: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Reg
> ionSegmentation.Rd:80: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sam
> pleChIAPETData.bam.Rd:23: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETs-class.Rd:32: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsBS-class.Rd:42: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsSegm-class.Rd:37: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sel
> fPETsSign-class.Rd:27: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sig
> nificanceCall.Rd:100: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/Sig
> nificanceCall.Rd:102: unknown macro '\insertRef'
> Warning in parse_Rd(manpage) :
>
> /var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/sum
> 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/Bioc
> Check.html#interpreting-bioccheck-output
>
>
>
>
>
>

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