[Bioc-devel] Question about sumbition process and biocviews

Tue Nov 8 14:26:55 CET 2016

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.vardaxis at math.ntnu.no>
wrote:

>
>
>
>
>
>On 07/11/16 13:43, "Martin Morgan" <martin.morgan at 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
>>>
>>>
>>>
>>>
>>>
>>>
>>
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