[Bioc-devel] Question about sumbition process and biocviews

Mon Nov 7 13:35:33 CET 2016

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.

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

-- 
Ioannis Vardaxis

Stipendiat IMF
NTNU

On 07/11/16 13:24, "Martin Morgan" <martin.morgan at roswellpark.org> wrote:

>On 11/07/2016 05:26 AM, Ioannis Vardaxis wrote:
>> Hi,
>>
>> I was Rechecking the  package folder and not the built version. Now it
>> works, thanks.
>>
>>
>> The warning I get for the references is the following:
>> Warning in parse_Rd(manpage) :
>>
>> 
>>/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpNOtV3V/MACPET/man/s
>>um
>> mary.Rd:78: unknown macro '\insertRef'
>>
>>
>
>you'll have to provide more detail here about what you're doing and
>where the warning is being generated. \insertRef is not part of base R
>so I guess it's from some package you're using. You say biocCheck but
>maybe you mean BiocCheck. BiocCheck performs a number of checks so of
>course it would help to know the specific check that causes the warning.
>It would also help to have a simple reproducible example or at least a
>simple help page that fully illustrates the use that you are trying for.
>
>Martin
>
>
>>
>>
>
>
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