[Bioc-devel] Question about sumbition process and biocviews

Sat Nov 12 18:28:37 CET 2016

Hi,

I don¹t get any error in R CMD build pkg at all, I only get a note in the
BiocCheck that the macro '\insertRef¹ is unknown. However it is only a
note, I have no errors nor warnings.
Is it ok if I submit the package like that? I can¹t  find any solution.

Output:

> system("R CMD check --no-build-vignettes pkg_0.99.0.tar.gz")
* using log directory
Œ/Users/vardaxis/Desktop/NTNU/NTNU.9.10.2014/Doktorgrad/Algoritmer/pkg.Rche
ck¹
* using R Under development (unstable) (2016-10-20 r71540)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option Œ--no-build-vignettes¹
* checking for file Œpkg/DESCRIPTION¹ ... OK
* this is package Œpkg¹ version Œ0.99.0¹
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package Œpkg¹ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking Œbuild¹ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ...
OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies
... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under Œinst/doc¹ ... OK
* checking installed files from Œinst/doc¹ ... OK
* checking files in Œvignettes¹ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in Œinst/doc¹ ... OK
* checking running R code from vignettes ...
   Œpkg.Rmd¹ using ŒUTF-8¹ ... OK
 NONE
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

While for BiocCheck:

> system("R CMD BiocCheck pkg_0.99.0.tar.gz")
* 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//RtmpEV2Sc8/pkg/man/Analys
isStatistics.Rd:114: unknown macro '\insertRef'
Warning in parse_Rd(infile) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/export
BS.Rd:78: unknown macro '\insertRef'
Warning in parse_Rd(infile) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/InterP
ETs-class.Rd:23: unknown macro '\insertRef'
Warning in parse_Rd(infile) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/IntraP
ETs-class.Rd:23: unknown macro '\insertRef'
Warning in parse_Rd(infile) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/MACPET
.Rd:76: unknown macro '\insertRef'
Warning in parse_Rd(infile) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/PeakCa
llerUlt.Rd:186: unknown macro '\insertRef'
Warning in parse_Rd(infile) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/PeakCa
llerUlt.Rd:188: 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...
* Checking for F...
* Checking for browser()...
* Checking for <<-...
* Checking for library/require of pkg...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking function lengths...............................
  The longest function is 302 lines long
  The longest 5 functions are:
      InfMatrix() (R/PeakFinderSubFunctions.R, line 813): 302 lines
      FitPeaks() (R/PeakFinderSubFunctions.R, line 212): 176 lines
      AnalysisStatistics() (R/AnalysisStatistics.R, line 111): 174 lines
      InputCheckPeakCallerUlt() (R/InputChecks.R, line 284): 152 lines
      RegionSegmentation() (R/RegionSegmentation.R, line 85): 139 lines
* Checking man pages...
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/Analys
isStatistics.Rd:114: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/export
BS.Rd:78: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/InterP
ETs-class.Rd:23: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/IntraP
ETs-class.Rd:23: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/MACPET
.Rd:76: unknown macro '\insertRef'
* Checking exported objects have runnable examples...
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/Analys
isStatistics.Rd:114: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/export
BS.Rd:78: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/InterP
ETs-class.Rd:23: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :

/var/folders/6n/6y8cjthx4sb0hk5k5w8q3lw40000gn/T//RtmpEV2Sc8/pkg/man/IntraP
ETs-class.Rd:23: unknown macro '\insertRef'
* Checking package NEWS...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 95 lines (1%) 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: 0
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 08/11/16 14:43, "Martin Morgan" <martin.morgan at roswellpark.org> wrote:

>On 11/08/2016 08:26 AM, Ioannis Vardaxis wrote:
>>
>> Create a folder \inst and place the REFERENCES.bib in it. (see attached)
>> Then in the R function add: #¹ @references \insertRef{ENCODE_1}{PkgA}.
>> You have to have the Rdpack installed.
>
>when I do that (see
>https://github.com/mtmorgan/PkgA/tree/parse-Rd-insertRef) and run R CMD
>build I see
>
>$ R CMD build PkgA
>* checking for file 'PkgA/DESCRIPTION' ... OK
>* preparing 'PkgA':
>* checking DESCRIPTION meta-information ... OK
>Warning: /tmp/RtmpFDYMzj/Rbuild2deb22881ea6/PkgA/man/fun.Rd:13: unknown
>macro '\insertRef'
>* checking for LF line-endings in source and make files
>* checking for empty or unneeded directories
>* building 'PkgA_0.0.1.tar.gz'
>
>so the problem reported by BiocCheck is already visible in R CMD build.
>
>Consulting the vignette for Rdpack
>
>https://cran.r-project.org/web/packages/Rdpack/vignettes/Inserting_bibtex_
>references.pdf
>
>I see that the solution is to add the line
>
>RdMacros: Rdpack
>
>to the DESCRIPTION file. I disagree with the package author that the
>Rdpack package does not need to be in the Suggests: field; if it were
>not there then how would something like the Bioconductor build system
>know that it needed to have the Rdpack available when the package is
>built?
>
>I updated the github repo with correct package.
>
>Martin
>
>
>>
>>
>
>
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