[Bioc-devel] Question about sumbition process and biocviews

Sun Nov 13 03:49:49 CET 2016

On 11/12/2016 12:28 PM, Ioannis Vardaxis wrote:
> 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.

yes, ignore the BiocCheck note. Thanks for your conscientious effort. Martin

>
>
> 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
>
>
>
>
>

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