Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘OGRE/DESCRIPTION’ ... OK
* preparing ‘OGRE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘OGRE_0.99.4.tar.gz’

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 BiocCheckGitClone('OGRE')

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This is BiocCheckGitClone version 1.31.19. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2431/42791c35fbb275302c46bdfffc695183178065e6/OGRE.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OGRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OGRE’ version ‘0.99.4’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OGRE’ can be installed ... [28s/28s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [29s/29s] NOTE
gvizPlot : <anonymous>: warning in AnnotationTrack(start =
  tmp$subjStart, end = tmp$subjEnd, chr = tmp$subjChr, name = x, id =
  regionLabels, fontsize.title = 24, featureAnnotation = "id",
  fontcolor.title = "black", fontcolor = "black", fontcolor.group =
  "black", fontcolor.item = "black", rotation.item = 20): partial
  argument match of 'chr' to 'chromosome'
addDataSetFromHub: no visible global function definition for
  'keepStandardChromosomes'
addDataSetFromHub: no visible global function definition for
  'seqlevelsStyle<-'
fOverlaps: no visible binding for global variable 'queryID'
fOverlaps: no visible binding for global variable 'subjID'
fOverlaps: no visible binding for global variable 'subjType'
gvizPlot : <anonymous>: no visible binding for global variable
  'subjType'
gvizPlot : <anonymous>: no visible binding for global variable
  'queryID'
sumPlot: no visible binding for global variable 'xtext'
sumPlot: no visible binding for global variable 'lab'
Undefined global functions or variables:
  keepStandardChromosomes lab queryID seqlevelsStyle<- subjID subjType
  xtext
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/61s] OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
addDataSetFromHub 15.206  1.557  31.841
gvizPlot           4.420  0.142  10.666
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2431/42791c35fbb275302c46bdfffc695183178065e6/OGRE.Rcheck/00check.log’
for details.






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 BiocCheck('OGRE_0.99.4.tar.gz')

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This is BiocCheck version 1.31.19. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 9 object(s) are initialized. Maybe
      they are part of a data set loaded with data(), or perhaps part
      of an object referenced in with() or within().
    function (object)
      addDataSetFromHub (keepStandardChromosomes)
      addDataSetFromHub (seqlevelsStyle<-)
      fOverlaps (queryID)
      fOverlaps (subjID)
      fOverlaps (subjType)
      gvizPlot  (subjType)
      gvizPlot  (queryID)
      sumPlot (xtext)
      sumPlot (lab)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
    * NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* 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 if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of OGRE...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/methods.R (line 163, column 9)
        R/methods.R (line 170, column 23)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        methods.R (line 227, column 42)
        methods.R (line 416, column 32)
        methods.R (line 418, column 27)
        methods.R (line 418, column 52)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        = in R/methods.R (line 28, column 10)
        = in R/methods.R (line 53, column 12)
        = in R/methods.R (line 61, column 10)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths    * NOTE: Recommended function length <= 50 lines.
      There are 1 functions > 50 lines.
      The longest 5 functions are:
        sumPlot() (R/methods.R, line 142): 54 lines
        gvizPlot() (R/methods.R, line 219): 49 lines
        fOverlaps() (R/methods.R, line 89): 39 lines
        addDataSetFromHub() (R/methods.R, line 315): 36 lines
        OGREDataSetFromDir() (R/main.R, line 16): 24 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 101 lines (10%) are > 80 characters
      long.
    First 6 lines:
      R/main.R:3 #' Builds a `OGREDataset` from user specified directories co...
      R/main.R:4 #' A `OGREDataset` is a `GenomicRangesList` with stores data...
      R/main.R:5 #' @param queryFolder A \code{character} path pointing to th...
      R/main.R:6 #' @param subjectFolder A \code{character} path pointing to ...
      R/main.R:13 #' mySubjectFolder <- file.path(system.file('extdata', pack...
      R/main.R:14 #' myOGRE <- OGREDataSetFromDir(queryFolder=myQueryFolder,s...
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    First 2 lines:
      vignettes/OGRE.Rmd:38 ```	
      vignettes/OGRE.Rmd:45 	install.packages("BiocManager")
    * NOTE: Consider multiples of 4 spaces for line indents, 226
      lines(23%) are not.
    First 6 lines:
      R/main.R:17   assertthat::assert_that(!is.null(queryFolder),msg="Please...
      R/main.R:18   assertthat::assert_that(!is.null(subjectFolder),msg="Plea...
      R/main.R:19   assertthat::assert_that(is(queryFolder,"character"),msg="...
      R/main.R:20   assertthat::assert_that(is(subjectFolder,"character"),msg...
      R/main.R:21   message("Initializing OGREDataSet... ")
      R/main.R:22   OGREDataSet <- GRangesList()
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 10
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output