Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘VSOLassoBag/DESCRIPTION’ ... OK
* preparing ‘VSOLassoBag’:
* 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
* building ‘VSOLassoBag_0.99.0.tar.gz’

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 BiocCheckGitClone('VSOLassoBag')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: VSOLassoBag
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2834/VSOLassoBag_20230222173713/VSOLassoBag
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2834/VSOLassoBag_20230222173713/VSOLassoBag.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VSOLassoBag/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VSOLassoBag’ version ‘0.99.0’
* 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 ‘VSOLassoBag’ can be installed ... 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [24s/24s] NOTE
VSOLassoBag : boot.once : boot.indiv: no visible global function
  definition for ‘is’
VSOLassoBag: no visible global function definition for ‘is’
singleFilter: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'VSOLassoBag.Rd':
  \examples lines wider than 100 characters:
     VSOLassoBag(ExpressionData, "label", bootN=100, a.family="binomial", bagFreq.sigMethod="PST", do.plot = FALSE, plot.freq = "not")
     VSOLassoBag(ExpressionData, "label", bootN=100, a.family="binomial", bagFreq.sigMethod="CEP", do.plot = FALSE, plot.freq = "not")
     VSOLassoBag(ExpressionData, "y", bootN=100, a.family="binomial", bagFreq.sigMethod="PST", do.plot = FALSE, plot.freq = "not")
     VSOLassoBag(ExpressionData, "y", bootN=100, a.family="binomial", bagFreq.sigMethod="CEP", do.plot = FALSE, plot.freq = "not")
     VSOLassoBag(ExpressionData, c("time","status"), bootN=100, a.family="binomial", bagFreq.sigMethod="PST", do.plot = FALSE, plot.freq = " ... [TRUNCATED]
     VSOLassoBag(ExpressionData, c("time","status"), bootN=100, a.family="binomial", bagFreq.sigMethod="CEP", do.plot = FALSE, plot.freq = " ... [TRUNCATED]
     VSOLassoBag(ExpressionData, c("multi.y.D_1","multi.y.D_2"), bootN=100, a.family="binomial", bagFreq.sigMethod="PST", do.plot = FALSE, p ... [TRUNCATED]
     VSOLassoBag(ExpressionData, c("multi.y.D_1","multi.y.D_2"), bootN=100, a.family="binomial", bagFreq.sigMethod="CEP", do.plot = FALSE, p ... [TRUNCATED]
     VSOLassoBag(ExpressionData, c("multi.label.D_1","multi.label.D_2"), bootN=100, a.family="binomial", bagFreq.sigMethod="PST", do.plot =  ... [TRUNCATED]
     VSOLassoBag(ExpressionData, c("multi.label.D_1","multi.label.D_2"), bootN=100, a.family="binomial", bagFreq.sigMethod="CEP", do.plot =  ... [TRUNCATED]
     VSOLassoBag(ExpressionData, "pois"), bootN=100, a.family="binomial", bagFreq.sigMethod="PST", do.plot = FALSE, plot.freq = "not")
     VSOLassoBag(ExpressionData, "pois"), bootN=100, a.family="binomial", bagFreq.sigMethod="CEP", do.plot = FALSE, plot.freq = "not")
     VSOLassoBag(ExpressionData, "y", bootN=100, a.family="binomial", bagFreq.sigMethod="PST", do.plot = FALSE, plot.freq = "not",bagFreq.si ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘test.df’
Undocumented data sets:
  ‘test.df’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [154s/154s] OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
VSOLassoBag 143.596  1.532 145.124
* 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 ... [5s/5s] OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2834/VSOLassoBag_20230222173713/VSOLassoBag.Rcheck/00check.log’
for details.






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 BiocCheck('VSOLassoBag_0.99.0.tar.gz')

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─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: VSOLassoBag
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp7roL3p/file10cb345380665/VSOLassoBag
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp7roL3p/file10cb3cb9c16c
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2834/VSOLassoBag_20230222173713/VSOLassoBag.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 3.6.0 to 4.3.0.
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Survival
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* 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 for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of VSOLassoBag...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 2 times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 48 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 20% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 248 lines (11%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 869 lines
      (38%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
    * WARNING: The package already exists on CRAN. Packages submitted
      to Bioconductor must be removed from CRAN before the next
      Bioconductor release.
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
1 ERRORS | 1 WARNINGS | 14 NOTES

See the VSOLassoBag.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir VSOLassoBag_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘VSOLassoBag’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (VSOLassoBag)