Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file DeProViR/DESCRIPTION ... OK
* preparing DeProViR:
* 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 DeProViR_0.99.29.tar.gz

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 BiocCheckGitClone('DeProViR')

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 BiocCheckVersion: 1.39.23
 BiocVersion: 3.19
 Package: DeProViR
 PackageVersion: 0.99.29
 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3148/dab9e14e6d194fa3331656e6783658987e0b7d55/DeProViR
 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...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

 BiocCheck results 
0 ERRORS | 0 WARNINGS | 1 NOTES

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




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 R CMD CHECK

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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3148/dab9e14e6d194fa3331656e6783658987e0b7d55/DeProViR.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file DeProViR/DESCRIPTION ... OK
* checking extension type ... Package
* this is package DeProViR version 0.99.29
* 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 serialization versions ... OK
* checking whether package DeProViR 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 ... NOTE
License stub is invalid DCF.
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [11s/11s] OK
* 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 files in vignettes ... OK
* checking examples ... [226s/225s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
encodeHostSeq    57.349  1.661  58.907
predInteractions 55.444  0.648  55.271
encodeViralSeq   49.662  0.684  50.343
gloveImport      49.176  0.572  49.744
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running runTests.R [63s/63s]
 [63s/63s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [2s/2s] OK
* DONE

Status: 1 NOTE
See
  /home/pkgbuild/packagebuilder/workers/jobs/3148/dab9e14e6d194fa3331656e6783658987e0b7d55/DeProViR.Rcheck/00check.log
for details.






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 BiocCheck('DeProViR_0.99.29.tar.gz')

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 BiocCheckVersion: 1.39.23
 BiocVersion: 3.19
 Package: DeProViR
 PackageVersion: 0.99.29
 sourceDir: /tmp/RtmpBiNtsf/file3348426fbf24d7/DeProViR
 installDir: /tmp/RtmpBiNtsf/file334842771fa998
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3148/dab9e14e6d194fa3331656e6783658987e0b7d55/DeProViR.BiocCheck
 platform: unix
 isTarBall: TRUE

* Installing package...
* 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...
* 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (8%).
* Checking for pinned package versions in DESCRIPTION...
* 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 DeProViR...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 3 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 methods overwritten by 'fmsb':
  method    from
  print.roc pROC
  plot.roc  pROC
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 5 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 616 lines
      (52%) 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...
* 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 is in the Support Site Watched Tags.

 BiocCheck results 
0 ERRORS | 0 WARNINGS | 9 NOTES

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