Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file DegCre/DESCRIPTION ... OK
* preparing DegCre:
* 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
* looking to see if a data/datalist file should be added
* building DegCre_0.99.1.tar.gz

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 BiocCheckGitClone('DegCre')

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 BiocCheckVersion: 1.39.22
 BiocVersion: 3.19
 Package: DegCre
 PackageVersion: 0.99.1
 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3265/5356d9df1761ded323b33f71f092360b0a455bab/DegCre
 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...
* Checking that provided CITATION file is correctly formatted...

 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 /home/pkgbuild/packagebuilder/workers/jobs/3265/5356d9df1761ded323b33f71f092360b0a455bab/DegCre.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 DegCre/DESCRIPTION ... OK
* checking extension type ... Package
* this is package DegCre version 0.99.1
* 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 DegCre 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 ... WARNING
Dependence on R version 4.2.1 not with patchlevel 0
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [35s/35s] OK
* checking Rd files ... [0s/0s] WARNING
checkRd: (7) DexNR3C1.Rd:30: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
checkRd: (7) DexNR3C1.Rd:32: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
checkRd: (7) DexNR3C1.Rd:34: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
checkRd: (7) plotBrowserDegCre.Rd:88: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/plotgardener.html}
checkRd: (7) plotBrowserDegCre.Rd:132: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/plotgardener.html}
checkRd: (7) runDegCre.Rd:127: Invalid URL: \url{https://bioconductor.org/packages/release/bioc/html/csaw.html}
* 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [12s/12s] ERROR
Running examples in DegCre-Ex.R failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calcAUC
> ### Title: Calculate Area Under the Curve (AUC)
> ### Aliases: calcAUC
> ### Keywords: internal
> 
> ### ** Examples
> 
> # Get AUC of quadratic curve.
> x <- seq_len(10)
> y <- x^2
> auc <- calcAUC(x, y)
Error in calcAUC(x, y) : could not find function "calcAUC"
Execution halted
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running testthat.R ERROR
TIMEOUT: R CMD check exceeded 15 mins






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 BiocCheck('DegCre_0.99.1.tar.gz')

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 BiocCheckVersion: 1.39.22
 BiocVersion: 3.19
 Package: DegCre
 PackageVersion: 0.99.1
 sourceDir: /tmp/RtmpJNrPga/file2397343810c7bc/DegCre
 installDir: /tmp/RtmpJNrPga/file239734c16ec7
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3265/5356d9df1761ded323b33f71f092360b0a455bab/DegCre.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...
    * NOTE: Update R version dependency from 4.2.1 to 4.4.0.
* 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 recommended DESCRIPTION fields...
    * NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (57%).
* 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 DegCre...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 12 functions greater than 50 lines.
* Checking man page documentation...
* 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; 24 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 572 lines
      (15%) 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 | 5 NOTES

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