Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘scoup/DESCRIPTION’ ... OK
* preparing ‘scoup’:
* 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 ‘scoup_0.99.13.tar.gz’

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 BiocCheckGitClone('scoup')

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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3502/5f38ad083cefdfc5c1999b91713d85384c7800f9/scoup
→ BiocVersion: 3.20
→ Package: scoup
→ PackageVersion: 0.99.13
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3502/5f38ad083cefdfc5c1999b91713d85384c7800f9/scoup.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3502/5f38ad083cefdfc5c1999b91713d85384c7800f9/scoup
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 0 NOTES
i 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/3502/5f38ad083cefdfc5c1999b91713d85384c7800f9/scoup.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scoup/DESCRIPTION’ ... OK
* this is package ‘scoup’ version ‘0.99.13’
* 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 ‘scoup’ 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 ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] 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 ... [14s/14s] 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 ... [19s/19s] OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
seqWriter 6.008  0.001   6.007
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘branchWise.R’ [15s/15s]
  Running ‘ouSensitivity.R’ [10s/10s]
  Running ‘sensitiveVnVs.R’ [15s/15s]
  Running ‘siteWise.R’ [10s/10s]
  Running ‘testthat.R’ [4s/4s]
 [55s/55s] 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 ... [4s/4s] OK
* DONE

Status: OK





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 BiocCheck('scoup_0.99.13.tar.gz')

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── Installing scoup ────────────────────────────────────────────────────────────
✔ Package installed successfully
── scoup session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0hZos1/file17167b26ad45c7/scoup
→ BiocVersion: 3.20
→ Package: scoup
→ PackageVersion: 0.99.13
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3502/5f38ad083cefdfc5c1999b91713d85384c7800f9/scoup.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmp0hZos1/file17167b26ad45c7/scoup
→ installDir: /tmp/Rtmp0hZos1/file17167b3da55f95
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scoup ──────────────────────────────────────────────────
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (33%).
* Checking for pinned package versions in DESCRIPTION...
* 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 scoup...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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...
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 0 NOTES
i See the scoup.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.