Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/katdetectr
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 20.04.4 LTS)/x86_64   WARNINGS     WARNINGS     skipped     OK  

nebbiolo2 Summary

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Package: katdetectr
Version: 0.99.5
RVersion: 4.2
BiocVersion: 3.16
BuildCommand: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data katdetectr
BuildTime: 1 minutes 5.06 seconds
CheckCommand: BiocCheckGitClone('katdetectr') && /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2676/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.install-out.txt katdetectr_0.99.5.tar.gz && BiocCheck('katdetectr_0.99.5.tar.gz', `new-package`=TRUE)
CheckTime: 3 minutes 29.53 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 1273.46 KiB
BuildID:: katdetectr_20220623134712
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: katdetectr. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0.

nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘katdetectr/DESCRIPTION’ ... OK
* preparing ‘katdetectr’:
* checking DESCRIPTION meta-information ... OK
Warning: /tmp/RtmpZSvsXc/Rbuild35b65e4a5d2be0/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
* installing the package to process help pages
Loading required namespace: katdetectr
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘katdetectr_0.99.5.tar.gz’


nebbiolo2 CHECK output

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===============================

 BiocCheckGitClone('katdetectr')

===============================

─ BiocCheckVersion: 1.33.9
─ BiocVersion: 3.16
─ Package: katdetectr
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output 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')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘katdetectr/DESCRIPTION’ ... OK
* this is package ‘katdetectr’ version ‘0.99.5’
* 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 ‘katdetectr’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.Rcheck/00install.out’ for details.
* 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 ... [26s/26s] OK
* checking Rd files ... [9s/9s] WARNING
prepare_Rd: ./man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
* 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 ... [24s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [23s/21s]
 [23s/21s] OK
* 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: 2 WARNINGs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.Rcheck/00check.log’
for details.






===============================

 BiocCheck('katdetectr_0.99.5.tar.gz')

===============================

─ BiocCheckVersion: 1.33.9
─ BiocVersion: 3.16
─ Package: katdetectr
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr
─ installDir: /tmp/RtmpbYZllB/file35bdac1de858f2
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
* 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...
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
* Checking for library/require of katdetectr...
* 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 70 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
* 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; 249 lines (13%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 26 lines
      (1%) 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 name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 3 NOTES

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

nebbiolo2 BUILD BIN output

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