Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/zenith
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   OK     OK     skipped     OK  
lconway macOS 12.2.1 Monterey/x86_64   OK     OK     OK     OK  

nebbiolo2 Summary

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Package: zenith
Version: 0.99.8
RVersion: 4.2
BiocVersion: 3.16
BuildCommand: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data zenith
BuildTime: 0 minutes 49.85 seconds
CheckCommand: BiocCheckGitClone('zenith') && /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2630/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith.install-out.txt zenith_0.99.8.tar.gz && BiocCheck('zenith_0.99.8.tar.gz', `new-package`=TRUE)
CheckTime: 2 minutes 51.57 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 4355.48 KiB
BuildID:: zenith_20220621173528
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: zenith. 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 ‘zenith/DESCRIPTION’ ... OK
* preparing ‘zenith’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: zenith
* 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 ‘zenith_0.99.8.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff’


nebbiolo2 CHECK output

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

 BiocCheckGitClone('zenith')

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

─ BiocCheckVersion: 1.33.8
─ BiocVersion: 3.16
─ Package: zenith
─ PackageVersion: 0.99.8
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith
─ 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/2630/72f870e31814680094205415ec98261862774ee7/zenith.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 ‘zenith/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘zenith’ version ‘0.99.8’
* 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 ... NOTE
Found the following non-portable file paths:
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘zenith’ 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 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 ... [21s/21s] OK
* checking Rd files ... [7s/7s] 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 ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith.Rcheck/00check.log’
for details.






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

 BiocCheck('zenith_0.99.8.tar.gz')

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

─ BiocCheckVersion: 1.33.8
─ BiocVersion: 3.16
─ Package: zenith
─ PackageVersion: 0.99.8
─ sourceDir: /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith
─ installDir: /tmp/Rtmp7FgPwY/file15cc5a2f7202a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith.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...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(infile) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(infile) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:86: unknown macro '\insertRef'
* Checking for library/require of zenith...
* Checking coding practice...
    * 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 19 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:86: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:86: unknown macro '\insertRef'
    * NOTE: Consider adding runnable examples to man pages that
      documentexported objects.
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /tmp/Rtmp7FgPwY/file15cc5a7230c5a6/zenith/man/zenith.Rd:86: 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; 100 lines (5%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 223 lines (11%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 196 lines
      (10%) 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 | 7 NOTES

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

nebbiolo2 BUILD BIN output

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lconway Summary

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Package: zenith
Version: 0.99.8
RVersion: 4.2
BiocVersion: 3.16
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data zenith
BuildTime: 0 minutes 50.42 seconds
CheckCommand: BiocCheckGitClone('zenith') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2630/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith.install-out.txt zenith_0.99.8.tar.gz && BiocCheck('zenith_0.99.8.tar.gz', `new-package`=TRUE)
CheckTime: 2 minutes 54.99 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh zenith_0.99.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 21.33 seconds
PackageFileSize: 4354.40 KiB
BuildID:: zenith_20220621173528
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: zenith. Starting Build package. Starting Check package. Starting Build 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. Build Package status: 0.

lconway BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘zenith/DESCRIPTION’ ... OK
* preparing ‘zenith’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
Loading required namespace: zenith
* 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 ‘zenith_0.99.8.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff’


lconway CHECK output

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

 BiocCheckGitClone('zenith')

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

─ BiocCheckVersion: 1.33.8
─ BiocVersion: 3.16
─ Package: zenith
─ PackageVersion: 0.99.8
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith
─ 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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zenith/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘zenith’ version ‘0.99.8’
* 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 ... NOTE
Found the following non-portable file paths:
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
  zenith/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘zenith’ 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 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 ... [20s/21s] OK
* checking Rd files ... [7s/7s] 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 ... [16s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith.Rcheck/00check.log’
for details.






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

 BiocCheck('zenith_0.99.8.tar.gz')

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

─ BiocCheckVersion: 1.33.8
─ BiocVersion: 3.16
─ Package: zenith
─ PackageVersion: 0.99.8
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e125e3ed1
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2630/72f870e31814680094205415ec98261862774ee7/zenith.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...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:86: unknown macro '\insertRef'
* Checking for library/require of zenith...
* Checking coding practice...
    * 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 19 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:86: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:86: unknown macro '\insertRef'
    * NOTE: Consider adding runnable examples to man pages that
      documentexported objects.
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:55: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith_gsa-methods.Rd:101: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:84: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmplt4Bjf/file233e38294f67/zenith/man/zenith.Rd:86: 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; 100 lines (5%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 223 lines (11%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 196 lines
      (10%) 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 | 7 NOTES

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

lconway BUILD BIN output

[top]

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir zenith_0.99.8.tar.gz'
>>>>>>> 

* installing *source* package ‘zenith’ ...
** using staged installation
** R
** 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 (zenith)