Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file bugphyzz/DESCRIPTION ... OK
* preparing bugphyzz:
* 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
Omitted LazyData from DESCRIPTION
* building bugphyzz_0.99.6.tar.gz

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 BiocCheckGitClone('bugphyzz')

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 sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3367/9dc230555d8581b5a4a198f81ff7d92d9c0c2ca5/bugphyzz
 BiocVersion: 3.20
 Package: bugphyzz
 PackageVersion: 0.99.6
 BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3367/9dc230555d8581b5a4a198f81ff7d92d9c0c2ca5/bugphyzz.BiocCheck
 BiocCheckVersion: 1.41.12
 sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3367/9dc230555d8581b5a4a198f81ff7d92d9c0c2ca5/bugphyzz
 installDir: NULL
 isTarBall: FALSE
 platform: unix
i Checking valid files...
 Checking valid files... [8ms]

i Checking for stray BiocCheck output folders...
 Checking for stray BiocCheck output folders... [10ms]

i Checking for inst/doc folders...
 Checking for inst/doc folders... [5ms]

i Checking if DESCRIPTION is well formatted...
 Checking if DESCRIPTION is well formatted... [5ms]

i Checking for valid maintainer...
 Checking for valid maintainer... [5ms]

i Checking CITATION...
 Checking CITATION... [5ms]

i N: (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 v1.41.12 results 
 0 ERRORS |  0 WARNINGS |  1 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3367/9dc230555d8581b5a4a198f81ff7d92d9c0c2ca5/bugphyzz.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file bugphyzz/DESCRIPTION ... OK
* this is package bugphyzz version 0.99.6
* 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 bugphyzz 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [2s/3s] 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 R/sysdata.rda ... OK
* checking files in vignettes ... OK
* checking examples ... [67s/123s] OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
physiologies       34.290  1.587  90.990
getTaxonSignatures 10.646  0.938  12.232
makeSignatures      8.527  0.481   9.152
importBugphyzz      8.234  0.482   8.889
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running testthat.R [93s/210s]
 [93s/210s] 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('bugphyzz_0.99.6.tar.gz')

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 Installing bugphyzz 
 Package installed successfully
 bugphyzz session metadata 
 sourceDir: /tmp/RtmpJ8iYqQ/file4e3d1af6b731/bugphyzz
 BiocVersion: 3.20
 Package: bugphyzz
 PackageVersion: 0.99.6
 BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3367/9dc230555d8581b5a4a198f81ff7d92d9c0c2ca5/bugphyzz.BiocCheck
 BiocCheckVersion: 1.41.12
 sourceDir: /tmp/RtmpJ8iYqQ/file4e3d1af6b731/bugphyzz
 installDir: /tmp/RtmpJ8iYqQ/file4e3d3b74ffcb
 isTarBall: TRUE
 platform: unix
 Running BiocCheck on bugphyzz 
i Checking for deprecated package usage...
 Checking for deprecated package usage... [10ms]

i Checking for remote package usage...
 Checking for remote package usage... [11ms]

i Checking for 'LazyData: true' usage...
 Checking for 'LazyData: true' usage... [5ms]

i Checking version number...
 Checking version number... [5ms]

i Checking for version number mismatch...
 Checking for version number mismatch... [8ms]

i Checking new package version number...
 Checking new package version number... [5ms]

i Checking R version dependency...
 Checking R version dependency... [5ms]

i Checking package size...
 Checking package size... [5ms]

i Checking individual file sizes...
 Checking individual file sizes... [5ms]

i Checking biocViews...
 Checking biocViews... [5ms]

i Checking that biocViews are present...
 Checking that biocViews are present... [5ms]

i Checking package type based on biocViews...
 Checking package type based on biocViews... [5ms]

 ExperimentData
i Checking for non-trivial biocViews...
 Checking for non-trivial biocViews... [5ms]

i Checking that biocViews come from the same category...
 Checking that biocViews come from the same category... [6ms]

i Checking biocViews validity...
 Checking biocViews validity... [5ms]

i Checking for recommended biocViews...
 Checking for recommended biocViews... [5ms]

i N: Consider adding these automatically suggested biocViews:
Escherichia_coli_Data
i Search 'biocViews' at https://contributions.bioconductor.org
i Checking build system compatibility...
 Checking build system compatibility... [5ms]

i Checking for proper Description: field...
 Checking for proper Description: field... [5ms]

i Checking if DESCRIPTION is well formatted...
 Checking if DESCRIPTION is well formatted... [5ms]

i Checking for whitespace in DESCRIPTION field names...
 Checking for whitespace in DESCRIPTION field names... [5ms]

i Checking that Package field matches directory/tarball name...
 Checking that Package field matches directory/tarball name... [5ms]

i Checking for Version: field...
 Checking for Version: field... [8ms]

i Checking License: for restrictive use...
 Checking License: for restrictive use... [5ms]

i Checking for recommended DESCRIPTION fields...
 Checking for recommended DESCRIPTION fields... [5ms]

i Checking for Bioconductor software dependencies...
 Checking for Bioconductor software dependencies... [5ms]

i Bioconductor dependencies found in Imports & Depends (20%).
i Checking for pinned package versions in DESCRIPTION...
 Checking for pinned package versions in DESCRIPTION... [5ms]

i Checking .Rbuildignore...
 Checking .Rbuildignore... [5ms]

i Checking for stray BiocCheck output folders...
 Checking for stray BiocCheck output folders... [5ms]

i Checking vignette directory...
 Checking vignette directory... [5ms]

i N: 'sessionInfo' not found in vignette(s)
i Checking whether vignette is built with 'R CMD build'...
 Checking whether vignette is built with 'R CMD build'... [9ms]

i Checking package installation calls in R code...
 Checking package installation calls in R code... [7ms]

i Checking for library/require of bugphyzz...
 Checking for library/require of bugphyzz... [20ms]

i Checking coding practice...
 Checking coding practice... [7ms]

i Checking parsed R code in R directory, examples, vignettes...
 Checking parsed R code in R directory, examples, vignettes... [6ms]

i Checking function lengths...
 Checking function lengths... [5ms]

i N: The recommended function length is 50 lines or less. There are 5 functions
greater than 50 lines.
i Checking man page documentation...
 Checking man page documentation... [5ms]

i Checking package NEWS...
 Checking package NEWS... [5ms]

i Checking unit tests...
 Checking unit tests... [5ms]

i Checking skip_on_bioc() in tests...
 Checking skip_on_bioc() in tests... [5ms]

i Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne...
 Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne...

i N: Consider shorter lines; 15 lines (1%) are > 80 characters long.
i N: Consider multiples of 4 spaces for line indents; 9 lines (1%) are not.
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
i Checking if package already exists in CRAN...
 Checking if package already exists in CRAN... [5ms]

i Checking if new package already exists in Bioconductor...
 Checking if new package already exists in Bioconductor... [6ms]

i Checking for bioc-devel mailing list subscription...
 Checking for bioc-devel mailing list subscription... [6ms]

i Maintainer is subscribed to bioc-devel.
i Checking for support site registration...
 Checking for support site registration... [5ms]

i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
 BiocCheck v1.41.12 results 
 0 ERRORS |  0 WARNINGS |  5 NOTES
i See the bugphyzz.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir bugphyzz_0.99.6.tar.gz'
>>>>>>> 

* installing *source* package bugphyzz ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (bugphyzz)