Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘tidysbml/DESCRIPTION’ ... OK
* preparing ‘tidysbml’:
* 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 ‘tidysbml_0.99.3.tar.gz’

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 BiocCheckGitClone('tidysbml')

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─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3319/a82f6c51feff6f69c509e6ce635be513f634e94f/tidysbml
─ BiocVersion: 3.20
─ Package: tidysbml
─ PackageVersion: 0.99.3
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3319/a82f6c51feff6f69c509e6ce635be513f634e94f/tidysbml.BiocCheck
─ BiocCheckVersion: 1.41.7
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3319/a82f6c51feff6f69c509e6ce635be513f634e94f/tidysbml
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix

* Checking valid files...
Warning in readLines(gitignore) :
  incomplete final line found on '/Users/pkgbuild/packagebuilder/workers/jobs/3319/a82f6c51feff6f69c509e6ce635be513f634e94f/tidysbml/.gitignore'
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
    * NOTE: (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 results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

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/3319/a82f6c51feff6f69c509e6ce635be513f634e94f/tidysbml.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 ‘tidysbml/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidysbml’ version ‘0.99.3’
* 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 serialization versions ... OK
* checking whether package ‘tidysbml’ 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] NOTE
as_value.annotation.creator: no visible binding for global variable
  ‘list_app’
as_value.annotation.creator: no visible binding for global variable
  ‘vec_tmp_i’
as_value.annotation.creator: no visible binding for global variable ‘m’
Undefined global functions or variables:
  list_app m vec_tmp_i
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'as_df.Rd':
  \examples lines wider than 100 characters:
     df <- as_df(sbml_list)  ## returns one dataframe with data about the species saved in the sbml document
     df <- as_df(sbml_list)  ## returns one list containing two dataframe with data about the reactions and the speciesReferences listed in  ... [TRUNCATED]

Rd file 'as_df.annotation.Rd':
  \examples lines wider than 100 characters:
     sbml_list <- sbml_as_list(system.file("extdata", "R-HSA-8937144.sbml", package = "tidysbml"), "species")
     df <- as_df.annotation(sbml_list)  ## returns one dataframe with one row for each species and one column for each descriptor in annotat ... [TRUNCATED]

Rd file 'as_df.attributes.Rd':
  \examples lines wider than 100 characters:
     sbml_list <- sbml_as_list(system.file("extdata", "R-HSA-8937144.sbml", package = "tidysbml"), "species")
     df <- as_df.attributes(sbml_list)   ## returns one dataframe with one row for each species and one column for each attribute

Rd file 'as_df.notes.Rd':
  \examples lines wider than 100 characters:
     sbml_list <- sbml_as_list(system.file("extdata", "R-HSA-8937144.sbml", package = "tidysbml"), "species")
     df <- as_df.notes(sbml_list)  ## returns the dataframe with only one column containing the notes' info

Rd file 'as_dfs.Rd':
  \examples lines wider than 100 characters:
     as_dfs(sbml_list)  ## returns a list of dataframes, giving in input the sbml already converted into a list

Rd file 'as_subdf.Rd':
  \examples lines wider than 100 characters:
     sbml_list <- sbml_as_list(system.file("extdata", "R-HSA-8937144.sbml", package = "tidysbml"), "reactions")
     df <- as_subdf(sbml_list)   ## returns one dataframe with one row for each species involved in each reaction

These lines will be truncated in the PDF manual.
* 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 ... [1s/1s] 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: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3319/a82f6c51feff6f69c509e6ce635be513f634e94f/tidysbml.Rcheck/00check.log’
for details.





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 BiocCheck('tidysbml_0.99.3.tar.gz')

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* Installing package...
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpDZ66QI/file174ec56a7eb21/tidysbml
─ BiocVersion: 3.20
─ Package: tidysbml
─ PackageVersion: 0.99.3
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3319/a82f6c51feff6f69c509e6ce635be513f634e94f/tidysbml.BiocCheck
─ BiocCheckVersion: 1.41.7
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpDZ66QI/file174ec56a7eb21/tidysbml
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpDZ66QI/file174ec2a3deff9
─ isTarBall: TRUE
─ platform: unix

* 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...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    * WARNING: No Bioconductor dependencies detected. Note that some
      infrastructure packages may not have Bioconductor dependencies.
      For more information, reach out to the Bioconductor community
      and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* 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...
* Checking for library/require of tidysbml...
* Checking coding practice...
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 2 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 190 lines (21%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 270 lines
      (30%) 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...
    * ERROR: Unable to find your email in the Support Site: HTTP 404
      Not Found.

─ BiocCheck results ──
1 ERRORS | 1 WARNINGS | 9 NOTES

See the tidysbml.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 tidysbml_0.99.3.tar.gz'
>>>>>>> 

* installing *source* package ‘tidysbml’ ...
** 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 (tidysbml)