===============================
R CMD BUILD
===============================
* 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_0.99.7.tar.gz’
===============================
BiocCheckGitClone('tidysbml')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3319/7a7d5dbf7eb02b6e5575d3b39febe323115950f8/tidysbml
→ BiocVersion: 3.20
→ Package: tidysbml
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3319/7a7d5dbf7eb02b6e5575d3b39febe323115950f8/tidysbml.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3319/7a7d5dbf7eb02b6e5575d3b39febe323115950f8/tidysbml
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3319/7a7d5dbf7eb02b6e5575d3b39febe323115950f8/tidysbml/.gitignore'
! W: System files in '/inst' should not be Git tracked.
• inst/.DS_Store
• inst/extdata/.DS_Store
✖ E: System files found that should not be Git tracked.
• tests/.DS_Store
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
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 v1.41.16 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3319/7a7d5dbf7eb02b6e5575d3b39febe323115950f8/tidysbml.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidysbml/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidysbml’ version ‘0.99.7’
* 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 ‘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 ... [3s/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 t ... [TRUNCATED]
Rd file 'as_dfs.Rd':
\examples lines wider than 100 characters:
as_dfs(sbml_list, type = "list") ## returns a list of dataframes, giving in input the sbml already converted into a list
Rd file 'sbml_validate.Rd':
\examples lines wider than 100 characters:
sbml_validate(xml_file) ## returns a boolean value as result of validation in addition to attribute containing errors details
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 ... [2s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[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 ... [2s/2s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3319/7a7d5dbf7eb02b6e5575d3b39febe323115950f8/tidysbml.Rcheck/00check.log’
for details.
===============================
BiocCheck('tidysbml_0.99.7.tar.gz')
===============================
── Installing tidysbml ─────────────────────────────────────────────────────────
✔ Package installed successfully
── tidysbml session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvcHOao/filec2e0e693bfb27/tidysbml
→ BiocVersion: 3.20
→ Package: tidysbml
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3319/7a7d5dbf7eb02b6e5575d3b39febe323115950f8/tidysbml.BiocCheck
→ BiocCheckVersion: 1.41.16
→ sourceDir: /tmp/RtmpvcHOao/filec2e0e693bfb27/tidysbml
→ installDir: /tmp/RtmpvcHOao/filec2e0e683f327c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on tidysbml ───────────────────────────────────────────────
* 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...
i N: Update R version dependency from 4.3.0 to 4.4.0.
* 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...
! W: 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...
* 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...
i N: Avoid sapply(); use vapply()
Found in files:
• R/as_df.notes.R (line 49, column 16)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i N: The recommended function length is 50 lines or less. There are 2 functions
greater than 50 lines.
The longest 5 functions are:
• as_subdf() (R/as_subdf.R): 165 lines
• as_df.annotation() (R/as_df.annotation.R): 88 lines
* 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...
i N: Consider shorter lines; 193 lines (22%) are > 80 characters long.
First few lines:
• R/as_df.annotation.R#L3 # Helper function for as_value.annotatio ...
• ...
• vignettes/tidysbml-introduction.Rmd#L193 df_mart_uniprot <- getBM( attributes
= c ...
i N: Consider multiples of 4 spaces for line indents; 249 lines (28%) are not.
First few lines:
• R/as_df.annotation.R#L11 if (descriptor_content_idx != 1) vec_v ...
• ...
• vignettes/tidysbml-introduction.Rmd#L196 mart = mart) ...
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.
* 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 v1.41.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | • 5 NOTES
i See the tidysbml.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.