===============================
R CMD BUILD
===============================
* checking for file ‘org.Hbacteriophora.eg.db/DESCRIPTION’ ... OK
* preparing ‘org.Hbacteriophora.eg.db’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘org.Hbacteriophora.eg.db_0.99.0.tar.gz’
===============================
BiocCheckGitClone('org.Hbacteriophora.eg.db')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3602/org.Hbacteriophora.eg.db_20250630182234/org.Hbacteriophora.eg.db
→ BiocVersion: 3.22
→ Package: org.Hbacteriophora.eg.db
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3602/org.Hbacteriophora.eg.db_20250630182234/org.Hbacteriophora.eg.db.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3602/org.Hbacteriophora.eg.db_20250630182234/org.Hbacteriophora.eg.db
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• org.Hbacteriophora.eg.db.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
* Checking CITATION...
i 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 v1.45.7 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3602/org.Hbacteriophora.eg.db_20250630182234/org.Hbacteriophora.eg.db.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘org.Hbacteriophora.eg.db/DESCRIPTION’ ... OK
* this is package ‘org.Hbacteriophora.eg.db’ version ‘0.99.0’
* 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 ‘org.Hbacteriophora.eg.db’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [16s/353s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking whether startup messages can be suppressed ... [13s/13s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘AnnotationHub’
All declared Imports should be used.
Unexported object imported by a ':::' call: ‘AnnotationDbi:::dbObjectName’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [41s/41s] NOTE
File ‘org.Hbacteriophora.eg.db/R/zzz.R’:
.onLoad calls:
message("Downloading H. bacteriophora annotation database (once per system)...")
packageStartupMessage(sprintf("%s.db loaded successfully\nSource: %s", sub(".db$", "", pkgname), ifelse(grepl("cache", dbfile), "Zenodo cache", "bundled package")))
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in '?.onAttach'.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] 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 ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3602/org.Hbacteriophora.eg.db_20250630182234/org.Hbacteriophora.eg.db.Rcheck/00check.log’
for details.
===============================
BiocCheck('org.Hbacteriophora.eg.db_0.99.0.tar.gz')
===============================
── Installing org.Hbacteriophora.eg.db ─────────────────────────────────────────
✔ Package installed successfully
── org.Hbacteriophora.eg.db session metadata ───────────────────────────────────
→ sourceDir: /tmp/RtmpRAJEV5/file12f1d948d90719/org.Hbacteriophora.eg.db
→ BiocVersion: 3.22
→ Package: org.Hbacteriophora.eg.db
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3602/org.Hbacteriophora.eg.db_20250630182234/org.Hbacteriophora.eg.db.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpRAJEV5/file12f1d948d90719/org.Hbacteriophora.eg.db
→ installDir: /tmp/RtmpRAJEV5/file12f1d9568cafd4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on org.Hbacteriophora.eg.db ───────────────────────────────
* 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 NOTE: Update R version dependency from 2.7.0 to 4.5.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ AnnotationData
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (33%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• Hbacteriophora_annotation_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of org.Hbacteriophora.eg.db...
* Checking coding practice...
✖ ERROR: Avoid downloads in '.onAttach' or '.onLoad' functions
Found in files:
• curl_download() in R/zzz.R (line 70, column 17)
• download.file() in R/zzz.R (line 78, column 18)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 1 times)
• <<- in R/zzz.R (line 52, column 13)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• .onLoad() (R/zzz.R): 89 lines
* Checking man page documentation...
org.Hbacteriophora.eg.db loaded successfully
Source: Zenodo cache
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• org.Hbacteriophora.egBASE.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
i 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...
i NOTE: Consider shorter lines; 11 lines (5%) are > 80 characters long.
First few lines:
• R/zzz.R#L5 org.Hbacteriophora.eg <- function() Anno ...
• ...
• vignettes/Hbacteriophora_annotation_vignette.Rmd#L64
select(org.Hbacteriophora.eg.db, keys=ke ...
i NOTE: Consider multiples of 4 spaces for line indents; 47 lines (22%) are
not.
First few lines:
• R/zzz.R#L18 AnnotationDbi::dbschema(datacache, fil ...
• ...
• vignettes/Hbacteriophora_annotation_vignette.Rmd#L59 dplyr::filter(ONTOLOGY
== "BP") ...
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the org.Hbacteriophora.eg.db.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.