===============================
R CMD BUILD
===============================
* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* preparing ‘OmicsMLRepoR’:
* 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 ‘OmicsMLRepoR_0.99.1.tar.gz’
===============================
BiocCheckGitClone('OmicsMLRepoR')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3551/87faed4ae5e4cbff01add86d602c09a25f481849/OmicsMLRepoR
→ BiocVersion: 3.20
→ Package: OmicsMLRepoR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3551/87faed4ae5e4cbff01add86d602c09a25f481849/OmicsMLRepoR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3551/87faed4ae5e4cbff01add86d602c09a25f481849/OmicsMLRepoR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3551/87faed4ae5e4cbff01add86d602c09a25f481849/OmicsMLRepoR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmicsMLRepoR’ version ‘0.99.1’
* 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 ‘OmicsMLRepoR’ can be installed ... WARNING
Found the following significant warnings:
Warning: OmicsMLRepoR.Rd:3: docType ‘_PACKAGE’ is unrecognized
See ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3551/87faed4ae5e4cbff01add86d602c09a25f481849/OmicsMLRepoR.Rcheck/00install.out’ for details.
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [6s/6s] NOTE
.getAllTargetForms: no visible binding for global variable ‘.’
.getOntos: no visible binding for global variable ‘.’
merge_vectors: no visible global function definition for ‘setNames’
ontoTreePlot: no visible binding for global variable ‘iri’
ontoTreePlot: no visible binding for global variable ‘text’
ontoTreePlot: no visible binding for global variable ‘parent’
ontoTreePlot: no visible binding for global variable ‘from’
ontoTreePlot: no visible binding for global variable ‘to’
Undefined global functions or variables:
. from iri parent setNames text to
Consider adding
importFrom("graphics", "text")
importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] WARNING
prepare_Rd: OmicsMLRepoR.Rd:3: docType ‘_PACKAGE’ is unrecognized
* 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 ... [7s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [17s/22s]
[18s/22s] 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 WARNINGs, 1 NOTE
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3551/87faed4ae5e4cbff01add86d602c09a25f481849/OmicsMLRepoR.Rcheck/00check.log’
for details.
===============================
BiocCheck('OmicsMLRepoR_0.99.1.tar.gz')
===============================
── Installing OmicsMLRepoR ─────────────────────────────────────────────────────
✔ Package installed successfully
── OmicsMLRepoR session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpaydaSM/filec479a1f0435c8/OmicsMLRepoR
→ BiocVersion: 3.20
→ Package: OmicsMLRepoR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3551/87faed4ae5e4cbff01add86d602c09a25f481849/OmicsMLRepoR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpaydaSM/filec479a1f0435c8/OmicsMLRepoR
→ installDir: /tmp/RtmpaydaSM/filec479a50344ae1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on OmicsMLRepoR ───────────────────────────────────────────
* 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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (13%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
✖ ERROR: Installation calls found in vignette(s)
Found in files:
• vignettes/Quickstart.Rmd (code line 10, column 5)
• vignettes/Quickstart.Rmd (code line 11, column 14)
• vignettes/Quickstart.Rmd (code line 10, column 5)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning: OmicsMLRepoR.Rd:3: docType ‘_PACKAGE’ is unrecognized
* Checking for library/require of OmicsMLRepoR...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/utils.R (line 162, column 16)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
The longest 5 functions are:
• tree_filter() (R/tree_filter.R): 66 lines
• ...
• getShortMetaTb() (R/manipulateMetadataTable.R): 54 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/OmicsMLRepoR.Rd
* 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 NOTE: Consider shorter lines; 10 lines (1%) are > 80 characters long.
First few lines:
• R/getMetadata.R#L2 cache <- tools::R_user_dir("OmicsMLR ...
• ...
• R/utils.R#L155 if (is.null(split_ontos)) {stop("The ...
i NOTE: Consider multiples of 4 spaces for line indents; 42 lines (3%) are not.
First few lines:
• R/availableTerms.R#L37 ontology = onto ...
• ...
• vignettes/Quickstart.Rmd#L23 warning = FALSE) ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | • 4 NOTES
i See the OmicsMLRepoR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.