===============================
R CMD BUILD
===============================
* checking for file bedbaser/DESCRIPTION ... OK
* preparing bedbaser:
* 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 bedbaser_0.99.8.tar.gz
===============================
BiocCheckGitClone('bedbaser')
===============================
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3527/58f6b285f975bf6fa0fb935fe1d0b7d0603e1045/bedbaser
BiocVersion: 3.20
Package: bedbaser
PackageVersion: 0.99.8
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3527/58f6b285f975bf6fa0fb935fe1d0b7d0603e1045/bedbaser.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3527/58f6b285f975bf6fa0fb935fe1d0b7d0603e1045/bedbaser
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/3527/58f6b285f975bf6fa0fb935fe1d0b7d0603e1045/bedbaser.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 bedbaser/DESCRIPTION ... OK
* this is package bedbaser version 0.99.8
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package bedbaser 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [33s/33s] NOTE
.format_metadata_files: no visible binding for global variable
access_methods
.format_metadata_files: no visible binding for global variable
access_url
.get_file: no visible binding for global variable name
.get_file: no visible binding for global variable access_id
bb_list_bedsets: no visible binding for global variable bed_ids
Undefined global functions or variables:
access_id access_methods access_url bed_ids name
* 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 ... [34s/46s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bb_to_grangeslist 8.668 0.487 15.809
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [29s/55s]
[29s/55s] 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: 2 NOTEs
See
/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3527/58f6b285f975bf6fa0fb935fe1d0b7d0603e1045/bedbaser.Rcheck/00check.log
for details.
===============================
BiocCheck('bedbaser_0.99.8.tar.gz')
===============================
Installing bedbaser
Package installed successfully
bedbaser session metadata
sourceDir: /tmp/RtmpnI0MJ8/file20fd630cf235f/bedbaser
BiocVersion: 3.20
Package: bedbaser
PackageVersion: 0.99.8
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3527/58f6b285f975bf6fa0fb935fe1d0b7d0603e1045/bedbaser.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /tmp/RtmpnI0MJ8/file20fd630cf235f/bedbaser
installDir: /tmp/RtmpnI0MJ8/file20fd6c0df16
isTarBall: TRUE
platform: unix
Running BiocCheck on bedbaser
* 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 (25%).
* 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 bedbaser...
* Checking coding practice...
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
utils.R (line 53, column 30)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
suppressWarnings() in R/bedbaser.R (line 52, column 5)
...
suppressMessages() in R/utils.R (line 173, column 13)
* Checking function lengths...
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/bb_save.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; 1 lines (0%) are > 80 characters long.
First few lines:
R/utils.R#L54 cached_file <- .download_to_cach ...
i NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
First few lines:
R/bedbaser.R#L93 x@cache ...
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
0 ERRORS | 2 WARNINGS | 3 NOTES
i See the bedbaser.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.