===============================
R CMD BUILD
===============================
* checking for file kmcut/DESCRIPTION ... OK
* preparing kmcut:
* 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 kmcut_0.99.3.tar.gz
===============================
BiocCheckGitClone('kmcut')
===============================
BiocCheckVersion: 1.41.0
BiocVersion: 3.19
Package: kmcut
PackageVersion: 0.99.3
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3018/afdda1a804e2c4ac211797536645c63bb18d1f71/kmcut
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* 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')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3018/afdda1a804e2c4ac211797536645c63bb18d1f71/kmcut.Rcheck
* using R version 4.4.0 (2024-04-24)
* 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 kmcut/DESCRIPTION ... OK
* checking extension type ... Package
* this is package kmcut 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 kmcut 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [20s/20s] NOTE
create_se_object: no visible global function definition for
read.delim
extract_columns: no visible global function definition for read.delim
extract_columns: no visible global function definition for
write.table
extract_rows: no visible global function definition for read.delim
extract_rows: no visible global function definition for write.table
km_opt_pcut: no visible global function definition for is
km_opt_pcut: no visible global function definition for pdf
km_opt_pcut: no visible global function definition for pchisq
km_opt_pcut: no visible global function definition for grid
km_opt_pcut: no visible global function definition for points
km_opt_pcut: no visible global function definition for legend
km_opt_pcut: no visible global function definition for dev.off
km_opt_pcut: no visible global function definition for p.adjust
km_opt_pcut: no visible global function definition for write.table
km_opt_scut: no visible global function definition for is
km_opt_scut: no visible global function definition for pdf
km_opt_scut: no visible global function definition for pchisq
km_opt_scut: no visible global function definition for grid
km_opt_scut: no visible global function definition for points
km_opt_scut: no visible global function definition for legend
km_opt_scut: no visible global function definition for dev.off
km_opt_scut: no visible global function definition for write.table
km_qcut: no visible global function definition for is
km_qcut: no visible global function definition for pdf
km_qcut: no visible global function definition for quantile
km_qcut: no visible global function definition for pchisq
km_qcut: no visible global function definition for grid
km_qcut: no visible global function definition for legend
km_qcut: no visible global function definition for dev.off
km_qcut: no visible global function definition for p.adjust
km_qcut: no visible global function definition for write.table
km_ucut: no visible global function definition for is
km_ucut: no visible global function definition for pdf
km_ucut: no visible global function definition for pchisq
km_ucut: no visible global function definition for grid
km_ucut: no visible global function definition for legend
km_ucut: no visible global function definition for dev.off
km_ucut: no visible global function definition for p.adjust
km_ucut: no visible global function definition for write.table
km_val_cut: no visible global function definition for is
km_val_cut: no visible global function definition for read.delim
km_val_cut: no visible global function definition for pdf
km_val_cut: no visible global function definition for pchisq
km_val_cut: no visible global function definition for grid
km_val_cut: no visible global function definition for legend
km_val_cut: no visible global function definition for p.adjust
km_val_cut: no visible global function definition for dev.off
km_val_cut: no visible global function definition for write.table
transpose_table: no visible global function definition for read.delim
transpose_table: no visible global function definition for
write.table
ucox_batch: no visible global function definition for is
ucox_batch: no visible global function definition for p.adjust
ucox_batch: no visible global function definition for write.table
ucox_pred: no visible global function definition for is
ucox_pred: no visible global function definition for as.formula
ucox_pred: no visible global function definition for predict
ucox_pred: no visible global function definition for p.adjust
ucox_pred: no visible global function definition for write.table
Undefined global functions or variables:
as.formula dev.off grid is legend p.adjust pchisq pdf points predict
quantile read.delim write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "grid", "legend", "points")
importFrom("methods", "is")
importFrom("stats", "as.formula", "p.adjust", "pchisq", "predict",
"quantile")
importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... [13s/13s] 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: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3018/afdda1a804e2c4ac211797536645c63bb18d1f71/kmcut.Rcheck/00check.log
for details.
===============================
BiocCheck('kmcut_0.99.3.tar.gz')
===============================
BiocCheckVersion: 1.41.0
BiocVersion: 3.19
Package: kmcut
PackageVersion: 0.99.3
sourceDir: /tmp/RtmpRClINt/file20f8ac4b397942/kmcut
installDir: /tmp/RtmpRClINt/file20f8ac17629535
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3018/afdda1a804e2c4ac211797536645c63bb18d1f71/kmcut.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* 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...
* NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
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 kmcut...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 10 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* 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; 10 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 137 lines
(5%) 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...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 0 WARNINGS | 6 NOTES
See the kmcut.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.