===============================
R CMD BUILD
===============================
* checking for file RUCova/DESCRIPTION ... OK
* preparing RUCova:
* 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 RUCova_0.99.6.tar.gz
===============================
BiocCheckGitClone('RUCova')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3620/849114e1f904ad570c1d1d8f5f2feccd8e7522ed/RUCova
BiocVersion: 3.21
Package: RUCova
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3620/849114e1f904ad570c1d1d8f5f2feccd8e7522ed/RUCova.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3620/849114e1f904ad570c1d1d8f5f2feccd8e7522ed/RUCova
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...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.43.2 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3620/849114e1f904ad570c1d1d8f5f2feccd8e7522ed/RUCova.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* 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 RUCova/DESCRIPTION ... OK
* this is package RUCova version 0.99.6
* 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 RUCova 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
ggcorrplot ggh4x ggplot2 ggpubr ggridges remotes
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [22s/22s] NOTE
calc_mean_BC: no visible global function definition for assay
calc_mean_BC: no visible binding for global variable quantile
calc_mean_BC: no visible global function definition for head
calc_mean_BC: no visible global function definition for DataFrame
calc_mean_DNA: no visible global function definition for assay
calc_mean_DNA: no visible binding for global variable quantile
calc_mean_DNA: no visible global function definition for DataFrame
heatmap_compare_corr: no visible global function definition for assay
heatmap_compare_corr: no visible global function definition for cor
rucova: no visible global function definition for assay
rucova: no visible global function definition for setNames
rucova : <anonymous>: no visible global function definition for
reformulate
rucova : <anonymous>: no visible global function definition for lm
rucova: no visible binding for global variable coef
rucova: no visible binding for global variable resid
rucova : <anonymous>: no visible global function definition for
residuals
rucova : <anonymous>: no visible global function definition for coef
rucova: no visible global function definition for reformulate
rucova: no visible binding for global variable marker
rucova: no visible binding for global variable coef_key
rucova: no visible binding for global variable surrogate
rucova: no visible binding for global variable value
rucova: no visible binding for global variable sd
rucova: no visible binding for global variable eff_value
rucova: no visible binding for global variable sd_x
rucova: no visible binding for global variable sd_y
rucova: no visible global function definition for assay<-
rucova: no visible global function definition for metadata
rucova: no visible global function definition for metadata<-
Undefined global functions or variables:
DataFrame assay assay<- coef coef_key cor eff_value head lm marker
metadata metadata<- quantile reformulate resid residuals sd sd_x sd_y
setNames surrogate value
Consider adding
importFrom("stats", "coef", "cor", "lm", "quantile", "reformulate",
"resid", "residuals", "sd", "setNames")
importFrom("utils", "head")
to your NAMESPACE file.
* 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 ... WARNING
Error in vapply(exprs, function(e) as.character(e[[1L]]), "") :
values must be length 1,
but FUN(X[[1]]) result is length 3
Calls: <Anonymous> -> vapply
Execution halted
* checking Rd \usage sections ... WARNING
Error in vapply(exprs, function(e) as.character(e[[1L]]), "") :
values must be length 1,
but FUN(X[[1]]) result is length 3
Calls: <Anonymous> -> vapply
Execution halted
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter Writing R documentation files in the Writing R
Extensions manual.
Error in vapply(exprs, function(e) as.character(e[[1L]]), "") :
values must be length 1,
but FUN(X[[1]]) result is length 3
Calls: <Anonymous> -> vapply
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [16s/16s] 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 WARNINGs, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3620/849114e1f904ad570c1d1d8f5f2feccd8e7522ed/RUCova.Rcheck/00check.log
for details.
===============================
BiocCheck('RUCova_0.99.6.tar.gz')
===============================
Installing RUCova
Package installed successfully
RUCova session metadata
sourceDir: /tmp/RtmpZmLm5R/file4fd1430981832/RUCova
BiocVersion: 3.21
Package: RUCova
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3620/849114e1f904ad570c1d1d8f5f2feccd8e7522ed/RUCova.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpZmLm5R/file4fd1430981832/RUCova
installDir: /tmp/RtmpZmLm5R/file4fd141d0f2739
isTarBall: TRUE
platform: unix
Running BiocCheck on RUCova
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (12%).
* 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 RUCova...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/rucova.R (line 135, column 29)
R/rucova.R (line 138, column 26)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/rucova.R (line 127, column 5)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/RUCova.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
rucova() (R/rucova.R): 213 lines
heatmap_compare_corr() (R/useful_functions.R): 88 lines
* Checking man page documentation...
* 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; 205 lines (16%) are > 80 characters long.
First few lines:
R/HNSCC_data.R#L3 #' Is a tibble containing mass cytometry ...
...
vignettes/RUCova.Rmd#L633 Here we just show one example, the least ...
i NOTE: Consider multiples of 4 spaces for line indents; 284 lines (23%) are
not.
First few lines:
R/rucova.R#L41 center_SU ...
...
vignettes/RUCova.Rmd#L660 xlab("eff_value (slope)") ...
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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 11 NOTES
i See the RUCova.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.