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R CMD BUILD
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* checking for file TraianProt/DESCRIPTION ... OK
* preparing TraianProt:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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 TraianProt_0.99.13.tar.gz
===============================
BiocCheckGitClone('TraianProt')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/f14dfe7150f40bcf581863c3ccd560860a72da0a/TraianProt
BiocVersion: 3.23
Package: TraianProt
PackageVersion: 0.99.13
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/f14dfe7150f40bcf581863c3ccd560860a72da0a/TraianProt.BiocCheck
BiocCheckVersion: 1.47.26
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/f14dfe7150f40bcf581863c3ccd560860a72da0a/TraianProt
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for remote package usage...
* Checking NAMESPACE...
* 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 v1.47.26 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4005/f14dfe7150f40bcf581863c3ccd560860a72da0a/TraianProt.Rcheck
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-27 08:14:51 UTC
* using option --no-vignettes
* checking for file TraianProt/DESCRIPTION ... OK
* this is package TraianProt version 0.99.13
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 TraianProt 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 ... WARNING
Found the following file with non-ASCII characters:
R/runTraianProt.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function tools::showNonASCIIfile can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
Namespace in Imports field not imported from: shinyjs
All declared Imports should be used.
Missing or unexported object: grDevices::my_heatmap
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [48s/49s] NOTE
barplot_func: no visible global function definition for barplot
identify_proteins: no visible global function definition for
complete.cases
my_heatmap_differential: no visible global function definition for
desc
my_heatmap_differential: no visible binding for global variable logFC
runTraianProt : server : <anonymous>: no visible global function
definition for write.table
runTraianProt : server : <anonymous>: no visible global function
definition for write.csv
runTraianProt : server : <anonymous>: no visible global function
definition for plot.new
runTraianProt : server : <anonymous>: no visible global function
definition for dev.off
runTraianProt : server: no visible global function definition for
gostplot_func
runTraianProt : server : <anonymous>: no visible global function
definition for pdf
runTraianProt : server: no visible global function definition for
datatable
Undefined global functions or variables:
barplot complete.cases datatable desc dev.off gostplot_func logFC pdf
plot.new write.csv write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "barplot", "plot.new")
importFrom("stats", "complete.cases")
importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'traianprot_power_curve.Rd':
\examples lines wider than 100 characters:
plot <- traianprot_power_curve(data, c("R1", "R2", "R3"), foldchange = 2, replicatespower = 5, alpha_level_choice = 1, alpha_level = 0. ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* 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 ... [69s/71s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [16s/16s]
[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 ... [4s/4s] OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4005/f14dfe7150f40bcf581863c3ccd560860a72da0a/TraianProt.Rcheck/00check.log
for details.
===============================
BiocCheck('TraianProt_0.99.13.tar.gz')
===============================
Installing TraianProt
Package installed successfully
TraianProt session metadata
sourceDir: /tmp/RtmpJx3kPO/file3d2af353aed5ab/TraianProt
BiocVersion: 3.23
Package: TraianProt
PackageVersion: 0.99.13
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/f14dfe7150f40bcf581863c3ccd560860a72da0a/TraianProt.BiocCheck
BiocCheckVersion: 1.47.26
sourceDir: /tmp/RtmpJx3kPO/file3d2af353aed5ab/TraianProt
installDir: /tmp/RtmpJx3kPO/file3d2af31e8aa989
isTarBall: TRUE
platform: unix
Running BiocCheck on TraianProt
* 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 (18%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
traianprot.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TraianProt...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/runTraianProt.R (line 909, column 18)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
runTraianProt.R (line 249, column 75)
...
runTraianProt.R (line 917, column 34)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/runTraianProt.R (line 920, column 9)
...
print() in R/runTraianProt.R (line 1569, column 11)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 8 times:
T in R/runTraianProt.R (line 1101, column 54)
...
F in R/runTraianProt.R (line 804, column 21)
* 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 12
functions greater than 50 lines.
The longest 5 functions are:
runTraianProt() (R/runTraianProt.R): 1815 lines
...
filter_valids() (R/functions.R): 81 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
Goterms_finder.Rd
...
interactions_up.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
Found in files:
Goterms_finder.Rd
...
interactions_up.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
interactions_up.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; 622 lines (11%) are > 80 characters long.
First few lines:
R/functions.R#L1 #################################### hel ...
...
vignettes/traianprot.Rmd#L425 > *Whether you are a beginner or exper
...
i NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
First few lines:
R/runTraianProt.R#L1401 info_box <- infoBox("Significant ...
i NOTE: Consider multiples of 4 spaces for line indents; 1011 lines (17%) are
not.
First few lines:
R/runTraianProt.R#L23 ui <- dashboardPage( ...
...
R/runTraianProt.R#L1834 return(shinyApp(ui = ui, server = serv ...
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 Unable to find your email in the Support Site: HTTP 504 Gateway Timeout.
BiocCheck v1.47.26 results
0 ERRORS | 1 WARNINGS | i 12 NOTES
i See the TraianProt.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.