===============================
BiocCheckGitClone('TraianProt')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/TraianProt_20260127133941/TraianProt
BiocVersion: 3.23
Package: TraianProt
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/TraianProt_20260127133941/TraianProt.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/TraianProt_20260127133941/TraianProt
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
TraianProt.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.47.16 results
1 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4005/TraianProt_20260127133941/TraianProt.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file TraianProt/DESCRIPTION ... OK
* this is package TraianProt version 0.99.5
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 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 ... 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 ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [28s/28s] NOTE
barplot_func: no visible global function definition for slot
barplot_func: no visible global function definition for slot<-
Undefined global functions or variables:
slot slot<-
Consider adding
importFrom("methods", "slot", "slot<-")
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 ... [9s/10s] ERROR
Running examples in TraianProt-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Goterms_finder
> ### Title: Find GO Terms (gprofiler2)
> ### Aliases: Goterms_finder
>
> ### ** Examples
>
>
> # Create synthetic data
> limma_df <- data.frame(
+ Protein = c("P04637", "P10415", "P00533"),
+ Protein_description = c("TP53", "CALCA", "EGFR"),
+ expression = c("Up-regulated", "Down-regulated", "Up-regulated"),
+ p.value = c(0.01, 0.02, 0.03)
+ )
> raw_df <- data.frame(
+ Protein = c("P04637", "P10415", "P00533", "P62258"),
+ Protein_description = c("TP53", "CALCA", "EGFR", "ACTB")
+ )
>
> # This example requires an internet connection and will be skipped on tests
>
> if (requireNamespace("gprofiler2")) {
+ go_res <- Goterms_finder(
+ df = limma_df,
+ raw = raw_df,
+ target = "ENSG",
+ numeric_ns = "ENTREZGENE_ACC",
+ mthreshold = 0.05,
+ filter_na = TRUE,
+ organismo = "hsapiens",
+ custombg = TRUE,
+ platform = 1
+ )
+ # Check the first result object
+ if (!is.null(go_res) && inherits(go_res[[1]], "compareClusterResult")) {
+ print(head(go_res[[1]]@compareClusterResult))
+ }
+ }
Detected custom background input, domain scope is set to 'custom'.
Error: Request to g:Profiler failed (HTTP 400). Please check your input or organism argument.
API message: Empty query
If the issue persists, please contact biit.support@ut.ee with a reproducible example.
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4005/TraianProt_20260127133941/TraianProt.Rcheck/00check.log
for details.
===============================
BiocCheck('TraianProt_0.99.5.tar.gz')
===============================
Installing TraianProt
Package installed successfully
TraianProt session metadata
sourceDir: /tmp/RtmpWeidq7/file2d39cf15a46ea3/TraianProt
BiocVersion: 3.23
Package: TraianProt
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4005/TraianProt_20260127133941/TraianProt.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /tmp/RtmpWeidq7/file2d39cf15a46ea3/TraianProt
installDir: /tmp/RtmpWeidq7/file2d39cf2d42fb6b
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...
i NOTE: Consider adding these automatically suggested biocViews: GO
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (19%).
* 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/functions.R (line 82, column 28)
...
R/functions.R (line 1996, column 65)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
functions.R (line 432, column 42)
...
functions.R (line 3094, column 69)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/functions.R (line 1619, column 7)
...
print() in R/run_traianprot.R (line 357, column 3)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/functions.R (line 997, column 53)
...
R/functions.R (line 1788, column 18)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/functions.R (line 2618, column 10)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/Goterms_finder.Rd
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 7
functions greater than 50 lines.
The longest 5 functions are:
statistical_analysis() (R/functions.R): 424 lines
...
filter_valids() (R/functions.R): 75 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
gostplot_func.Rd
...
run_traianprot.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
Found in files:
gostplot_func.Rd
...
run_traianprot.Rd
* Checking package NEWS...
* 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; 368 lines (9%) are > 80 characters long.
First few lines:
R/functions.R#L2 #################################### hel ...
...
vignettes/traianprot.Rmd#L401 > *Whether you are a beginner or exper ...
i NOTE: Consider multiples of 4 spaces for line indents; 928 lines (23%) are
not.
First few lines:
R/functions.R#L54 intensity_names <- metadata$intensity_ ...
...
vignettes/traianprot.Rmd#L286 limma <- limma %>% ...
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 v1.47.16 results
0 ERRORS | 0 WARNINGS | i 15 NOTES
i See the TraianProt.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.