===============================
R CMD BUILD
===============================
* checking for file ‘EMTscoreData/DESCRIPTION’ ... OK
* preparing ‘EMTscoreData’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘EMTscoreData_0.99.4.tar.gz’
===============================
BiocCheckGitClone('EMTscoreData')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4031/a9d05d62a0faf17d9b6800f707da755b4a032102/EMTscoreData
→ BiocVersion: 3.23
→ Package: EMTscoreData
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4031/a9d05d62a0faf17d9b6800f707da755b4a032102/EMTscoreData.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4031/a9d05d62a0faf17d9b6800f707da755b4a032102/EMTscoreData
→ 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 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 v1.47.7 results ───────────────────────────────────────────────────
✖ 0 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/4031/a9d05d62a0faf17d9b6800f707da755b4a032102/EMTscoreData.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘EMTscoreData/DESCRIPTION’ ... OK
* this is package ‘EMTscoreData’ version ‘0.99.4’
* 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 ‘EMTscoreData’ can be installed ... WARNING
Found the following significant warnings:
Warning: previous export '‘MCF7_TNF’' is being replaced
See ‘/home/pkgbuild/packagebuilder/workers/jobs/4031/a9d05d62a0faf17d9b6800f707da755b4a032102/EMTscoreData.Rcheck/00install.out’ for details.
* 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] NOTE
Warning: previous export '‘MCF7_TNF’' is being replaced
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking whether startup messages can be suppressed ... [13s/13s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘SummarizedExperiment’
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 ... [40s/40s] OK
* 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 ... WARNING
Undocumented code objects:
‘MCF7_EGF’ ‘MCF7_TGFB1’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [22s/165s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MCF7_TNF 5.18 2.088 149.763
* 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/4031/a9d05d62a0faf17d9b6800f707da755b4a032102/EMTscoreData.Rcheck/00check.log’
for details.
===============================
BiocCheck('EMTscoreData_0.99.4.tar.gz')
===============================
── Installing EMTscoreData ─────────────────────────────────────────────────────
✔ Package installed successfully
── EMTscoreData session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1GI4GM/filef9b193ccf5cc1/EMTscoreData
→ BiocVersion: 3.23
→ Package: EMTscoreData
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4031/a9d05d62a0faf17d9b6800f707da755b4a032102/EMTscoreData.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /tmp/Rtmp1GI4GM/filef9b193ccf5cc1/EMTscoreData
→ installDir: /tmp/Rtmp1GI4GM/filef9b1928fa2f49
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EMTscoreData ───────────────────────────────────────────
* 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...
→ ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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...
i 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (67%).
* 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:
• EMTscoreData.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of EMTscoreData...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/zzz.R (line 40, column 6)
• R/zzz.R (line 41, column 10)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/EMTscoreData.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
* Checking man page documentation...
Warning: previous export '‘MCF7_TNF’' is being replaced
* 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; 11 lines (4%) are > 80 characters long.
First few lines:
• R/EMTscoreData.R#L4 #' Cook DP, Vanderhyden BC (2020). Conte ...
• ...
• vignettes/EMTscoreData.Rmd#L147 p_AUCell <- plot_EMT_from_objects(seurat ...
i NOTE: Consider multiples of 4 spaces for line indents; 37 lines (15%) are
not.
First few lines:
• R/zzz.R#L40 fl = system.file("extdata", "metadata. ...
• ...
• vignettes/EMTscoreData.Rmd#L143 return(p) ...
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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/workflows/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/workflows
* Checking for bioc-devel mailing list subscription...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.47.7 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the EMTscoreData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.