===============================
R CMD BUILD
===============================
* checking for file ‘leapR/DESCRIPTION’ ... OK
* preparing ‘leapR’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘leapR_0.99.5.tar.gz’
===============================
BiocCheckGitClone('leapR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/d721db968a6ad9cdf916630c5d1326fa1a44ebc4/leapR
→ BiocVersion: 3.22
→ Package: leapR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/d721db968a6ad9cdf916630c5d1326fa1a44ebc4/leapR.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/d721db968a6ad9cdf916630c5d1326fa1a44ebc4/leapR
→ 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 v1.47.1 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/3866/d721db968a6ad9cdf916630c5d1326fa1a44ebc4/leapR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘leapR/DESCRIPTION’ ... OK
* this is package ‘leapR’ version ‘0.99.5’
* 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 ‘leapR’ 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 ... NOTE
License stub is invalid DCF.
* 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 ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] 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 ... NOTE
Namespaces in Imports field not imported from:
‘gplots’ ‘methods’ ‘tibble’
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 ... [20s/20s] NOTE
calcTTest: no visible global function definition for ‘is’
calcTTest : <anonymous>: no visible global function definition for
‘t.test’
cluster_enrichment: no visible global function definition for ‘is’
combine_omics: no visible global function definition for ‘as’
correlation_comparison_enrichment: no visible global function
definition for ‘is’
correlation_comparison_enrichment: no visible global function
definition for ‘cor’
correlation_enrichment: no visible global function definition for ‘is’
correlation_enrichment: no visible global function definition for ‘cor’
difference_enrichment_in_relationships: no visible global function
definition for ‘is’
difference_enrichment_in_relationships : <anonymous>: no visible global
function definition for ‘t.test’
difference_enrichment_in_relationships : <anonymous>: no visible global
function definition for ‘is’
enrichment_by_fishers: no visible global function definition for
‘fisher.test’
enrichment_in_abundance: no visible global function definition for ‘is’
enrichment_in_abundance : <anonymous>: no visible global function
definition for ‘t.test’
enrichment_in_abundance : <anonymous>: no visible global function
definition for ‘is’
enrichment_in_groups: no visible global function definition for ‘is’
enrichment_in_groups : <anonymous>: no visible global function
definition for ‘ks.test’
enrichment_in_relationships: no visible global function definition for
‘is’
enrichment_in_relationships : <anonymous>: no visible global function
definition for ‘t.test’
enrichment_in_relationships : <anonymous>: no visible global function
definition for ‘is’
leapR: no visible global function definition for ‘is’
Undefined global functions or variables:
as cor fisher.test is ks.test t.test
Consider adding
importFrom("methods", "as", "is")
importFrom("stats", "cor", "fisher.test", "ks.test", "t.test")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/66s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
leapR 5.887 0.122 9.570
cluster_enrichment 2.431 0.089 10.401
combine_omics 2.229 0.228 30.152
calcTTest 0.836 0.040 6.358
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [71s/89s]
[71s/89s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3866/d721db968a6ad9cdf916630c5d1326fa1a44ebc4/leapR.Rcheck/00check.log’
for details.
===============================
BiocCheck('leapR_0.99.5.tar.gz')
===============================
── Installing leapR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── leapR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmppchy7l/file2e144b495bed5a/leapR
→ BiocVersion: 3.22
→ Package: leapR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/d721db968a6ad9cdf916630c5d1326fa1a44ebc4/leapR.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/Rtmppchy7l/file2e144b495bed5a/leapR
→ installDir: /tmp/Rtmppchy7l/file2e144b37047b46
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on leapR ──────────────────────────────────────────────────
* 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (14%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* 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 leapR...
* Checking coding practice...
* 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 9
functions greater than 50 lines.
The longest 5 functions are:
• enrichment_in_groups() (R/enrichment_in_groups.R): 145 lines
• ...
• _anonymous_.45() (R/enrichment_in_abundance.R): 82 lines
* Checking man page documentation...
* 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 multiples of 4 spaces for line indents; 693 lines (28%) are
not.
First few lines:
• R/calcTTest.R#L36 stopifnot(is(eset,'SummarizedExperimen ...
• ...
• vignettes/leapR.Rmd#L837 horiz = TRUE, names.arg = rownames(kse ...
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 v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 3 NOTES
i See the leapR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.