===============================
BiocCheckGitClone('leapR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/leapR_20250804163926/leapR
→ BiocVersion: 3.22
→ Package: leapR
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/leapR_20250804163926/leapR.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/leapR_20250804163926/leapR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• leapR.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.45.12 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/3866/leapR_20250804163926/leapR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leapR/DESCRIPTION’ ... OK
* this is package ‘leapR’ version ‘0.99.0’
* 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 ... [6s/6s] 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 ... [21s/21s] NOTE
calcTTest : <anonymous>: no visible binding for global variable
‘shortlist’
calcTTest : <anonymous>: no visible binding for global variable
‘longlist’
calcTTest : <anonymous>: no visible global function definition for
‘t.test’
combine_omics: no visible global function definition for ‘as’
correlation_comparison_enrichment: no visible global function
definition for ‘cor’
correlation_enrichment: no visible global function definition for ‘cor’
difference_enrichment_in_relationships: no visible global function
definition for ‘detag’
difference_enrichment_in_relationships: no visible global function
definition for ‘t.test’
difference_enrichment_in_relationships: 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
‘t.test’
enrichment_in_abundance: no visible global function definition for ‘is’
enrichment_in_groups: no visible global function definition for
‘ks.test’
enrichment_in_relationships: no visible global function definition for
‘detag’
enrichment_in_relationships: no visible global function definition for
‘t.test’
enrichment_in_relationships: no visible global function definition for
‘is’
Undefined global functions or variables:
as cor detag fisher.test is ks.test longlist shortlist 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 ... NOTE
Rd file 'calcTTest.Rd':
\examples lines wider than 100 characters:
tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",method='libcurl',destfile='transData.rda')
Rd file 'cluster_enrichment.Rd':
\examples lines wider than 100 characters:
tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",method='libcurl',destfile='transData.rda')
# for the example we will limit the number of transcripts considered - arbitrarily in this case
transdata.hc.enrichment = leapR::cluster_enrichment(geneset=ncipid, clusters=clust.list, background=rownames(transdata))
Rd file 'combine_omics.Rd':
\examples lines wider than 100 characters:
pdata <- download.file('https://api.figshare.com/v2/file/download/56536217',method='libcurl',destfile='protData.rda')
tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",method='libcurl',destfile='transData.rda')
phdata<-download.file('https://api.figshare.com/v2/file/download/56536211',method='libcurl',destfile = 'phosData.rda')
Rd file 'leapR.Rd':
\examples lines wider than 100 characters:
tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",method='libcurl',destfile='transData.rda')
# use enrichment_comparison to calculate enrichment in one set of conditions (shortlist) and another
short_v_long = leapR(geneset=ncipid, assay_name='transcriptomics', enrichment_method='enrichment_comparison',
# use enrichment_in_sets to calculate the most enriched pathways from the highest abundance proteins
onept_sets = leapR(geneset=ncipid, assay_name='transcriptomics', enrichment_method='enrichment_in_sets',
# the previous example uses a hard threshold to get a short list of most abundant proteins
# and calculates enrichment based on set overlap. The results are likely to be similar - but
onept_order = leapR(geneset=ncipid, assay_name='transcriptomics', enrichment_method='enrichment_in_order',
short_pathways = leapR(geneset=ncipid, assay_name='transcriptomics',enrichment_method='enrichment_in_pathway',
short_correlation_pathways = leapR(geneset=ncipid, assay_name='transcriptomics', enrichment_method='correlation_enrichment',
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [10s/10s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/60s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
leapR 6.452 0.217 9.919
combine_omics 2.205 0.409 29.306
cluster_enrichment 2.006 0.051 6.051
calcTTest 0.782 0.033 5.045
* 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: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3866/leapR_20250804163926/leapR.Rcheck/00check.log’
for details.
===============================
BiocCheck('leapR_0.99.0.tar.gz')
===============================
── Installing leapR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── leapR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmparcJPJ/file2a49ce1f2741e2/leapR
→ BiocVersion: 3.22
→ Package: leapR
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3866/leapR_20250804163926/leapR.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/RtmparcJPJ/file2a49ce1f2741e2/leapR
→ installDir: /tmp/RtmparcJPJ/file2a49ce73051874
→ 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...
i NOTE: Update R version dependency from 4.4.0 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...
i NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Transcriptomics
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...
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...
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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• leapR.Rmd
* 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...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/calcTTest.R (line 33, column 12)
• ...
• R/get_pathway_information.R (line 32, column 24)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• cluster_enrichment.R (line 47, column 59)
• ...
• read_gene_sets.R (line 65, column 25)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/cluster_enrichment.R (line 43, column 5)
• ...
• R/read_gene_sets.R (line 69, column 17)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/helper_functions.R (line 18, column 16)
• ...
• R/leapR.R (line 172, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/enrichment_in_groups.R (line 141, column 46)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/enrichment_in_groups.R (line 138, column 13)
* 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:
• .enrichment_wrapper() (R/leapR.R): 229 lines
• ...
• enrichment_in_relationships() (R/enrichment_in_relationships.R): 113 lines
* Checking man page documentation...
* 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; 423 lines (18%) are > 80 characters long.
First few lines:
• R/calcTTest.R#L4 #' append results to ExpressionSet with ...
• ...
• vignettes/leapR.Rmd#L612 ksea_result = phosphodata.ksea.corr.svl[ ...
i NOTE: Consider multiples of 4 spaces for line indents; 730 lines (32%) are
not.
First few lines:
• R/calcTTest.R#L31 exprdata <- SummarizedExperiment::assa ...
• ...
• vignettes/leapR.Rmd#L622 horiz=TRUE, names.arg=rownames( ...
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...
✖ 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 v1.45.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 15 NOTES
i See the leapR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.