===============================
BiocCheckGitClone('linkSet')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/926b77f509e09defe746aaaedb3ebaeb46e43f3c/linkSet
→ BiocVersion: 3.21
→ Package: linkSet
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/926b77f509e09defe746aaaedb3ebaeb46e43f3c/linkSet.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/926b77f509e09defe746aaaedb3ebaeb46e43f3c/linkSet
→ 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 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 v1.43.12 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/3634/926b77f509e09defe746aaaedb3ebaeb46e43f3c/linkSet.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘linkSet/DESCRIPTION’ ... OK
* this is package ‘linkSet’ version ‘0.99.7’
* 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 ‘linkSet’ 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 ... OK
* 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 ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [14s/15s] 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 ... [75s/91s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'Convert.Rd':
\examples lines wider than 100 characters:
gi <- GInteractions(anchor1 = c(1, 2), anchor2 = c(3, 4), regions = GRanges(seqnames = c("chr1", "chr1", "chr2", "chr2"),
Rd file 'annotatePromoter-linkSet-method.Rd':
\examples lines wider than 100 characters:
annotated_ls <- suppressWarnings(annotatePromoter(ls, genome = "hg38", upstream = 500,overwrite = TRUE))
Rd file 'linkSet-GRange-Methods.Rd':
\examples lines wider than 100 characters:
flank_bait <- flankRegions(linkExample, width = 100, start = TRUE, both = FALSE, use.names = TRUE, ignore.strand = FALSE, region = "bai ... [TRUNCATED]
Rd file 'linkSet-subset-methods.Rd':
\examples lines wider than 100 characters:
subset_bait_regions <- GRanges(seqnames = "chr1", ranges = IRanges(start = c(100, 200), end = c(150, 250)))
subset_oe_regions <- GRanges(seqnames = "chr1", ranges = IRanges(start = c(300, 400), end = c(350, 450)))
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 ... [26s/31s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [90s/112s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotatePromoter-linkSet-method 1.991 0.055 5.386
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [38s/43s]
[38s/43s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
> test_check("linkSet")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 158 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_statistic.R:4:3'): run_chicane processes linkSet correctly ─────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'countInteractibility': object 'linkExample' not found
Backtrace:
▆
1. ├─linkSet::countInteractibility(linkExample) at test_statistic.R:4:3
2. └─base::.handleSimpleError(...)
3. └─base (local) h(simpleError(msg, call))
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 158 ]
Error: Test failures
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, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3634/926b77f509e09defe746aaaedb3ebaeb46e43f3c/linkSet.Rcheck/00check.log’
for details.
===============================
BiocCheck('linkSet_0.99.7.tar.gz')
===============================
── Installing linkSet ──────────────────────────────────────────────────────────
✔ Package installed successfully
── linkSet session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpuBAMmx/file37c5a6364a4dbb/linkSet
→ BiocVersion: 3.21
→ Package: linkSet
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/926b77f509e09defe746aaaedb3ebaeb46e43f3c/linkSet.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/RtmpuBAMmx/file37c5a6364a4dbb/linkSet
→ installDir: /tmp/RtmpuBAMmx/file37c5a658788c36
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on linkSet ────────────────────────────────────────────────
* 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 2.10 to 4.6.0.
* 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: Sequencing,
SingleCell, Coverage
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 (37%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of linkSet...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/formatConverter.R (line 482, column 12)
• ...
• R/formatConverter.R (line 588, column 19)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• formatConverter.R (line 367, column 20)
• ...
• visualization.R (line 113, column 30)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/formatConverter.R (line 278, column 16)
• ...
• R/statical.R (line 156, column 25)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/annotate.R (line 55, column 17)
• ...
• R/visualization.R (line 675, column 15)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/annotate.R (line 124, column 19)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/statical.R (line 346, column 47)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
The longest 5 functions are:
• ggplot_add.interSet() (R/visualization.R): 191 lines
• ...
• readvalidPairs() (R/formatConverter.R): 114 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/dot-convert_to_grange.Rd
• ...
• man/show.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• geom_linkset.Rd
• ...
• withTxDb.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
Found in files:
• withTxDb.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• withTxDb.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 386 lines (7%) are > 80 characters long.
First few lines:
• R/AllGenerics.R#L44 setGeneric("unchecked_regions<-", functi ...
• ...
• vignettes/linkSet.Rmd#L320 You can choose the oe-centric views to v ...
i NOTE: Consider 4 spaces instead of tabs; 873 lines (16%) contain tabs.
First few lines:
• R/statical.R#L50 replicate.merging.method = 'sum', ...
• ...
• R/statical.R#L1322 } ...
i NOTE: Consider multiples of 4 spaces for line indents; 1127 lines (20%) are
not.
First few lines:
• R/AllGenerics.R#L50 standardGeneric("subsetBait") ...
• ...
• vignettes/linkSet.Rmd#L289 strand = "+") ...
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 404 Not Found.
── BiocCheck v1.43.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 17 NOTES
i See the linkSet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.