===============================
BiocCheckGitClone('linkSet')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/bdf62a667f48c5a61d07f08d71f921f7bf445be5/linkSet
→ BiocVersion: 3.21
→ Package: linkSet
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/bdf62a667f48c5a61d07f08d71f921f7bf445be5/linkSet.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/bdf62a667f48c5a61d07f08d71f921f7bf445be5/linkSet
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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 v1.43.2 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/bdf62a667f48c5a61d07f08d71f921f7bf445be5/linkSet.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘linkSet/DESCRIPTION’ ... OK
* this is package ‘linkSet’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] NOTE
Warning: no function found corresponding to methods exports from ‘linkSet’ for: ‘flank’, ‘narrow’, ‘promoters’, ‘resize’, ‘show’, ‘trim’
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 ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘DBI’ ‘doParallel’
'loadNamespace' or 'requireNamespace' call not declared from: ‘GenomicInteractions’
'library' or 'require' calls in package code:
‘TxDb.Hsapiens.UCSC.hg38.knownGene’
‘TxDb.Mmusculus.UCSC.mm10.knownGene’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘Matrix’ ‘dplyr’
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 ... [38s/38s] NOTE
linkSet,GRanges-GRanges-character_Or_missing: warning in
.new_LK(anchor1 = anchor1, anchor2 = anchor2, nameBait = nameBait,
region = regions, metadata = metadata): partial argument match of
'region' to 'regions'
.convert_to_grange: no visible global function definition for ‘Rle’
.exist_distance: no visible global function definition for ‘mcols’
.exist_inter: no visible global function definition for ‘mcols’
.exportToLinkSet: no visible binding for global variable ‘otherEndID’
.exportToLinkSet: no visible binding for global variable ‘baitID’
.filter.fragments: no visible global function definition for ‘mcols’
.get_dist_output: no visible global function definition for ‘seqnames’
.makeNakedMatFromGInteractions: no visible global function definition
for ‘mcols’
.makeNakedMatFromGInteractions: no visible binding for global variable
‘showAsCell’
.new_LK: no visible global function definition for
‘make_zero_col_DFrame’
.new_LK: no visible binding for global variable ‘gr1’
.pasteAnchor: no visible global function definition for ‘seqnames’
.pasteAnchor: no visible global function definition for ‘showAsCell’
.pasteAnchor: no visible global function definition for ‘ranges’
.safeNMcols: no visible global function definition for ‘mcols’
.verify.linkSet: no visible global function definition for ‘is’
.verify.linkSet: no visible global function definition for ‘mcols’
.verify.linkSet: no visible global function definition for ‘mcols<-’
fit.glm: no visible global function definition for ‘POtr’
fit.glm : <anonymous>: no visible global function definition for
‘pPOtr’
fit.glm: no visible global function definition for ‘NBItr’
fit.glm : <anonymous>: no visible global function definition for
‘pNBItr’
fit.model: no visible global function definition for ‘mcols’
ggplot_add.interSet: no visible global function definition for
‘seqnames’
ggplot_add.interSet: no visible global function definition for ‘mcols’
plotBaits: no visible global function definition for ‘is’
plotBaits: no visible global function definition for ‘seqnames’
plotBaits: no visible global function definition for ‘strand’
plotBaits: no visible binding for global variable ‘oe_middle’
plotBaits: no visible binding for global variable ‘.data’
plotBaits: no visible binding for global variable ‘color_factor’
readvalidPairs: no visible global function definition for ‘mcols’
readvalidPairs: no visible global function definition for ‘mcols<-’
run.model.fitting: no visible binding for global variable ‘distance’
run.model.fitting: no visible binding for global variable ‘temp.data’
run.model.fitting: no visible binding for global variable ‘expected’
run.model.fitting: no visible binding for global variable ‘p.value’
run.model.fitting: no visible global function definition for
‘create.modelfit.plot’
$,linkSet: no visible global function definition for ‘mcols’
$<-,linkSet: no visible global function definition for ‘mcols’
$<-,linkSet: no visible global function definition for ‘mcols<-’
Convert,ANY: no visible binding for global variable ‘baitCol’
Convert,ANY: no visible global function definition for ‘mcols<-’
Convert,GInteractions: no visible global function definition for
‘mcols<-’
Convert,Pairs: no visible global function definition for ‘mcols<-’
Convert,data.frame: no visible global function definition for ‘mcols<-’
annotateInter,linkSet: no visible global function definition for
‘seqnames’
annotateInter,linkSet: no visible global function definition for
‘mcols’
annotateInter,linkSet: no visible global function definition for
‘mcols<-’
annotatePromoter,linkSet: no visible global function definition for
‘mcols<-’
as.GInteractions,linkSet: no visible global function definition for
‘mcols’
as.GInteractions,linkSet: no visible global function definition for
‘mcols<-’
as.data.frame,linkSet: no visible global function definition for
‘mcols’
baitGInteractions,GInteractions-GRanges-GRanges: no visible global
function definition for ‘mcols’
baitGInteractions,GInteractions-GRanges-GRanges: no visible global
function definition for ‘mcols<-’
countInteractibility,linkSet: no visible global function definition for
‘mcols’
countInteractions,linkSet: no visible global function definition for
‘mcols’
countInteractions,linkSet: no visible global function definition for
‘mcols<-’
crossGeneEnhancer,linkSet: no visible global function definition for
‘mcols’
crossGeneEnhancer,linkSet: no visible global function definition for
‘.’
crossGeneEnhancer,linkSet: no visible binding for global variable ‘N’
crossGeneEnhancer,linkSet: no visible global function definition for
‘mcols<-’
diagnoseLinkSet,linkSet: no visible global function definition for
‘mcols’
diagnoseLinkSet,linkSet: no visible binding for global variable ‘prop’
exportInterBed,linkSet: no visible global function definition for
‘mcols’
exportInterBed,linkSet: no visible global function definition for
‘write.table’
exportWashU,linkSet: no visible global function definition for ‘mcols’
exportWashU,linkSet: no visible global function definition for
‘write.table’
filterLinks,linkSet: no visible global function definition for
‘seqnames’
flank,linkSet: no visible binding for global variable ‘flank’
flankRegions,linkSet: no visible binding for global variable ‘flank’
linkSet,GRanges-GRanges-character_Or_missing: no visible global
function definition for ‘mcols’
linkSet,GRanges-GRanges-character_Or_missing: no visible global
function definition for ‘mcols<-’
linkSet,GRanges-GRanges-character_Or_missing: no visible global
function definition for ‘make_zero_col_DFrame’
linkSet,character-GRanges-character_Or_missing: no visible global
function definition for ‘mcols’
linkSet,character-GRanges-character_Or_missing: no visible global
function definition for ‘mcols<-’
linkSet,character-GRanges-character_Or_missing: no visible global
function definition for ‘make_zero_col_DFrame’
names<-,linkSet: no visible global function definition for
‘validObject’
narrow,linkSet: no visible binding for global variable ‘narrow’
narrowRegions,linkSet: no visible binding for global variable ‘narrow’
oe<-,linkSet: no visible global function definition for ‘is’
oe<-,linkSet: no visible global function definition for ‘mcols’
oe<-,linkSet: no visible global function definition for ‘mcols<-’
orderLinks,linkSet: no visible global function definition for ‘mcols’
pairdist,linkSet: no visible global function definition for ‘mcols’
pairdist,linkSet: no visible global function definition for ‘mcols<-’
parallel_slot_names,linkSet: no visible global function definition for
‘callNextMethod’
plot_genomic_ranges,linkSet: no visible global function definition for
‘is’
plot_genomic_ranges,linkSet: no visible global function definition for
‘mcols’
plot_genomic_ranges,linkSet: no visible binding for global variable
‘xstart’
plot_genomic_ranges,linkSet: no visible binding for global variable
‘xend’
plot_genomic_ranges,linkSet: no visible binding for global variable
‘region’
promoterRegions,linkSet: no visible binding for global variable
‘promoters’
promoters,linkSet: no visible binding for global variable ‘promoters’
reduceRegions,linkSet: no visible global function definition for
‘subjectHits’
regions<-,linkSet: no visible global function definition for
‘validObject’
regionsBait<-,linkSet: no visible global function definition for ‘is’
regionsBait<-,linkSet: no visible global function definition for
‘mcols’
regionsBait<-,linkSet: no visible global function definition for
‘mcols<-’
resize,linkSet: no visible binding for global variable ‘resize’
resizeRegions,linkSet: no visible binding for global variable ‘resize’
run_chicane,linkSet: no visible binding for global variable ‘q.value’
run_chicane,linkSet: no visible binding for global variable ‘p.value’
run_chicane,linkSet: no visible global function definition for ‘mcols’
run_chicane,linkSet: no visible global function definition for
‘mcols<-’
showLinkSet,linkSet: no visible global function definition for
‘makePrettyMatrixForCompactPrinting’
showLinkSet,linkSet: no visible global function definition for
‘getSlots’
showLinkSet,linkSet: no visible global function definition for
‘makeClassinfoRowForCompactPrinting’
subsetBaitRegion,linkSet: no visible global function definition for
‘queryHits’
subsetOE,linkSet: no visible global function definition for ‘queryHits’
trim,linkSet: no visible global function definition for ‘trim’
Undefined global functions or variables:
. .data N NBItr POtr Rle baitCol baitID callNextMethod color_factor
create.modelfit.plot distance expected flank getSlots gr1 is
makeClassinfoRowForCompactPrinting makePrettyMatrixForCompactPrinting
make_zero_col_DFrame mcols mcols<- narrow oe_middle otherEndID
p.value pNBItr pPOtr promoters prop q.value queryHits ranges region
resize seqnames showAsCell strand subjectHits temp.data trim
validObject write.table xend xstart
Consider adding
importFrom("methods", "callNextMethod", "getSlots", "is",
"validObject")
importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'linkSet':
‘linkSet-class.Rd’ ‘linkSet.Rd’
* 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 'baitGInteractions-GInteractions-GRanges-GRanges-method.Rd':
\examples lines wider than 100 characters:
geneGr <- GRanges(seqnames = "chr1", ranges = IRanges(start = c(100, 200), end = c(150, 250)), geneSymbol = c("Gene1", "Gene2"))
Rd file 'chicane.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 ... WARNING
Missing link or links in Rd file 'linkSet-class.Rd':
‘linkSet-methods’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘anchor1<-’ ‘anchor2<-’ ‘anchorIds’ ‘anchors’ ‘as.GInteractions’
‘bait’ ‘bait<-’ ‘baitGInteractions’ ‘clean_unused_regions’
‘countInteractibility’ ‘countInteractions’ ‘exportInterBed’
‘exportWashU’ ‘fit.model’ ‘geom_linkset’ ‘linkExample’ ‘oe’ ‘oe<-’
‘plotBaits’ ‘reduceRegions’ ‘regions<-’ ‘regionsBait’ ‘regionsBait<-’
‘run_chicane’ ‘showLinkSet’ ‘unchecked_anchor1<-’
‘unchecked_anchor2<-’ ‘unchecked_regions<-’ ‘withTxDb’
Undocumented data sets:
‘linkExample’
Undocumented S4 classes:
‘character_Or_missing’
Undocumented S4 methods:
generic '$' and siglist 'linkSet'
generic '$<-' and siglist 'linkSet'
generic 'anchorIds' and siglist 'linkSet'
generic 'anchors' and siglist 'linkSet'
generic 'bait' and siglist 'linkSet'
generic 'bait<-' and siglist 'linkSet'
generic 'first' and siglist 'linkSet'
generic 'linkSet' and siglist 'GRanges,GRanges,character_Or_missing'
generic 'linkSet' and siglist
'character,GRanges,character_Or_missing'
generic 'names' and siglist 'linkSet'
generic 'names<-' and siglist 'linkSet'
generic 'oe' and siglist 'linkSet'
generic 'oe<-' and siglist 'linkSet'
generic 'regions<-' and siglist 'linkSet'
generic 'regionsBait' and siglist 'linkSet'
generic 'regionsBait<-' and siglist 'linkSet'
generic 'second' and siglist 'linkSet'
generic 'unchecked_anchor1<-' and siglist 'linkSet'
generic 'unchecked_anchor2<-' and siglist 'linkSet'
generic 'unchecked_regions<-' and siglist 'linkSet'
All user-level objects in a package (including S4 classes and methods)
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 ... WARNING
Undocumented arguments in Rd file 'Convert.Rd'
‘source’ ‘oeCol’
Documented arguments not in \usage in Rd file 'Convert.Rd':
‘specificCol’
Undocumented arguments in Rd file 'baitGInteractions-GInteractions-GRanges-GRanges-method.Rd'
‘x’
Documented arguments not in \usage in Rd file 'baitGInteractions-GInteractions-GRanges-GRanges-method.Rd':
‘gi’
Undocumented arguments in Rd file 'clean_unused_regions-linkSet-method.Rd'
‘x’
Undocumented arguments in Rd file 'countInteractions-linkSet-method.Rd'
‘baitRegions’
Undocumented arguments in Rd file 'crossGeneEnhancer-linkSet-method.Rd'
‘x’
Undocumented arguments in Rd file 'diagnoseLinkSet-linkSet-method.Rd'
‘x’
Undocumented arguments in Rd file 'filterLinks-linkSet-method.Rd'
‘x’
Undocumented arguments in Rd file 'geom_linkset-linkSet-method.Rd'
‘linkSet’
Documented arguments not in \usage in Rd file 'geom_linkset-linkSet-method.Rd':
‘link.file’ ‘file.type’ ‘plot.curve’
Undocumented arguments in Rd file 'geom_range.Rd'
‘bait_col’ ‘oe_col’ ‘default_col’ ‘minimal_width’
Undocumented arguments in Rd file 'linkSet-GRange-Methods.Rd'
‘width’ ‘fix’ ‘...’ ‘region’ ‘start’ ‘end’ ‘shift’ ‘both’
‘ignore.strand’ ‘upstream’ ‘downstream’ ‘drop.empty.ranges’
Undocumented arguments in Rd file 'linkSet-theme.Rd'
‘x.range’ ‘margin.len’ ‘show.rect’
Undocumented arguments in Rd file 'orderLinks-linkSet-method.Rd'
‘x’
Undocumented arguments in Rd file 'reduceRegions-linkSet-method.Rd'
‘region’
Documented arguments not in \usage in Rd file 'reduceRegions-linkSet-method.Rd':
‘reduceBait’ ‘reduceOE’
Undocumented arguments in Rd file 'show.Rd'
‘object’ ‘x’ ‘margin’ ‘print.seqinfo’ ‘print.classinfo’ ‘baitRegion’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [11s/11s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [41s/41s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/22s]
[23s/23s] 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 ... [5s/5s] OK
* DONE
Status: 5 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3634/bdf62a667f48c5a61d07f08d71f921f7bf445be5/linkSet.Rcheck/00check.log’
for details.
===============================
BiocCheck('linkSet_0.99.2.tar.gz')
===============================
── Installing linkSet ──────────────────────────────────────────────────────────
✔ Package installed successfully
── linkSet session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8ZRibU/file14598c783ce883/linkSet
→ BiocVersion: 3.21
→ Package: linkSet
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/bdf62a667f48c5a61d07f08d71f921f7bf445be5/linkSet.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/Rtmp8ZRibU/file14598c783ce883/linkSet
→ installDir: /tmp/Rtmp8ZRibU/file14598c6a9e961a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on linkSet ────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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 4.5.0.
* 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: 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/hic_workthrough.Rmd (code line 51, column 41)
• ...
• vignettes/linkSet.Rmd (code line 190, column 71)
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/hic_workthrough.Rmd
• vignettes/linkSet.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of linkSet...
! WARNING: Avoid the use of 'library' or 'require' in R code
Found in files:
• require() in R/annotate.R (line 23, column 5)
• require() in R/annotate.R (line 26, column 5)
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/formatConverter.R (line 51, column 12)
• ...
• R/formatConverter.R (line 587, column 19)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• formatConverter.R (line 366, column 20)
• ...
• visualization.R (line 133, column 30)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/count.R (line 180, column 21)
• ...
• R/visualization.R (line 161, column 25)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/annotate.R (line 46, column 17)
• ...
• R/visualization.R (line 665, column 15)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/annotate.R (line 115, column 19)
i NOTE: Avoid system() ; use system2()
Found in files:
• system() in R/formatConverter.R (line 328, column 21)
• system() in R/formatConverter.R (line 330, column 21)
* 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 352, 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/clean_unused_regions-linkSet-method.Rd
• ...
• man/show.Rd
Warning: no function found corresponding to methods exports from ‘linkSet’ for: ‘flank’, ‘narrow’, ‘promoters’, ‘resize’, ‘trim’
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• geom_range.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; 370 lines (7%) are > 80 characters long.
First few lines:
• R/AllGenerics.R#L38 setGeneric("unchecked_regions<-", functi ...
• ...
• vignettes/linkSet.Rmd#L314 You can choose the oe-centric views to v ...
i NOTE: Consider 4 spaces instead of tabs; 917 lines (18%) contain tabs.
First few lines:
• R/statical.R#L4 #' This function adapts the \code{chican ...
• ...
• R/statical.R#L1357 } ...
i NOTE: Consider multiples of 4 spaces for line indents; 1110 lines (21%) are
not.
First few lines:
• R/AllGenerics.R#L44 standardGeneric("subsetBait") ...
• ...
• vignettes/linkSet.Rmd#L283 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...
✖ 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 Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | i 17 NOTES
i See the linkSet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.