===============================
R CMD BUILD
===============================
* checking for file ‘linkSet/DESCRIPTION’ ... OK
* preparing ‘linkSet’:
* 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 ‘linkSet_0.99.9.tar.gz’
===============================
BiocCheckGitClone('linkSet')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/da47adfb09e9424ea126e9c9a24a3d4c5755ba38/linkSet
→ BiocVersion: 3.22
→ Package: linkSet
→ PackageVersion: 0.99.9
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/da47adfb09e9424ea126e9c9a24a3d4c5755ba38/linkSet.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/da47adfb09e9424ea126e9c9a24a3d4c5755ba38/linkSet
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3634/da47adfb09e9424ea126e9c9a24a3d4c5755ba38/linkSet/.gitignore'
✖ ERROR: System files found that should not be Git tracked.
• linkSet.Rcheck/00check.log
* 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...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
* 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 v1.45.7 results ───────────────────────────────────────────────────
✖ 2 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/da47adfb09e9424ea126e9c9a24a3d4c5755ba38/linkSet.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘0.99.9’
* 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 ‘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 ... [11s/11s] OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [38s/38s] NOTE
Convert,ANY: no visible global function definition for
‘.exportToLinkSet’
Undefined global functions or variables:
.exportToLinkSet
* 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:
‘checkPackages’ ‘checkSplitDataNumericalFit’ ‘cleanUnusedRegions’
‘collateGRanges’ ‘convertToGrange’ ‘createSampleLinkSet’
‘distanceSplit’ ‘enforceOrder’ ‘existDistance’ ‘existInter’
‘exportToLinkSet’ ‘extractDataFromLinkset’ ‘filterFragments’
‘fitModel’ ‘geomRange’ ‘getDbConnection’ ‘getDistOutput’
‘modelTryCatch’ ‘plotGenomicRanges’ ‘runModelFitting’
‘unchecked_anchor1<-’ ‘unchecked_anchor2<-’
Undocumented S4 methods:
generic 'cleanUnusedRegions' and siglist 'linkSet'
generic 'plotGenomicRanges' 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 ... WARNING
Functions or methods with usage in Rd file 'Embryo_body.Rd' but not in code:
‘system.file’
Functions or methods with usage in Rd file 'dot-check.split.data.numerical.fit.Rd' but not in code:
‘.check.split.data.numerical.fit’
Functions or methods with usage in Rd file 'dot-convert_to_grange.Rd' but not in code:
‘.convert_to_grange’
Functions or methods with usage in Rd file 'dot-exportToLinkSet.Rd' but not in code:
‘.exportToLinkSet’
Functions or methods with usage in Rd file 'dot-pasteAnchor.Rd' but not in code:
‘.pasteAnchor’
Functions or methods with usage in Rd file 'geom_range.Rd' but not in code:
‘geom_range’
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'Embryo_body.Rd'
‘extdata’ ‘Embryo_body.bed’ ‘package’
Objects in \usage without \alias in Rd file 'Embryo_body.Rd':
‘system.file’
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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/42s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/22s]
[22s/22s] 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 ... [4s/4s] OK
* DONE
Status: 3 WARNINGs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3634/da47adfb09e9424ea126e9c9a24a3d4c5755ba38/linkSet.Rcheck/00check.log’
for details.
===============================
BiocCheck('linkSet_0.99.9.tar.gz')
===============================
── Installing linkSet ──────────────────────────────────────────────────────────
✔ Package installed successfully
── linkSet session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpLcyXdY/file1cd1eb3387dc1b/linkSet
→ BiocVersion: 3.22
→ Package: linkSet
→ PackageVersion: 0.99.9
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/da47adfb09e9424ea126e9c9a24a3d4c5755ba38/linkSet.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpLcyXdY/file1cd1eb3387dc1b/linkSet
→ installDir: /tmp/RtmpLcyXdY/file1cd1eb1818814d
→ 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 4.0.0 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...
Warning in FUN(X[[i]], ...) :
incomplete final line found on '/tmp/RtmpLcyXdY/file1cd1eb3387dc1b/linkSet/man/Embryo_body.Rd'
* 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 (40%).
* 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:
• hic_workthrough.Rmd
• linkSet.Rmd
* 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 483, column 12)
• ...
• R/formatConverter.R (line 589, column 19)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• formatConverter.R (line 368, column 20)
• ...
• visualization.R (line 650, column 18)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/formatConverter.R (line 279, 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 765, 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 18
functions greater than 50 lines.
The longest 5 functions are:
• _anonymous_.372() (R/visualization.R): 210 lines
• ...
• modelTryCatch() (R/statical.R): 140 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/linkSet-GRanges-GRanges-character_Or_missing-method.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• chicane.Rd
• geom_linkset.Rd
• withTxDb.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
Found in files:
• geom_linkset.Rd
• withTxDb.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• geom_linkset.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; 407 lines (7%) are > 80 characters long.
First few lines:
• R/AllGenerics.R#L44 setGeneric("unchecked_regions<-", functi ...
• ...
• vignettes/linkSet.Rmd#L377 You can choose the oe-centric views to v ...
i NOTE: Consider 4 spaces instead of tabs; 873 lines (15%) 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; 1381 lines (23%) are
not.
First few lines:
• R/AllGenerics.R#L50 standardGeneric("subsetBait") ...
• ...
• vignettes/linkSet.Rmd#L346 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 v1.45.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 17 NOTES
i See the linkSet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.