===============================
BiocCheckGitClone('linkSet')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/linkSet_20241127195704/linkSet
→ BiocVersion: 3.21
→ Package: linkSet
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/linkSet_20241127195704/linkSet.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3634/linkSet_20241127195704/linkSet
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• lkObj.Rproj
* 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 ───────────────────────────────────────────────────
✖ 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/3634/linkSet_20241127195704/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 ‘0.99.1’
* 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 ... [12s/12s] 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] 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 ... [0s/0s] WARNING
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Error: package ‘S4Vectors’ required by ‘GenomicRanges’ could not be found
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: there is no package called ‘S4Vectors’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: there is no package called ‘S4Vectors’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error: there is no package called ‘S4Vectors’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error: there is no package called ‘S4Vectors’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [3s/3s] NOTE
Error: there is no package called ‘S4Vectors’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘S4Vectors’
Calls: <Anonymous>
Execution halted
* 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
Error: package ‘S4Vectors’ required by ‘GenomicRanges’ could not be found
Call sequence:
5: stop(gettextf("package %s required by %s could not be found",
sQuote(pkg), sQuote(pkgname)), call. = FALSE, domain = NA)
4: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
3: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Error: package ‘S4Vectors’ required by ‘GenomicRanges’ could not be found
Call sequence:
5: stop(gettextf("package %s required by %s could not be found",
sQuote(pkg), sQuote(pkgname)), call. = FALSE, domain = NA)
4: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
3: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package ‘S4Vectors’ required by ‘GenomicRanges’ could not be found
Call sequence:
5: stop(gettextf("package %s required by %s could not be found",
sQuote(pkg), sQuote(pkgname)), call. = FALSE, domain = NA)
4: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
3: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package ‘S4Vectors’ required by ‘GenomicRanges’ could not be found
Call sequence:
5: stop(gettextf("package %s required by %s could not be found",
sQuote(pkg), sQuote(pkgname)), call. = FALSE, domain = NA)
4: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
3: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
* 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.
Error: there is no package called ‘S4Vectors’
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
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 ... [0s/0s] WARNING
Failed with error: 'there is no package called 'S4Vectors''
Error loading dataset 'linkExample':
Error in .requirePackage(package) :
unable to load required package 'linkSet'
The dataset(s) may use package(s) not declared in Depends/Imports.
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] ERROR
Running examples in ‘linkSet-Ex.R’ failed
The error occurred in:
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> pkgname <- "linkSet"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "linkSet-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+ options(OutDec = '.')
+ format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
>
> ### * </HEADER>
> library('linkSet')
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Error: package ‘S4Vectors’ required by ‘GenomicRanges’ could not be found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Error: package 'S4Vectors' required by 'GenomicRanges' could not be found
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 ... [5s/5s] OK
* DONE
Status: 2 ERRORs, 9 WARNINGs, 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3634/linkSet_20241127195704/linkSet.Rcheck/00check.log’
for details.
===============================
BiocCheck('linkSet_0.99.1.tar.gz')
===============================
Error: package or namespace load failed for ‘BiocCheck’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘RBGL’
Execution halted