===============================
BiocCheckGitClone('SARC')
===============================
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.231
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3071/190c4ad3ba5e18a0924d347709dd5e8eff7bdc23/SARC
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3071/190c4ad3ba5e18a0924d347709dd5e8eff7bdc23/SARC.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SARC’ version ‘0.99.231’
* 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 ‘SARC’ 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] 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 ... [12s/12s] 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 ... NOTE
Error: there is no package called ‘Matrix’
Call sequence:
23: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
21: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
20: loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
19: asNamespace(ns)
18: asNamespace(ns)
17: namespaceImportFrom(self, asNamespace(ns), vars, from = from)
16: namespaceImportClasses(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), imp[[2L]], from = package)
15: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
14: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
13: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
12: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
11: loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [17s/17s] NOTE
Error: there is no package called ‘Matrix’
Call sequence:
23: doWithOneRestart(return(expr), restart)
22: withOneRestart(expr, restarts[[1L]])
21: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
20: loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
19: asNamespace(ns)
18: asNamespace(ns)
17: namespaceImportFrom(self, asNamespace(ns), vars, from = from)
16: namespaceImportClasses(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), imp[[2L]], from = package)
15: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
14: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
13: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
12: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
11: loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[
Execution halted
Error in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘Matrix’
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘Matrix’
Calls: <Anonymous> -> lapply -> FUN -> find.package
Execution halted
* checking for missing documentation entries ... WARNING
Error: package ‘RaggedExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
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 ‘RaggedExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
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 ‘RaggedExperiment’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
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 in find.package(package, lib.loc) :
there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
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 in find.package(package, lib.loc) :
there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
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 ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) :
there is no package called ‘SARC’
Execution halted
* checking contents of ‘data’ directory ... WARNING
Output for data("test_cnv", package = "SARC"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘SARC’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("test_cnv2", package = "SARC"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘SARC’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
Output for data("test_cov", package = "SARC"):
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called ‘SARC’
Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
Execution halted
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] ERROR
Running examples in ‘SARC-Ex.R’ failed
The error occurred in:
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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 <- "SARC"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "SARC-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('SARC')
Loading required package: RaggedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘RaggedExperiment’ in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘Matrix’
Error: package ‘RaggedExperiment’ could not be loaded
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [3s/3s]
[3s/3s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for 'RaggedExperiment' in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'Matrix'
Error: package 'RaggedExperiment' could not be loaded
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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: 2 ERRORs, 7 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3071/190c4ad3ba5e18a0924d347709dd5e8eff7bdc23/SARC.Rcheck/00check.log’
for details.
===============================
BiocCheck('SARC_0.99.231.tar.gz')
===============================
cmd: /home/biocbuild/bbs-3.18-bioc/R/bin/R
args: --vanilla CMD INSTALL --no-test-load --library=/tmp/RtmpfbiXfx/file5a69a5269c60e/lib '/home/pkgbuild/packagebuilder/workers/jobs/3071/190c4ad3ba5e18a0924d347709dd5e8eff7bdc23/SARC_0.99.231.tar.gz'
stderr:
* installing *source* package ‘SARC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
ERROR: lazy loading failed for package ‘SARC’
* removing ‘/tmp/RtmpfbiXfx/file5a69a5269c60e/lib/SARC’
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3071/190c4ad3ba5e18a0924d347709dd5e8eff7bdc23/SARC_0.99.231.tar.gz
must be installable.
cmd: /home/biocbuild/bbs-3.18-bioc/R/bin/R
args: --vanilla -e 'library(SARC)'
stderr:
Loading required package: RaggedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘RaggedExperiment’ in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘Matrix’
Error: package ‘RaggedExperiment’ could not be loaded
Execution halted
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3071/190c4ad3ba5e18a0924d347709dd5e8eff7bdc23/SARC_0.99.231.tar.gz
must be loadable.
─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.231
─ sourceDir: /tmp/RtmpfbiXfx/file5a69a43c14f46/SARC
─ installDir: /tmp/RtmpfbiXfx/file5a69a5269c60e
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3071/190c4ad3ba5e18a0924d347709dd5e8eff7bdc23/SARC.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Coverage
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
no package 'SARC' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted