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This page was generated on 2025-09-22 12:05 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1866/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SARC 1.7.1  (landing page)
Krutik Patel
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/SARC
git_branch: devel
git_last_commit: 1115634
git_last_commit_date: 2025-07-24 10:08:10 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for SARC on lconway

To the developers/maintainers of the SARC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SARC.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SARC
Version: 1.7.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SARC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SARC_1.7.1.tar.gz
StartedAt: 2025-09-21 23:49:49 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 23:59:09 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 560.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SARC.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SARC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SARC_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SARC.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SARC’ version ‘1.7.1’
* 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 ‘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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
addExonsGenes: no visible global function definition for ‘metadata’
addExonsGenes: no visible global function definition for ‘metadata<-’
anovaOnCNV: no visible global function definition for ‘metadata’
anovaOnCNV: no visible global function definition for ‘metadata<-’
cnvConfidence: no visible global function definition for ‘metadata’
cnvConfidence: no visible global function definition for ‘metadata<-’
pasteExonsGenes: no visible global function definition for ‘metadata’
pasteExonsGenes: no visible global function definition for ‘metadata<-’
phDunnetonCNV: no visible global function definition for ‘metadata’
phDunnetonCNV: no visible global function definition for ‘metadata<-’
plotCovPrep: no visible global function definition for ‘metadata’
plotCovPrep: no visible global function definition for ‘metadata<-’
prepAnova: no visible global function definition for ‘metadata’
prepAnova: no visible global function definition for ‘metadata<-’
regionGrangeMake: no visible global function definition for ‘metadata’
regionGrangeMake: no visible global function definition for
  ‘metadata<-’
regionMean: no visible global function definition for ‘metadata’
regionMean: no visible global function definition for ‘metadata<-’
regionQuantiles: no visible global function definition for ‘metadata’
regionQuantiles: no visible global function definition for ‘metadata<-’
regionSet: no visible global function definition for ‘sortSeqlevels’
regionSet: no visible global function definition for ‘metadata’
regionSet: no visible global function definition for ‘metadata<-’
regionSplit: no visible global function definition for ‘metadata’
regionSplit: no visible global function definition for ‘metadata<-’
setQDplot: no visible global function definition for ‘metadata’
setQDplot: no visible global function definition for ‘metadata<-’
setupCNVplot: no visible global function definition for ‘metadata’
setupCNVplot: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
  metadata metadata<- sortSeqlevels
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
addExonsGenes   44.566  1.545  46.450
setupCNVplot    36.424  0.918  37.553
plotCNV         35.535  0.943  36.671
pasteExonsGenes 34.283  1.070  35.584
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in x$.self$finalize() : attempt to apply non-function
  Error in x$.self$finalize() : attempt to apply non-function
  [1] "All CNVs are fine for further evaluation"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plotCNV.R:19:1'): (code run outside of `test_that()`) ────────
  class(p)[[1]] not equal to "gg".
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
  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 ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SARC.Rcheck/00check.log’
for details.


Installation output

SARC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SARC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SARC’ ...
** this is package ‘SARC’ version ‘1.7.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'SARC' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'SARC' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (SARC)

Tests output

SARC.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

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.

> #test SARC unit tests
> #unit test check
> library(testthat)
> library(SARC)
Loading required package: RaggedExperiment
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

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: Seqinfo
Warning message:
In fun(libname, pkgname) :
  Package 'SARC' is deprecated and will be removed from Bioconductor
  version 3.23
> test_check(package = "SARC")
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
[1] "All CNVs are fine for further evaluation"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plotCNV.R:19:1'): (code run outside of `test_that()`) ────────
class(p)[[1]] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 27 ]
Error: Test failures
Execution halted

Example timings

SARC.Rcheck/SARC-Ex.timings

nameusersystemelapsed
addExonsGenes44.566 1.54546.450
anovaOnCNV1.2030.0491.262
cnvConfidence1.7320.1181.859
pasteExonsGenes34.283 1.07035.584
plotCNV35.535 0.94336.671
plotCovPrep0.2510.0160.268
prepAnova1.0990.0551.160
regionGrangeMake0.5400.0840.629
regionMean1.0370.0371.080
regionQuantiles2.1120.1832.322
regionSet0.3890.0400.432
regionSplit0.3790.0330.414
seeDist1.9720.2732.257
setQDplot0.7950.1450.961
setupCNVplot36.424 0.91837.553
test_cnv0.0010.0020.003
test_cnv20.0010.0010.002
test_cov0.0750.0090.084