Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-11 11:44 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 704/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
extraChIPs 1.12.0  (landing page)
Stevie Pederson
Snapshot Date: 2025-08-07 13:40 -0400 (Thu, 07 Aug 2025)
git_url: https://git.bioconductor.org/packages/extraChIPs
git_branch: RELEASE_3_21
git_last_commit: 73770ee
git_last_commit_date: 2025-04-15 12:50:15 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for extraChIPs on merida1

To the developers/maintainers of the extraChIPs package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/extraChIPs.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: extraChIPs
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings extraChIPs_1.12.0.tar.gz
StartedAt: 2025-08-08 03:30:43 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 03:44:20 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 816.5 seconds
RetCode: 0
Status:   OK  
CheckDir: extraChIPs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings extraChIPs_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/extraChIPs.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘extraChIPs/DESCRIPTION’ ... OK
* this is package ‘extraChIPs’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'BiocParallel', 'GenomicRanges', 'ggplot2', 'ggside',
  'SummarizedExperiment', 'tibble'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘extraChIPs’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... 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 ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'extraChIPs-package.Rd':
  ‘[limma:EList]{limma::EList}’

Non-topic package-anchored link(s) in Rd file 'fitAssayDiff-methods.Rd':
  ‘[DESeq2]{estimateSizeFactors}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
defineRegions        8.733  0.032   8.933
plotPairwise         7.472  0.040   7.821
plotOverlaps-methods 7.388  0.061   8.032
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/extraChIPs.Rcheck/00check.log’
for details.


Installation output

extraChIPs.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘extraChIPs’ ...
** this is package ‘extraChIPs’ version ‘1.12.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c HMPfuns.c -o HMPfuns.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c lookup_tables.c -o lookup_tables.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o extraChIPs.so HMPfuns.o init.o lookup_tables.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-extraChIPs/00new/extraChIPs/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (extraChIPs)

Tests output

extraChIPs.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "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.

> library(testthat)
> library(extraChIPs)
Loading required package: BiocParallel
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: GenomeInfoDb
Loading required package: ggplot2
Loading required package: ggside
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: tibble
> 
> test_check("extraChIPs")
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Getting coverage across all 1 peaks...done (1.31s)
Finding centres by chromosome...done (0.75s)
Getting coverage across all 1 peaks...done (1.09s)
Finding centres by chromosome...done (0.70s)
Getting coverage across all 1 peaks...done (1.04s)
Finding centres by chromosome...done (0.72s)
Getting coverage across all 1 peaks...done (0.70s)
Finding centres by chromosome...done (0.74s)
Creating DESeqDataSet...
converting counts to integer mode
Calculating none normalisation factors...
Estimating dispersions using fitType = local...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895
Creating DGE list...
Calculating experiment-wide normalisation factors...
Estimating dispersions...
Running glmQLFit...
Creating DGE list...
Calculating experiment-wide normalisation factors...
Estimating dispersions...
Running glmQLFit...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 602 ]
> 
> proc.time()
   user  system elapsed 
171.756   9.317 186.668 

Example timings

extraChIPs.Rcheck/extraChIPs-Ex.timings

nameusersystemelapsed
addDiffStatus-methods0.4660.0170.533
as_tibble1.0470.1331.290
bestOverlap-methods2.1480.0082.166
centrePeaks-methods1.0770.0151.181
chopMC0.4190.0030.456
colToRanges-methods0.4400.0030.483
collapseGenes0.0040.0010.005
cytobands0.0230.0120.035
defineRegions8.7330.0328.933
defineSeqinfo0.0210.0050.026
distinctMC0.7520.0040.758
dualFilter000
ex_datasets0.0320.0060.038
fitAssayDiff-methods0.4460.0070.454
fixed_width_datasets0.0910.0110.101
getProfileData-methods2.7630.0432.818
grlToSE-methods1.0270.0051.033
importPeaks0.3090.0090.319
makeConsensus2.3650.2762.705
mapByFeature1.4660.0111.501
mapGrlCols3.6660.0553.810
mergeByCol-methods0.7500.0060.793
mergeByHMP-methods1.1300.0071.185
mergeBySig-methods0.9930.0071.021
partitionRanges-methods2.5650.0122.617
plotAssayDensities-methods2.2170.0332.315
plotAssayHeatmap-methods0.8530.0100.872
plotAssayPCA-methods1.7620.0171.905
plotAssayRle-methods1.8490.0161.877
plotGrlCol3.5620.0353.652
plotHFGC0.0000.0010.001
plotOverlaps-methods7.3880.0618.032
plotPairwise7.4720.0407.821
plotPie-methods3.3990.0423.665
plotProfileHeatmap-methods0.0000.0000.001
plotSplitDonut-methods2.8890.0142.934
propOverlap-methods0.6490.0020.686
reduceMC0.6130.0030.648
setoptsMC-methods2.2710.0112.474
stitchRanges0.6590.0030.689
voomWeightsFromCPM0.5570.0100.601