Xiaosai Yao
| Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/epiregulon |
| git_branch: devel |
| git_last_commit: 591e442 |
| git_last_commit_date: 2025-10-16 15:43:25 -0400 (Thu, 16 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-18 12:03 -0400 (Sat, 18 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 681/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epiregulon 1.99.2 (landing page) Xiaosai Yao
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the epiregulon package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epiregulon.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. |
| Package: epiregulon |
| Version: 1.99.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:epiregulon.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings epiregulon_1.99.2.tar.gz |
| StartedAt: 2025-10-17 23:33:32 -0400 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 23:54:03 -0400 (Fri, 17 Oct 2025) |
| EllapsedTime: 1230.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: epiregulon.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:epiregulon.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings epiregulon_1.99.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/epiregulon.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘epiregulon/DESCRIPTION’ ... OK
* this is package ‘epiregulon’ version ‘1.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘epiregulon’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘beachmat’ ‘bluster’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addFDR: no visible global function definition for ‘ecdf’
.addFDR: no visible global function definition for ‘p.adjust’
.aggregateCells: no visible global function definition for ‘reducedDim’
aggregateAcrossCellsFast: no visible global function definition for
‘spritnf’
optimizeMetacellNumber: no visible global function definition for
‘assay<-’
optimizeMetacellNumber: no visible global function definition for ‘lm’
optimizeMetacellNumber: no visible global function definition for
‘optim’
optimizeMetacellNumber : <anonymous>: no visible global function
definition for ‘predict’
plot,CellNumSol-ANY: no visible global function definition for ‘points’
plot,CellNumSol-ANY: no visible global function definition for ‘lines’
Undefined global functions or variables:
assay<- ecdf lines lm optim p.adjust points predict reducedDim
spritnf
Consider adding
importFrom("graphics", "lines", "points")
importFrom("stats", "ecdf", "lm", "optim", "p.adjust", "predict")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'calculateActivity.Rd'
‘method’
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 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
getTFMotifInfo 22.623 0.843 23.738
addMotifScore 17.385 0.730 18.485
calculateP2G 5.061 0.097 5.160
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/epiregulon.Rcheck/00check.log’
for details.
epiregulon.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL epiregulon
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘epiregulon’ ...
** this is package ‘epiregulon’ version ‘1.99.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c binom.c -o binom.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fast_chisq.cpp -o fast_chisq.o
fast_chisq.cpp: In function ‘Rcpp::List fast_chisq(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericMatrix, int, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericMatrix, int, Rcpp::IntegerVector)’:
fast_chisq.cpp:27:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
27 | if (nrows != tf_by_peak.size()) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~
fast_chisq.cpp:30:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
30 | if (nrows != target_by_peak.size()) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
fast_chisq.cpp:33:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
33 | if (nrows != target_ordered.size()) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fast_wilcox.cpp -o fast_wilcox.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o epiregulon.so RcppExports.o binom.o fast_chisq.o fast_wilcox.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-epiregulon/00new/epiregulon/libs
** R
** 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
** 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 (epiregulon)
epiregulon.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.
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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(epiregulon)
Loading required package: SingleCellExperiment
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: 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
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
>
> test_check("epiregulon")
adding weights using wilcoxon...
adding weights using wilcoxon...
adding weights using wilcoxon...
adding weights using wilcoxon...
adding weights using MI...
calculating average expression across clusters...
computing weights...
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adding weights using corr...
calculating average expression across clusters...
computing weights...
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calculating TF activity from regulon using
aggregating regulons...
creating weight matrix...
calculating activity scores...
normalize by the number of targets...
calculating TF activity from regulon using
aggregating regulons...
creating weight matrix...
calculating activity scores...
normalize by the number of targets...
calculating TF activity from regulon using
aggregating regulons...
creating weight matrix...
calculating activity scores...
normalize by mean...
normalize by the number of targets...
calculating TF activity from regulon using
aggregating regulons...
creating weight matrix...
calculating frequency...
calculating activity scores...
normalize by number of targets...
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An issue detected during estimation optimal number of metacells.Consider at least one of the following actions:1. Change of the `cellNumMin` and `cellNumMax` paramaters2. Increasing the number of evaluation points (`n_evaluation_points` argument)3. Increasing the number of iterations (`n_iter` argument)4. Increasing the number of false connections used to compute p-valuenull distribution (`nRandConns` argument)
Solution not found using quadratic regression. Using cluster size with the lowest mean p-value.
Retrieving chip-seq data, version 2
see ?scMultiome and browseVignettes('scMultiome') for documentation
loading from cache
Computing overlap...
Success!
Retrieving chip-seq data, version 2
see ?scMultiome and browseVignettes('scMultiome') for documentation
loading from cache
Retrieving chip-seq data, version 2
see ?scMultiome and browseVignettes('scMultiome') for documentation
loading from cache
annotating peaks with motifs
see ?scMultiome and browseVignettes('scMultiome') for documentation
loading from cache
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'rtracklayer'
The following object is masked from 'package:AnnotationHub':
hubUrl
pruning network with binom tests using a regulon cutoff of pval<2
pruning regulons
binarizing matrices
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pruning network with chi.sq tests using a regulon cutoff of pval<2
pruning regulons
pruning network with binom tests using a regulon cutoff of pval<2
pruning regulons
binarizing matrices
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pruning network with chi.sq tests using a regulon cutoff of pval<2
pruning regulons
pruning network with chi.sq tests using a regulon cutoff of pval<0.05
pruning regulons
pruning network with binom tests using a regulon cutoff of pval<2
pruning regulons
binarizing matrices
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pruning network with chi.sq tests using a regulon cutoff of pval<2
pruning regulons
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 69 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 69 ]
>
> proc.time()
user system elapsed
485.144 8.331 446.254
epiregulon.Rcheck/epiregulon-Ex.timings
| name | user | system | elapsed | |
| addLogFC | 2.039 | 0.109 | 2.153 | |
| addMotifScore | 17.385 | 0.730 | 18.485 | |
| addTFMotifInfo | 0.228 | 0.028 | 0.257 | |
| addWeights | 4.210 | 0.293 | 4.506 | |
| aggregateAcrossCellsFast | 0.553 | 0.090 | 0.643 | |
| calculateActivity | 1.548 | 0.065 | 1.613 | |
| calculateP2G | 5.061 | 0.097 | 5.160 | |
| getRegulon | 0.258 | 0.008 | 0.266 | |
| getTFMotifInfo | 22.623 | 0.843 | 23.738 | |
| pruneRegulon | 1.448 | 0.139 | 1.586 | |