Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 662/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epiregulon 1.2.0 (landing page) Xiaosai Yao
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 1.2.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:epiregulon.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings epiregulon_1.2.0.tar.gz |
StartedAt: 2024-12-19 23:21:26 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:35:58 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 872.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: epiregulon.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:epiregulon.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings epiregulon_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/epiregulon.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 * checking for file ‘epiregulon/DESCRIPTION’ ... OK * this is package ‘epiregulon’ version ‘1.2.0’ * 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 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 ... 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 ... 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 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 20.702 1.134 22.098 addMotifScore 16.933 0.463 17.696 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/epiregulon.Rcheck/00check.log’ for details.
epiregulon.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL epiregulon ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘epiregulon’ ... ** 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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c aggregate_across_cells.cpp -o aggregate_across_cells.o aggregate_across_cells.cpp: In function ‘SEXPREC* aggregate_across_cells(SEXP, Rcpp::List, int)’: aggregate_across_cells.cpp:19:26: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 19 | if (groups[g].size() != NC) { | ~~~~~~~~~~~~~~~~~^~~~~ In file included from aggregate_across_cells.cpp:2: AggregateAcrossCells.h: In instantiation of ‘void scran::AggregateAcrossCells::compute_row(Index_, Index_, const Contents_&, const Factor_*, std::vector<IndexIn_>&, std::vector<Sum_*>&, std::vector<Detected_>&, std::vector<Detected_*>&) [with bool sparse_ = true; Index_ = int; Contents_ = tatami::SparseRange<double, int>; Factor_ = int; Sum_ = double; Detected_ = int]’: AggregateAcrossCells.h:150:30: required from ‘void scran::AggregateAcrossCells::compute(const tatami::Matrix<Value_, Index_>*, const Factor_*, std::vector<Detected_*>&, std::vector<Detected_*>&) [with bool row_ = true; bool sparse_ = true; Data_ = double; Index_ = int; Factor_ = int; Sum_ = double; Detected_ = int]’ AggregateAcrossCells.h:210:28: required from ‘void scran::AggregateAcrossCells::run(const tatami::Matrix<Value_, Index_>*, const Factor*, std::vector<Sum*>, std::vector<Sum_*>) [with Data = double; Index = int; Factor = int; Sum = double; Detected = int]’ aggregate_across_cells.cpp:52:13: required from here AggregateAcrossCells.h:109:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 109 | for (Index_ l = 0; l < tmp_sums.size(); ++l) { | ~~^~~~~~~~~~~~~~~~~ AggregateAcrossCells.h:127:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 127 | for (Index_ l = 0; l < tmp_detected.size(); ++l) { | ~~^~~~~~~~~~~~~~~~~~~~~ AggregateAcrossCells.h: In instantiation of ‘void scran::AggregateAcrossCells::compute_row(Index_, Index_, const Contents_&, const Factor_*, std::vector<IndexIn_>&, std::vector<Sum_*>&, std::vector<Detected_>&, std::vector<Detected_*>&) [with bool sparse_ = false; Index_ = int; Contents_ = const double*; Factor_ = int; Sum_ = double; Detected_ = int]’: AggregateAcrossCells.h:152:31: required from ‘void scran::AggregateAcrossCells::compute(const tatami::Matrix<Value_, Index_>*, const Factor_*, std::vector<Detected_*>&, std::vector<Detected_*>&) [with bool row_ = true; bool sparse_ = false; Data_ = double; Index_ = int; Factor_ = int; Sum_ = double; Detected_ = int]’ AggregateAcrossCells.h:212:29: required from ‘void scran::AggregateAcrossCells::run(const tatami::Matrix<Value_, Index_>*, const Factor*, std::vector<Sum*>, std::vector<Sum_*>) [with Data = double; Index = int; Factor = int; Sum = double; Detected = int]’ aggregate_across_cells.cpp:52:13: required from here AggregateAcrossCells.h:109:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 109 | for (Index_ l = 0; l < tmp_sums.size(); ++l) { | ~~^~~~~~~~~~~~~~~~~ AggregateAcrossCells.h:127:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 127 | for (Index_ l = 0; l < tmp_detected.size(); ++l) { | ~~^~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c binom.c -o binom.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c fast_wilcox.cpp -o fast_wilcox.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o epiregulon.so RcppExports.o aggregate_across_cells.o binom.o fast_chisq.o fast_wilcox.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. 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 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, saveRDS, setdiff, 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 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 MI... calculating average expression across clusters... computing weights... | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% adding weights using corr... calculating average expression across clusters... computing weights... | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% calculating TF activity from regulon using weightedmean aggregating regulons... creating weight matrix... calculating activity scores... normalize by the number of targets... calculating TF activity from regulon using weightedmean aggregating regulons... creating weight matrix... calculating activity scores... normalize by mean... normalize by the number of targets... calculating TF activity from regulon using weightedmean aggregating regulons... creating weight matrix... calculating frequency... calculating activity scores... normalize by number of targets... Using epiregulon to compute peak to gene links... performing k means clustering to form metacells Computing correlation see ?scMultiome and browseVignettes('scMultiome') for documentation loading from cache Computing overlap... Success! see ?scMultiome and browseVignettes('scMultiome') for documentation loading from cache 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:BiocIO': FileForFormat 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 | | | 0% | |=================================== | 50% | |======================================================================| 100% 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 | | | 0% | |=================================== | 50% | |======================================================================| 100% 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 | | | 0% | |=================================== | 50% | |======================================================================| 100% pruning network with chi.sq tests using a regulon cutoff of pval<2 pruning regulons [ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ] > > proc.time() user system elapsed 221.007 8.494 230.674
epiregulon.Rcheck/epiregulon-Ex.timings
name | user | system | elapsed | |
addLogFC | 2.317 | 0.068 | 2.386 | |
addMotifScore | 16.933 | 0.463 | 17.696 | |
addTFMotifInfo | 0.193 | 0.056 | 0.249 | |
addWeights | 2.709 | 0.173 | 2.881 | |
aggregateAcrossCells | 0.042 | 0.038 | 0.082 | |
aggregateAcrossCellsFast | 1.888 | 0.704 | 2.593 | |
calculateActivity | 1.519 | 0.061 | 1.580 | |
calculateP2G | 1.653 | 0.110 | 1.763 | |
getRegulon | 0.223 | 0.018 | 0.241 | |
getTFMotifInfo | 20.702 | 1.134 | 22.098 | |
pruneRegulon | 1.361 | 0.072 | 1.433 | |