Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 666/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epiregulon 1.0.1  (landing page)
Xiaosai Yao
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/epiregulon
git_branch: RELEASE_3_19
git_last_commit: a281375
git_last_commit_date: 2024-06-06 17:05:24 -0400 (Thu, 06 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'motifmatchr' which is only available as a source package that needs compilation


CHECK results for epiregulon on nebbiolo1

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.

raw results


Summary

Package: epiregulon
Version: 1.0.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epiregulon.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epiregulon_1.0.1.tar.gz
StartedAt: 2024-06-19 22:56:32 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 23:05:37 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 545.1 seconds
RetCode: 0
Status:   OK  
CheckDir: epiregulon.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epiregulon.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epiregulon_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/epiregulon.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘epiregulon/DESCRIPTION’ ... OK
* this is package ‘epiregulon’ version ‘1.0.1’
* 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 ‘epiregulon’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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
addMotifScore  24.048  1.324  30.039
getTFMotifInfo 21.275  0.320  21.894
addLogFC        7.806  0.352   8.863
addWeights      4.868  0.364   5.234
* 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-3.19-bioc/meat/epiregulon.Rcheck/00check.log’
for details.


Installation output

epiregulon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL epiregulon
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘epiregulon’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/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<InputIndex_>&, 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<InputIndex_>&, 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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c binom.c -o binom.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/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-3.19-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-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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)

Tests output

epiregulon.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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, 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...

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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 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
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
DataFrame with 4 rows and 6 columns
           tf      target   idxATAC                           pval
  <character> <character> <integer>                       <matrix>
1           A           B         1 1.0000000:1.00000000:1.0000000
2           A           B         2 0.0191648:0.03523071:1.0000000
3           A           C         3 0.7082253:0.82677153:0.2675027
4           C           B         4 0.0877076:0.00167859:0.0740225
                       stats                          qval
                    <matrix>                      <matrix>
1 0.000000:0.0000000:0.00000 1.0000000:1.00000000:1.000000
2 5.486415:4.4339583:0.00000 0.0766592:0.10569214:1.000000
3 0.140056:0.0478927:1.22951 1.0000000:1.00000000:0.802508
4 2.915952:9.8714953:3.19149 0.2631229:0.00671436:0.296090
pruning network with chi.sq tests using a regulon cutoff of pval<0.05
pruning regulons
DataFrame with 2 rows and 6 columns
           tf      target   idxATAC                           pval
  <character> <character> <integer>                       <matrix>
1           A           B         2 0.0191648:0.03523071:1.0000000
2           C           B         4 0.0877076:0.00167859:0.0740225
                    stats                         qval
                 <matrix>                     <matrix>
1 5.48642:4.43396:0.00000 0.0766592:0.10569214:1.00000
2 2.91595:9.87150:3.19149 0.2631229:0.00671436:0.29609
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 0 | SKIP 0 | PASS 45 ]
> 
> proc.time()
   user  system elapsed 
 31.384   1.673  33.047 

Example timings

epiregulon.Rcheck/epiregulon-Ex.timings

nameusersystemelapsed
addLogFC7.8060.3528.863
addMotifScore24.048 1.32430.039
addTFMotifInfo0.2960.0470.342
addWeights4.8680.3645.234
aggregateAcrossCells0.0360.0080.045
aggregateAcrossCellsFast1.0200.0081.029
calculateActivity1.6730.0201.694
calculateP2G3.8920.0923.983
getRegulon0.3020.0040.306
getTFMotifInfo21.275 0.32021.894
pruneRegulon2.1080.0162.124