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This page was generated on 2021-12-06 13:04:56 -0500 (Mon, 06 Dec 2021).

CHECK results for DEScan2 on nebbiolo2

To the developers/maintainers of the DEScan2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEScan2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 493/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEScan2 1.14.1  (landing page)
Dario Righelli
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/DEScan2
git_branch: RELEASE_3_14
git_last_commit: 750fd91
git_last_commit_date: 2021-11-18 04:40:05 -0500 (Thu, 18 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DEScan2
Version: 1.14.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DEScan2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DEScan2_1.14.1.tar.gz
StartedAt: 2021-12-05 07:36:41 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 07:43:57 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 435.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DEScan2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DEScan2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DEScan2_1.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/DEScan2.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEScan2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEScan2’ version ‘1.14.1’
* 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 ‘DEScan2’ 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 ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... NOTE
.addScoreCol: no visible global function definition for 'mcols<-'
Undefined global functions or variables:
  mcols<-
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
findOverlapsOverSamples      44.641  2.181  16.292
fromSamplesToChrsGRangesList 36.201  3.937   0.289
binnedCoverage               13.954  0.607  15.098
finalRegions                  2.611  0.071  33.095
findPeaks                     0.519  0.036  41.578
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/DEScan2.Rcheck/00check.log’
for details.



Installation output

DEScan2.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DEScan2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘DEScan2’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rcpparma_max_win.cpp -o rcpparma_max_win.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o DEScan2.so RcppExports.o rcpparma_max_win.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-DEScan2/00new/DEScan2/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 (DEScan2)

Tests output

DEScan2.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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("DEScan2")
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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("DEScan2")
Maximizing with zthresh: 10	sigwin: 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
 52.138   5.961  58.315 

Example timings

DEScan2.Rcheck/DEScan2-Ex.timings

nameusersystemelapsed
RleListToRleMatrix0.1650.0000.166
binnedCoverage13.954 0.60715.098
constructBedRanges0.4760.0280.504
countFinalRegions3.8060.0643.873
createGranges0.1390.0040.142
cutGRangesPerChromosome0.0700.0000.069
divideEachSampleByChromosomes0.1770.0120.189
finalRegions 2.611 0.07133.095
findOverlapsOverSamples44.641 2.18116.292
findPeaks 0.519 0.03641.578
fromSamplesToChrsGRangesList36.201 3.937 0.289
keepRelevantChrs0.0410.0160.057
readBamAsBed0.0950.0120.108
readBedFile0.1250.0040.130
readFilesAsGRangesList3.3320.1883.530
saveGRangesAsBed0.1060.0040.110
saveGRangesAsTsv0.0160.0040.020
setGRGenomeInfo0.1450.0040.149