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This page was generated on 2024-03-02 11:35:40 -0500 (Sat, 02 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 547/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEScan2 1.22.0  (landing page)
Dario Righelli
Snapshot Date: 2024-03-01 14:05:09 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/DEScan2
git_branch: RELEASE_3_18
git_last_commit: 9abfdf1
git_last_commit_date: 2023-10-24 11:03:24 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for DEScan2 on nebbiolo2


To the developers/maintainers of the DEScan2 package:
- 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 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: DEScan2
Version: 1.22.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DEScan2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DEScan2_1.22.0.tar.gz
StartedAt: 2024-03-01 21:36:10 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 21:43:33 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 443.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DEScan2.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DEScan2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DEScan2_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DEScan2.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘DEScan2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEScan2’ version ‘1.22.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: saveGRangesAsTsv.Rd:34: unknown macro '\t'
See ‘/home/biocbuild/bbs-3.18-bioc/meat/DEScan2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 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 ... NOTE
.addScoreCol: no visible global function definition for ‘mcols<-’
Undefined global functions or variables:
  mcols<-
* checking Rd files ... WARNING
prepare_Rd: saveGRangesAsTsv.Rd:34: unknown macro '\t'
* 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      21.747  0.776   8.339
fromSamplesToChrsGRangesList 19.252  2.955   0.209
binnedCoverage               12.275  0.563  13.433
finalRegions                  4.121  0.112  18.339
findPeaks                     0.415  0.036  22.324
* 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 ...
  ‘DEScan2.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DEScan2.Rcheck/00check.log’
for details.



Installation output

DEScan2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL DEScan2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘DEScan2’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-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-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-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-3.18-bioc/R/lib -L/usr/local/lib -o DEScan2.so RcppExports.o rcpparma_max_win.o -llapack -L/home/biocbuild/bbs-3.18-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-DEScan2/00new/DEScan2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: saveGRangesAsTsv.Rd:34: unknown macro '\t'
*** 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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 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, 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, sort, 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
> 
> test_check("DEScan2")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
 37.253   3.549  50.873 

Example timings

DEScan2.Rcheck/DEScan2-Ex.timings

nameusersystemelapsed
RleListToRleMatrix0.1630.0010.163
binnedCoverage12.275 0.56313.433
constructBedRanges0.4130.0040.417
countFinalRegions3.2380.0843.324
createGranges0.1420.0040.146
cutGRangesPerChromosome0.0480.0040.052
divideEachSampleByChromosomes0.1220.0120.134
finalRegions 4.121 0.11218.339
findOverlapsOverSamples21.747 0.776 8.339
findPeaks 0.415 0.03622.324
fromSamplesToChrsGRangesList19.252 2.955 0.209
keepRelevantChrs0.0360.0000.037
readBamAsBed0.0860.0000.085
readBedFile0.0920.0160.108
readFilesAsGRangesList2.7160.1282.844
saveGRangesAsBed0.0700.0080.078
saveGRangesAsTsv0.0110.0000.011
setGRGenomeInfo0.1200.0000.121