Back to Multiple platform build/check report for BioC 3.16:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-03-27 11:04:54 -0400 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4480
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4276
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4304
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

CHECK results for chromstaR on nebbiolo2


To the developers/maintainers of the chromstaR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromstaR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 325/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.24.0  (landing page)
Aaron Taudt
Snapshot Date: 2023-03-24 14:00:04 -0400 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/chromstaR
git_branch: RELEASE_3_16
git_last_commit: a38e62b
git_last_commit_date: 2022-11-01 11:13:56 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chromstaR
Version: 1.24.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings chromstaR_1.24.0.tar.gz
StartedAt: 2023-03-24 19:32:36 -0400 (Fri, 24 Mar 2023)
EndedAt: 2023-03-24 19:43:15 -0400 (Fri, 24 Mar 2023)
EllapsedTime: 638.9 seconds
RetCode: 0
Status:   OK  
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings chromstaR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/chromstaR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.24.0’
* 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 ‘chromstaR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
* 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
Chromstar: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
combineMultivariates  21.629  0.288  21.919
enrichment_analysis   14.980  0.928  19.001
callPeaksMultivariate 10.322  0.400  10.723
unis2pseudomulti       8.876  0.328   9.273
callPeaksReplicates    8.805  0.256   9.062
plotGenomeBrowser      7.114  0.392   7.522
Chromstar              5.856  0.685  39.967
combinatorialStates    5.706  0.140   5.846
changePostCutoff       5.680  0.108   5.789
readCustomBedFile      5.331  0.248   5.745
plotExpression         2.254  0.216   5.836
* 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 ...
  ‘chromstaR.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/chromstaR.Rcheck/00check.log’
for details.



Installation output

chromstaR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL chromstaR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘chromstaR’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-chromstaR/00new/chromstaR/libs
** R
** data
** 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 (chromstaR)

Tests output

chromstaR.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
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(chromstaR)
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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: chromstaRData

Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.

> 
> test_check("chromstaR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
 18.821   0.713  20.024 

Example timings

chromstaR.Rcheck/chromstaR-Ex.timings

nameusersystemelapsed
Chromstar 5.856 0.68539.967
binReads0.5010.0630.566
callPeaksMultivariate10.322 0.40010.723
callPeaksReplicates8.8050.2569.062
callPeaksUnivariate1.7690.0121.781
changeMaxPostCutoff4.0810.1404.221
changePostCutoff5.6800.1085.789
collapseBins0.5190.0080.526
combinatorialStates5.7060.1405.846
combineMultivariates21.629 0.28821.919
conversion0.0010.0000.000
enrichment_analysis14.980 0.92819.001
experiment.table0.0030.0000.003
exportFiles1.0920.0241.116
exportGRangesAsBedFile0.8020.0400.843
fixedWidthBins0.0630.0040.066
genes_rn40.0980.0040.102
genomicFrequencies0.1970.0200.218
getCombinations0.2410.0000.242
getDistinctColors0.0160.0040.020
getStateColors0.0140.0000.014
heatmapCombinations0.4530.0520.504
heatmapCountCorrelation0.3480.0280.375
heatmapTransitionProbs0.3460.0040.350
loadHmmsFromFiles1.6780.0961.836
model.combined0.2760.0200.296
model.multivariate0.2290.0120.241
model.univariate0.0820.0000.081
multiHMM0.1840.0240.208
plotExpression2.2540.2165.836
plotGenomeBrowser7.1140.3927.522
plotHistogram2.1010.1442.270
readBamFileAsGRanges0.6690.0200.689
readBedFileAsGRanges1.3010.0641.365
readCustomBedFile5.3310.2485.745
removeCondition2.4740.1042.578
state.brewer0.0090.0000.009
stateBrewer0.0280.0000.028
transitionFrequencies0.2780.0280.306
unis2pseudomulti8.8760.3289.273
variableWidthBins1.6310.0361.667