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This page was generated on 2023-05-31 05:44:31 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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 kunpeng1


To the developers/maintainers of the chromstaR package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 335/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.27.0  (landing page)
Aaron Taudt
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/chromstaR
git_branch: devel
git_last_commit: 468f990
git_last_commit_date: 2023-04-25 14:47:44 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: chromstaR
Version: 1.27.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings chromstaR_1.27.0.tar.gz
StartedAt: 2023-05-30 03:26:09 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 03:44:18 -0000 (Tue, 30 May 2023)
EllapsedTime: 1089.6 seconds
RetCode: 0
Status:   OK  
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings chromstaR_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/chromstaR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.27.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... NOTE
  installed size is  5.7Mb
  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 startup messages can be suppressed ... 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  33.271  0.236  33.517
enrichment_analysis   17.945  0.596  71.568
callPeaksMultivariate 14.765  0.264  15.033
callPeaksReplicates   12.605  0.180  12.793
plotGenomeBrowser     11.477  0.364  11.842
unis2pseudomulti      10.994  0.224  11.218
combinatorialStates    8.936  0.032   8.968
changePostCutoff       8.858  0.088   8.946
Chromstar              6.771  0.473  51.101
changeMaxPostCutoff    6.429  0.076   6.506
plotExpression         2.898  0.244  47.447
* 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-3.18-bioc/meat/chromstaR.Rcheck/00check.log’
for details.



Installation output

chromstaR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL chromstaR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘chromstaR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fPIC  -g -O2  -c R_interface.cpp -o R_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fPIC  -g -O2  -c densities.cpp -o densities.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fPIC  -g -O2  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fPIC  -g -O2  -c scalehmm.cpp -o scalehmm.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fPIC  -g -O2  -c utility.cpp -o utility.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 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: 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 
 28.535   1.082  29.602 

Example timings

chromstaR.Rcheck/chromstaR-Ex.timings

nameusersystemelapsed
Chromstar 6.771 0.47351.101
binReads0.6360.0300.670
callPeaksMultivariate14.765 0.26415.033
callPeaksReplicates12.605 0.18012.793
callPeaksUnivariate2.8180.0162.833
changeMaxPostCutoff6.4290.0766.506
changePostCutoff8.8580.0888.946
collapseBins0.7570.0000.757
combinatorialStates8.9360.0328.968
combineMultivariates33.271 0.23633.517
conversion0.0000.0000.001
enrichment_analysis17.945 0.59671.568
experiment.table0.0020.0020.004
exportFiles1.2330.0411.276
exportGRangesAsBedFile1.0010.0231.024
fixedWidthBins0.0960.0000.096
genes_rn40.1120.0040.116
genomicFrequencies0.2290.0200.250
getCombinations0.2310.0160.247
getDistinctColors0.0220.0040.026
getStateColors0.0150.0040.019
heatmapCombinations0.6110.0240.635
heatmapCountCorrelation0.5230.0280.550
heatmapTransitionProbs0.4130.0120.426
loadHmmsFromFiles2.5000.0682.569
model.combined0.220.020.24
model.multivariate0.1940.0120.206
model.univariate0.0730.0000.072
multiHMM0.2020.0040.206
plotExpression 2.898 0.24447.447
plotGenomeBrowser11.477 0.36411.842
plotHistogram2.8030.0562.859
readBamFileAsGRanges0.8920.0360.928
readBedFileAsGRanges1.9960.0522.049
readCustomBedFile3.9940.1084.103
removeCondition1.6340.0241.658
state.brewer0.0140.0000.014
stateBrewer0.0420.0000.042
transitionFrequencies0.3380.0000.338
unis2pseudomulti10.994 0.22411.218
variableWidthBins3.5650.0683.634