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CHECK report for chromstaR on malbec1

This page was generated on 2020-04-15 12:11:31 -0400 (Wed, 15 Apr 2020).

Package 287/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.12.0
Aaron Taudt
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/chromstaR
Branch: RELEASE_3_10
Last Commit: b37e9bf
Last Changed Date: 2019-10-29 13:09:48 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromstaR
Version: 1.12.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chromstaR_1.12.0.tar.gz
StartedAt: 2020-04-15 03:55:48 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:03:28 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 460.6 seconds
RetCode: 0
Status:  OK 
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chromstaR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/chromstaR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.12.0’
* 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  5.6Mb
  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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
combineMultivariates  30.528  0.104  31.675
enrichment_analysis   16.176  0.136  20.013
callPeaksMultivariate 13.616  0.088  13.874
callPeaksReplicates   11.884  0.036  12.185
unis2pseudomulti      11.288  0.040  11.539
changePostCutoff      10.640  0.056  10.804
plotGenomeBrowser      9.824  0.020  10.032
combinatorialStates    9.668  0.020   9.869
readCustomBedFile      9.092  0.044   9.252
Chromstar              7.700  0.612  53.318
changeMaxPostCutoff    6.724  0.040   6.804
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/chromstaR.Rcheck/00check.log’
for details.



Installation output

chromstaR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL chromstaR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘chromstaR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 22.028   0.480  23.253 

Example timings

chromstaR.Rcheck/chromstaR-Ex.timings

nameusersystemelapsed
Chromstar 7.700 0.61253.318
binReads0.8120.0160.888
callPeaksMultivariate13.616 0.08813.874
callPeaksReplicates11.884 0.03612.185
callPeaksUnivariate3.0880.0083.116
changeMaxPostCutoff6.7240.0406.804
changePostCutoff10.640 0.05610.804
collapseBins0.8920.0160.912
combinatorialStates9.6680.0209.869
combineMultivariates30.528 0.10431.675
conversion0.0040.0000.000
enrichment_analysis16.176 0.13620.013
experiment.table0.0040.0000.004
exportFiles1.5080.0121.552
exportGRangesAsBedFile1.4240.0161.449
fixedWidthBins0.0800.0000.079
genes_rn40.1640.0000.169
genomicFrequencies0.3360.0120.353
getCombinations0.3360.0040.344
getDistinctColors0.0240.0000.026
getStateColors0.0200.0000.019
heatmapCombinations0.6560.0040.678
heatmapCountCorrelation0.5600.0080.568
heatmapTransitionProbs0.5560.0120.581
loadHmmsFromFiles2.3960.0082.440
model.combined0.3760.0080.387
model.multivariate0.3440.0080.355
model.univariate0.120.000.12
multiHMM0.3080.0200.338
plotExpression2.7600.0084.397
plotGenomeBrowser 9.824 0.02010.032
plotHistogram3.3600.0043.578
readBamFileAsGRanges1.1080.0081.159
readBedFileAsGRanges2.1720.0202.349
readCustomBedFile9.0920.0449.252
removeCondition1.9400.0202.035
state.brewer0.0160.0000.016
stateBrewer0.0480.0040.052
transitionFrequencies0.4360.0160.454
unis2pseudomulti11.288 0.04011.539
variableWidthBins3.4120.0083.429