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CHECK report for chromstaR on merida1

This page was generated on 2019-04-16 11:59:43 -0400 (Tue, 16 Apr 2019).

Package 259/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.8.1
Aaron Taudt
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/chromstaR
Branch: RELEASE_3_8
Last Commit: 2d75cac
Last Changed Date: 2019-01-04 13:25:27 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromstaR_1.8.1.tar.gz
StartedAt: 2019-04-15 22:59:51 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:07:30 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 458.7 seconds
RetCode: 0
Status:  OK 
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromstaR_1.8.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/chromstaR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.1’
* 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  5.2Mb
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
combineMultivariates  23.971  2.220  26.479
enrichment_analysis   17.119  1.152  25.521
callPeaksMultivariate 11.711  0.797  12.610
callPeaksReplicates    9.839  0.807  10.744
readCustomBedFile     10.034  0.211  10.401
plotGenomeBrowser      9.985  0.206  10.332
unis2pseudomulti       8.378  0.638   9.085
changePostCutoff       7.904  0.789   8.770
Chromstar              6.960  0.474  47.423
combinatorialStates    6.511  0.570   7.165
changeMaxPostCutoff    6.071  0.567   6.688
plotExpression         2.112  0.155   8.407
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/chromstaR.Rcheck/00check.log’
for details.



Installation output

chromstaR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chromstaR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘chromstaR’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c R_interface.cpp -o R_interface.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c densities.cpp -o densities.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c utility.cpp -o utility.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (chromstaR)

Tests output

chromstaR.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 20.337   0.968  21.507 

Example timings

chromstaR.Rcheck/chromstaR-Ex.timings

nameusersystemelapsed
Chromstar 6.960 0.47447.423
binReads0.7270.0590.801
callPeaksMultivariate11.711 0.79712.610
callPeaksReplicates 9.839 0.80710.744
callPeaksUnivariate2.2490.2142.493
changeMaxPostCutoff6.0710.5676.688
changePostCutoff7.9040.7898.770
collapseBins0.8640.0530.929
combinatorialStates6.5110.5707.165
combineMultivariates23.971 2.22026.479
conversion0.0000.0000.001
enrichment_analysis17.119 1.15225.521
experiment.table0.0050.0020.006
exportFiles1.2890.0571.366
exportGRangesAsBedFile1.2320.0681.310
fixedWidthBins0.0870.0030.091
genes_rn40.1590.0080.168
genomicFrequencies0.3160.0350.354
getCombinations0.3340.0300.367
getDistinctColors0.0360.0040.040
getStateColors0.0230.0000.023
heatmapCombinations0.6710.0250.704
heatmapCountCorrelation0.6200.0620.701
heatmapTransitionProbs0.5460.0190.571
loadHmmsFromFiles2.0210.1952.238
model.combined0.3140.0360.354
model.multivariate0.2970.0340.333
model.univariate0.1100.0140.126
multiHMM0.2670.0230.291
plotExpression2.1120.1558.407
plotGenomeBrowser 9.985 0.20610.332
plotHistogram2.8210.2463.101
readBamFileAsGRanges0.9280.1011.040
readBedFileAsGRanges2.2560.1522.439
readCustomBedFile10.034 0.21110.401
removeCondition2.3880.2012.612
state.brewer0.0190.0010.019
stateBrewer0.0590.0030.062
transitionFrequencies0.4420.0490.501
unis2pseudomulti8.3780.6389.085
variableWidthBins2.5350.3812.934