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BioC 3.5: CHECK report for chromstaR on malbec2

This page was generated on 2017-08-16 13:17:41 -0400 (Wed, 16 Aug 2017).

Package 220/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.2.0
Aaron Taudt
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/chromstaR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromstaR
Version: 1.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_1.2.0.tar.gz
StartedAt: 2017-08-15 21:56:38 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:02:30 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 351.3 seconds
RetCode: 0
Status:  OK 
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.2.0’
* 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 ... 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
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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
combineMultivariates  11.200  0.036  11.316
enrichment_analysis    9.924  0.012  14.500
readCustomBedFile      9.544  0.012   9.563
Chromstar              7.068  0.376  35.233
transitionFrequencies  6.212  0.244  44.740
callPeaksMultivariate  6.300  0.032   6.406
plotExpression         2.236  0.012   5.787
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck/00check.log’
for details.


chromstaR.Rcheck/00install.out:

* installing *source* package ‘chromstaR’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck/chromstaR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chromstaR)

chromstaR.Rcheck/chromstaR-Ex.timings:

nameusersystemelapsed
Chromstar 7.068 0.37635.233
binReads0.3720.0000.428
callPeaksMultivariate6.3000.0326.406
callPeaksReplicates4.2680.0124.330
callPeaksUnivariate1.6160.0041.620
changeFDR2.9200.0122.937
changePostCutoff2.3680.0042.375
collapseBins0.4160.0040.421
combinatorialStates3.2640.0083.273
combineMultivariates11.200 0.03611.316
combined_model0.1840.0120.193
conversion0.0000.0000.001
enrichment_analysis 9.924 0.01214.500
experiment.table0.0000.0040.004
exportFiles0.5040.0120.515
exportGRangesAsBedFile0.5720.0000.572
fixedWidthBins0.0560.0000.053
genes_rn40.1040.0120.117
genomicFrequencies0.1360.0120.147
getCombinations0.1640.0080.175
getDistinctColors0.0160.0040.019
getStateColors0.0160.0000.014
heatmapCombinations0.3920.0120.403
heatmapCountCorrelation0.2760.0160.292
heatmapTransitionProbs0.3240.0000.325
loadHmmsFromFiles1.3440.0001.346
multiHMM0.1080.0080.114
multivariate_model0.1000.0120.112
plotExpression2.2360.0125.787
plotHistogram1.3320.0001.332
readBamFileAsGRanges1.2760.0041.280
readBedFileAsGRanges4.4200.0284.468
readCustomBedFile9.5440.0129.563
removeCondition0.5320.0000.533
state.brewer0.0080.0000.010
stateBrewer0.0320.0000.029
transitionFrequencies 6.212 0.24444.740
unis2pseudomulti3.4360.0363.473
variableWidthBins2.4280.0162.444