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BioC 3.5: CHECK report for chromstaR on veracruz2

This page was generated on 2017-10-18 14:34:45 -0400 (Wed, 18 Oct 2017).

Package 220/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.2.0
Aaron Taudt
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/chromstaR
Branch: RELEASE_3_5
Last Commit: 6471020
Last Changed Date: 2017-04-24 15:45:44 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.2.0.tar.gz
StartedAt: 2017-10-18 01:43:41 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:50:33 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 412.3 seconds
RetCode: 0
Status:  OK 
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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
enrichment_analysis   13.246  0.393  17.708
readCustomBedFile     10.863  0.172  11.302
combineMultivariates  10.242  0.535  11.078
Chromstar              8.231  0.288  44.534
callPeaksMultivariate  6.477  0.266   7.005
transitionFrequencies  5.676  0.311  49.462
plotExpression         2.491  0.060   5.761
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck/00check.log’
for details.


chromstaR.Rcheck/00install.out:

* 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 /Users/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 8.231 0.28844.534
binReads0.9530.0311.081
callPeaksMultivariate6.4770.2667.005
callPeaksReplicates3.2790.1833.607
callPeaksUnivariate1.5430.0741.670
changeFDR2.7600.1163.005
changePostCutoff2.2230.1172.431
collapseBins0.9470.0241.002
combinatorialStates2.9690.1263.184
combineMultivariates10.242 0.53511.078
combined_model0.1860.0150.204
conversion0.0010.0000.001
enrichment_analysis13.246 0.39317.708
experiment.table0.0040.0010.007
exportFiles0.5940.0160.637
exportGRangesAsBedFile0.7180.0360.768
fixedWidthBins0.0810.0050.087
genes_rn40.1180.0070.132
genomicFrequencies0.1160.0100.130
getCombinations0.1720.0110.187
getDistinctColors0.0300.0040.034
getStateColors0.020.000.02
heatmapCombinations0.5020.0150.533
heatmapCountCorrelation0.3250.0100.340
heatmapTransitionProbs0.3460.0090.396
loadHmmsFromFiles0.8220.0370.890
multiHMM0.1170.0120.132
multivariate_model0.1120.0120.126
plotExpression2.4910.0605.761
plotHistogram1.4530.0791.570
readBamFileAsGRanges0.8540.0620.944
readBedFileAsGRanges4.7070.1254.951
readCustomBedFile10.863 0.17211.302
removeCondition1.0940.0731.195
state.brewer0.0150.0000.016
stateBrewer0.0400.0020.044
transitionFrequencies 5.676 0.31149.462
unis2pseudomulti2.8220.1533.054
variableWidthBins2.3970.3482.820